From 83db6c794605229a70a0ce345074dd49d7a5aeec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 19 Oct 2024 11:37:34 +0200 Subject: [PATCH 01/59] Bundle assembly resources --- hugo/content/species/foo_bar/_index.md | 55 ++++++ .../species/foo_bar/assembly/_index.md | 6 + .../species/foo_bar/assembly/assembly.yaml | 15 ++ .../species/foo_bar/assembly/contrib.md | 14 ++ .../species/foo_bar/assembly/stats.yaml | 24 +++ hugo/content/species/foo_bar/download.md | 6 + hugo/content/species/foo_bar/taxonomy.json | 58 ++++++ hugo/layouts/species/assembly.html | 175 ++++++++++++++++++ 8 files changed, 353 insertions(+) create mode 100644 hugo/content/species/foo_bar/_index.md create mode 100644 hugo/content/species/foo_bar/assembly/_index.md create mode 100644 hugo/content/species/foo_bar/assembly/assembly.yaml create mode 100644 hugo/content/species/foo_bar/assembly/contrib.md create mode 100644 hugo/content/species/foo_bar/assembly/stats.yaml create mode 100644 hugo/content/species/foo_bar/download.md create mode 100644 hugo/content/species/foo_bar/taxonomy.json create mode 100644 hugo/layouts/species/assembly.html diff --git a/hugo/content/species/foo_bar/_index.md b/hugo/content/species/foo_bar/_index.md new file mode 100644 index 00000000..7506ad6a --- /dev/null +++ b/hugo/content/species/foo_bar/_index.md @@ -0,0 +1,55 @@ +--- +# Required params below +title: "*Clupea harengus*" +subtitle: "Atlantic herring" + +last_updated: "15/05/2024" + +cover_image: "/img/species/clupea_harengus.webp" +img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" +img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" + + +# The params below were auto-generated, you should not need to edit them... +# unless you were warned by the add-new-species.py script. +layout: "species_intro" +banner_title: "Species overview" +url: "clupea_harengus" +weight: 1 +science_name: "Clupea harengus" +lineage_data_path: "clupea_harengus/taxonomy" + +gbif_taxon_id: "8351946" +goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" + + +# Optional params below, +# remove them if you don't want them or they are not relevant. +iucn_category: "Least Concern" +iucn_link: "https://www.iucnredlist.org/species/155123/4717767" + +swe_red_list: "Viable" +swe_red_list_link: "https://artfakta.se/taxa/206089/" + +# These 3 params define the initial view for the map +# latitude and longitude are for the map center. +latitude: 60 +longitude: -40 +initialZoom: 1 +--- + +### Description + +Write some content here in markdown for the introduction tab of the species page. + +#### Genome reference + +[EDIT] + +#### References + +- [EDIT] + +#### Changelog + +- DD/MM/YYYY - Species first published on the Portal diff --git a/hugo/content/species/foo_bar/assembly/_index.md b/hugo/content/species/foo_bar/assembly/_index.md new file mode 100644 index 00000000..59c22e0a --- /dev/null +++ b/hugo/content/species/foo_bar/assembly/_index.md @@ -0,0 +1,6 @@ +--- +title: "Genome assembly" +layout: assembly +--- + +### Methods diff --git a/hugo/content/species/foo_bar/assembly/assembly.yaml b/hugo/content/species/foo_bar/assembly/assembly.yaml new file mode 100644 index 00000000..21f063cc --- /dev/null +++ b/hugo/content/species/foo_bar/assembly/assembly.yaml @@ -0,0 +1,15 @@ +name: + label: "Assembly Name" + value: "Foobarus" +type: + label: "Assembly Type" + value: "" +level: + label: "Assembly Level" + value: "" +representation: + label: "Assembly Representation" + value: "" +accession: + label: "Assembly Accession" + value: "" diff --git a/hugo/content/species/foo_bar/assembly/contrib.md b/hugo/content/species/foo_bar/assembly/contrib.md new file mode 100644 index 00000000..97e53c71 --- /dev/null +++ b/hugo/content/species/foo_bar/assembly/contrib.md @@ -0,0 +1,14 @@ +--- +build: + list: never + publishResources: false + render: never +--- + +### Contributor(s) + +### Publication(s) + +### Funding + +### Acknowledgements diff --git a/hugo/content/species/foo_bar/assembly/stats.yaml b/hugo/content/species/foo_bar/assembly/stats.yaml new file mode 100644 index 00000000..0b6aa3d3 --- /dev/null +++ b/hugo/content/species/foo_bar/assembly/stats.yaml @@ -0,0 +1,24 @@ +assembly: + - "Assembly length (Mbp)": [EDIT] + - "GC %": [EDIT] + - "Contig #": [EDIT] + - "Contig N50 (Mbp)": [EDIT] + - "Contig L50": [EDIT] + - "Contig N90 (Mbp)": [EDIT] + - "Contig L90": [EDIT] + - "Scaffold #": [EDIT] + - "Scaffold N50 (Mbp)": [EDIT] + - "Scaffold L50": [EDIT] + - "Scaffold N90 (Mbp)": [EDIT] + - "Scaffold L90": [EDIT] + - "Scaffolds >= 10 kb": [EDIT] + - "BUSCO % [EDIT]": "[EDIT]" + +annotation: + - "Gene #": [EDIT] + - "Transcript #": [EDIT] + - "Avg exons per transcript": [EDIT] + - "Avg gene length (bp)": [EDIT] + - "Avg transcript length (bp)": [EDIT] + - "Avg exon length (bp)": [EDIT] + - "Avg intron length (bp)": [EDIT] diff --git a/hugo/content/species/foo_bar/download.md b/hugo/content/species/foo_bar/download.md new file mode 100644 index 00000000..be355e9c --- /dev/null +++ b/hugo/content/species/foo_bar/download.md @@ -0,0 +1,6 @@ +--- +title: "Download" +layout: "species_download" +url: "clupea_harengus/download" +weight: 3 +--- diff --git a/hugo/content/species/foo_bar/taxonomy.json b/hugo/content/species/foo_bar/taxonomy.json new file mode 100644 index 00000000..d64f3d63 --- /dev/null +++ b/hugo/content/species/foo_bar/taxonomy.json @@ -0,0 +1,58 @@ +{ + "Species": { + "science_name": "Clupea harengus", + "tax_id": "7950", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7950", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7950", + "display_order": 1 + }, + "Genus": { + "science_name": "Clupea", + "tax_id": "7949", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", + "display_order": 2 + }, + "Family": { + "science_name": "Clupeidae", + "tax_id": "55118", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", + "display_order": 3 + }, + "Order": { + "science_name": "Clupeiformes", + "tax_id": "32446", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", + "display_order": 4 + }, + "Class": { + "science_name": "Actinopteri", + "tax_id": "186623", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", + "display_order": 5 + }, + "Phylum": { + "science_name": "Chordata", + "tax_id": "7711", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", + "display_order": 6 + }, + "Kingdom": { + "science_name": "Metazoa", + "tax_id": "33208", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", + "display_order": 7 + }, + "Superkingdom": { + "science_name": "Eukaryota", + "tax_id": "2759", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", + "display_order": 8 + } +} diff --git a/hugo/layouts/species/assembly.html b/hugo/layouts/species/assembly.html new file mode 100644 index 00000000..18faeae0 --- /dev/null +++ b/hugo/layouts/species/assembly.html @@ -0,0 +1,175 @@ +{{ define "main" }} + +{{ partial "species_title.html" . }} + +{{ partial "species_nav.html" . }} + + +{{ $stats_file := (split .Params.stats_data_path "/") }} +{{ $stats_contents := index .Site.Data $stats_file }} + + +{{ $.Scratch.Add "accession" "" }} +{{ range .Params.key_info }} + {{ if isset . "Accession" }} + {{ $.Scratch.Set "accession" .Accession }} + {{ end }} +{{ end }} +{{ $accession := $.Scratch.Get "accession" }} + +{{ $ena_link := print "https://www.ebi.ac.uk/ena/browser/view/" $accession }} +{{ $ncbi_link := print "https://www.ncbi.nlm.nih.gov/datasets/genome/" $accession }} + + + +{{ $content := .Content }} +{{ $contrib := .Resources.Get "contrib.md" }} + + +
+ +
+
+

Description

+
    + {{ with .Resources.Get "assembly.yaml" }} + {{ $metadata := transform.Unmarshal . }} + {{ range slice "name" "type" "level" "representation" "accession" }} + {{ $entry := index $metadata . }} +
  • {{ $entry.label }}: {{ $entry.value }}
    • + {{ end }} + {{ end }} +
+
+
+
+ + + +
+
+ + + +
+
+ +
+ + +
+
+ {{ $content | safeHTML }} +
+
+ +
+ + +
+

Assembly Statistics

+ + {{ if .Params.stats_data_path }} +
+ + + + + + + + + + + {{ range $idx, $statistic := $stats_contents.assembly }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+ {{ else }} +

No assembly data has been provided for this species

+ {{ end }} +
+ + +
+

Annotation Statistics

+ + {{ if .Params.stats_data_path }} +
+ + + + + + + + + + + {{ range $idx, $statistic := $stats_contents.annotation }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+ {{ else }} +

No annotation data has been provided for this species

+ {{ end }} +
+ +
+
+ + +
+
+ {{ $contrib | safeHTML }} +
+
+ +{{ partial "last_updated.html" . }} + + +{{ end }} + +{{ define "scripts" }} + + + +{{ end }} From a78ee2cdc69a65585e9b0667918b9d48aa83aa14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 19 Oct 2024 14:07:13 +0200 Subject: [PATCH 02/59] Simplify species assembly layout --- .../species/foo_bar/assembly/assembly.yaml | 4 +- hugo/layouts/species/assembly.html | 291 ++++++++---------- 2 files changed, 135 insertions(+), 160 deletions(-) diff --git a/hugo/content/species/foo_bar/assembly/assembly.yaml b/hugo/content/species/foo_bar/assembly/assembly.yaml index 21f063cc..3bd79ccd 100644 --- a/hugo/content/species/foo_bar/assembly/assembly.yaml +++ b/hugo/content/species/foo_bar/assembly/assembly.yaml @@ -11,5 +11,5 @@ representation: label: "Assembly Representation" value: "" accession: - label: "Assembly Accession" - value: "" + label: "Accession" + value: "GCA_XXX" diff --git a/hugo/layouts/species/assembly.html b/hugo/layouts/species/assembly.html index 18faeae0..c1574139 100644 --- a/hugo/layouts/species/assembly.html +++ b/hugo/layouts/species/assembly.html @@ -1,175 +1,150 @@ {{ define "main" }} -{{ partial "species_title.html" . }} - -{{ partial "species_nav.html" . }} - - -{{ $stats_file := (split .Params.stats_data_path "/") }} -{{ $stats_contents := index .Site.Data $stats_file }} - - -{{ $.Scratch.Add "accession" "" }} -{{ range .Params.key_info }} - {{ if isset . "Accession" }} - {{ $.Scratch.Set "accession" .Accession }} - {{ end }} -{{ end }} -{{ $accession := $.Scratch.Get "accession" }} - -{{ $ena_link := print "https://www.ebi.ac.uk/ena/browser/view/" $accession }} -{{ $ncbi_link := print "https://www.ncbi.nlm.nih.gov/datasets/genome/" $accession }} - - - -{{ $content := .Content }} -{{ $contrib := .Resources.Get "contrib.md" }} - - -
- -
-
-

Description

-
    - {{ with .Resources.Get "assembly.yaml" }} - {{ $metadata := transform.Unmarshal . }} - {{ range slice "name" "type" "level" "representation" "accession" }} - {{ $entry := index $metadata . }} -
  • {{ $entry.label }}: {{ $entry.value }}
    • - {{ end }} - {{ end }} -
-
-
-
- - - -
- -
+ {{ partial "species_title.html" . }} + + {{ partial "species_nav.html" . }} + +
+ {{ with .Resources.Get "assembly.yaml" }} + {{ $metadata := transform.Unmarshal . }} +
+
+

Description

+
    + {{ range slice "name" "type" "level" "representation" "accession" }} + {{ $entry := index $metadata . }} +
  • {{ $entry.label }}: {{ $entry.value }}
    • + {{ end }} +
+
+
+
+ + + +
+ +
+
+ {{ else }} + No metadata was provided for this assembly. + {{ end }} + +
+
+ {{ .Content }} +
+
+ +
+ {{ with .Resources.Get "stats.yaml" }} + {{ $stats := transform.Unmarshal . }} + + +
+

Assembly Statistics

+
+ + + + + + + + + + + {{ range $idx, $statistic := $stats.assembly }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+
+ + +
+

Annotation Statistics

+ +
+ + + + + + + + + + + {{ range $idx, $statistic := $stats.annotation }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+
+ {{ else }} +

No assembly and annotation statistics have been provided for this species

+ {{ end }} +
-
- {{ $content | safeHTML }} -
-
- -
- - -
-

Assembly Statistics

- - {{ if .Params.stats_data_path }} -
- - - - - - - - - - - {{ range $idx, $statistic := $stats_contents.assembly }} - {{ range $stat_name, $value := $statistic }} - - - - - {{ end }} - {{ end }} - - -
StatisticValue
{{ $stat_name }} {{ $value }}
-
- {{ else }} -

No assembly data has been provided for this species

- {{ end }} -
- - -
-

Annotation Statistics

- - {{ if .Params.stats_data_path }} -
- - - - - - - - - - - {{ range $idx, $statistic := $stats_contents.annotation }} - {{ range $stat_name, $value := $statistic }} - - - - - {{ end }} - {{ end }} - - -
StatisticValue
{{ $stat_name }} {{ $value }}
-
- {{ else }} -

No annotation data has been provided for this species

- {{ end }} -
- -
-
- - -
-
- {{ $contrib | safeHTML }} +
+ {{ with .Resources.Get "contrib.md" }} + {{ .Content }} + {{ end }} +
-
-{{ partial "last_updated.html" . }} + {{ partial "last_updated.html" . }} {{ end }} {{ define "scripts" }} - + {{ end }} From 700abd443f6980c4b53d976d3799661290dca0a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 21 Oct 2024 09:45:41 +0200 Subject: [PATCH 03/59] Add archetype stub --- hugo/archetypes/species/_index.md | 55 +++++++++++++++++ hugo/archetypes/species/assembly/_index.md | 5 ++ .../archetypes/species/assembly/assembly.yaml | 15 +++++ hugo/archetypes/species/assembly/contrib.md | 17 ++++++ hugo/archetypes/species/assembly/stats.yaml | 24 ++++++++ hugo/archetypes/species/download.md | 6 ++ hugo/archetypes/species/taxonomy.json | 58 ++++++++++++++++++ hugo/content/species/_index.md | 4 +- hugo/content/species/foo_bar/_index.md | 7 ++- .../foo_bar/assembly/{_index.md => index.md} | 0 hugo/layouts/species/browser.html | 60 +++++++++++++++++++ 11 files changed, 246 insertions(+), 5 deletions(-) create mode 100644 hugo/archetypes/species/_index.md create mode 100644 hugo/archetypes/species/assembly/_index.md create mode 100644 hugo/archetypes/species/assembly/assembly.yaml create mode 100644 hugo/archetypes/species/assembly/contrib.md create mode 100644 hugo/archetypes/species/assembly/stats.yaml create mode 100644 hugo/archetypes/species/download.md create mode 100644 hugo/archetypes/species/taxonomy.json rename hugo/content/species/foo_bar/assembly/{_index.md => index.md} (100%) create mode 100644 hugo/layouts/species/browser.html diff --git a/hugo/archetypes/species/_index.md b/hugo/archetypes/species/_index.md new file mode 100644 index 00000000..7506ad6a --- /dev/null +++ b/hugo/archetypes/species/_index.md @@ -0,0 +1,55 @@ +--- +# Required params below +title: "*Clupea harengus*" +subtitle: "Atlantic herring" + +last_updated: "15/05/2024" + +cover_image: "/img/species/clupea_harengus.webp" +img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" +img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" + + +# The params below were auto-generated, you should not need to edit them... +# unless you were warned by the add-new-species.py script. +layout: "species_intro" +banner_title: "Species overview" +url: "clupea_harengus" +weight: 1 +science_name: "Clupea harengus" +lineage_data_path: "clupea_harengus/taxonomy" + +gbif_taxon_id: "8351946" +goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" + + +# Optional params below, +# remove them if you don't want them or they are not relevant. +iucn_category: "Least Concern" +iucn_link: "https://www.iucnredlist.org/species/155123/4717767" + +swe_red_list: "Viable" +swe_red_list_link: "https://artfakta.se/taxa/206089/" + +# These 3 params define the initial view for the map +# latitude and longitude are for the map center. +latitude: 60 +longitude: -40 +initialZoom: 1 +--- + +### Description + +Write some content here in markdown for the introduction tab of the species page. + +#### Genome reference + +[EDIT] + +#### References + +- [EDIT] + +#### Changelog + +- DD/MM/YYYY - Species first published on the Portal diff --git a/hugo/archetypes/species/assembly/_index.md b/hugo/archetypes/species/assembly/_index.md new file mode 100644 index 00000000..7630469e --- /dev/null +++ b/hugo/archetypes/species/assembly/_index.md @@ -0,0 +1,5 @@ +--- +title: "Genome assembly" +--- + +### Methods diff --git a/hugo/archetypes/species/assembly/assembly.yaml b/hugo/archetypes/species/assembly/assembly.yaml new file mode 100644 index 00000000..1a49687b --- /dev/null +++ b/hugo/archetypes/species/assembly/assembly.yaml @@ -0,0 +1,15 @@ +name: + label: "Assembly Name" + value: "" +type: + label: "Assembly Type" + value: "" +level: + label: "Assembly Level" + value: "" +representation: + label: "Assembly Representation" + value: "" +accession: + label: "Assembly Accession" + value: "" diff --git a/hugo/archetypes/species/assembly/contrib.md b/hugo/archetypes/species/assembly/contrib.md new file mode 100644 index 00000000..c76ea97a --- /dev/null +++ b/hugo/archetypes/species/assembly/contrib.md @@ -0,0 +1,17 @@ +--- +build: + list: never + publishResources: false + render: never +--- + +### Contributor(s) + + +### Publication(s) + + +### Funding + + +### Acknowledgements diff --git a/hugo/archetypes/species/assembly/stats.yaml b/hugo/archetypes/species/assembly/stats.yaml new file mode 100644 index 00000000..0b6aa3d3 --- /dev/null +++ b/hugo/archetypes/species/assembly/stats.yaml @@ -0,0 +1,24 @@ +assembly: + - "Assembly length (Mbp)": [EDIT] + - "GC %": [EDIT] + - "Contig #": [EDIT] + - "Contig N50 (Mbp)": [EDIT] + - "Contig L50": [EDIT] + - "Contig N90 (Mbp)": [EDIT] + - "Contig L90": [EDIT] + - "Scaffold #": [EDIT] + - "Scaffold N50 (Mbp)": [EDIT] + - "Scaffold L50": [EDIT] + - "Scaffold N90 (Mbp)": [EDIT] + - "Scaffold L90": [EDIT] + - "Scaffolds >= 10 kb": [EDIT] + - "BUSCO % [EDIT]": "[EDIT]" + +annotation: + - "Gene #": [EDIT] + - "Transcript #": [EDIT] + - "Avg exons per transcript": [EDIT] + - "Avg gene length (bp)": [EDIT] + - "Avg transcript length (bp)": [EDIT] + - "Avg exon length (bp)": [EDIT] + - "Avg intron length (bp)": [EDIT] diff --git a/hugo/archetypes/species/download.md b/hugo/archetypes/species/download.md new file mode 100644 index 00000000..be355e9c --- /dev/null +++ b/hugo/archetypes/species/download.md @@ -0,0 +1,6 @@ +--- +title: "Download" +layout: "species_download" +url: "clupea_harengus/download" +weight: 3 +--- diff --git a/hugo/archetypes/species/taxonomy.json b/hugo/archetypes/species/taxonomy.json new file mode 100644 index 00000000..d64f3d63 --- /dev/null +++ b/hugo/archetypes/species/taxonomy.json @@ -0,0 +1,58 @@ +{ + "Species": { + "science_name": "Clupea harengus", + "tax_id": "7950", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7950", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7950", + "display_order": 1 + }, + "Genus": { + "science_name": "Clupea", + "tax_id": "7949", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", + "display_order": 2 + }, + "Family": { + "science_name": "Clupeidae", + "tax_id": "55118", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", + "display_order": 3 + }, + "Order": { + "science_name": "Clupeiformes", + "tax_id": "32446", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", + "display_order": 4 + }, + "Class": { + "science_name": "Actinopteri", + "tax_id": "186623", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", + "display_order": 5 + }, + "Phylum": { + "science_name": "Chordata", + "tax_id": "7711", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", + "display_order": 6 + }, + "Kingdom": { + "science_name": "Metazoa", + "tax_id": "33208", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", + "display_order": 7 + }, + "Superkingdom": { + "science_name": "Eukaryota", + "tax_id": "2759", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", + "display_order": 8 + } +} diff --git a/hugo/content/species/_index.md b/hugo/content/species/_index.md index ba412b29..7d50b2ff 100644 --- a/hugo/content/species/_index.md +++ b/hugo/content/species/_index.md @@ -1,7 +1,7 @@ --- # This prevents the species folder from generating a html file for the path [webaddress]/species/ -_build: +build: render: never list: never publishResources: false ---- \ No newline at end of file +--- diff --git a/hugo/content/species/foo_bar/_index.md b/hugo/content/species/foo_bar/_index.md index 7506ad6a..7d08497c 100644 --- a/hugo/content/species/foo_bar/_index.md +++ b/hugo/content/species/foo_bar/_index.md @@ -1,10 +1,12 @@ --- # Required params below -title: "*Clupea harengus*" -subtitle: "Atlantic herring" +title: "*Foo barus*" +subtitle: "Pacifc herring" last_updated: "15/05/2024" +# TODO Place image in bundle and use metadata for uniform naming +# TODO Extract non-standard fields under params key cover_image: "/img/species/clupea_harengus.webp" img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" @@ -14,7 +16,6 @@ img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg # unless you were warned by the add-new-species.py script. layout: "species_intro" banner_title: "Species overview" -url: "clupea_harengus" weight: 1 science_name: "Clupea harengus" lineage_data_path: "clupea_harengus/taxonomy" diff --git a/hugo/content/species/foo_bar/assembly/_index.md b/hugo/content/species/foo_bar/assembly/index.md similarity index 100% rename from hugo/content/species/foo_bar/assembly/_index.md rename to hugo/content/species/foo_bar/assembly/index.md diff --git a/hugo/layouts/species/browser.html b/hugo/layouts/species/browser.html new file mode 100644 index 00000000..ae2abb84 --- /dev/null +++ b/hugo/layouts/species/browser.html @@ -0,0 +1,60 @@ +{{ define "main" }} + +
+
+
+
+ + + +
+ +{{ if hugo.IsDevelopment }} + +{{ end }} + + + + +{{ end }} From f1fdc666b87692939d97d8da06a50985009a4da2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 09:37:45 +0200 Subject: [PATCH 04/59] Start halloween experiment --- .../{species => halloween}/_index.md | 0 .../{species => halloween}/assembly/_index.md | 0 .../assembly/assembly.yaml | 0 .../assembly/contrib.md | 0 .../assembly/stats.yaml | 0 .../{species => halloween}/download.md | 0 .../{species => halloween}/taxonomy.json | 0 .../{species => halloween}/foo_bar/_index.md | 0 .../foo_bar/assembly/assembly.yaml | 0 .../foo_bar/assembly/contrib.md | 0 .../foo_bar/assembly/index.md | 0 .../foo_bar/assembly/stats.yaml | 0 .../foo_bar/download.md | 0 .../foo_bar/taxonomy.json | 0 .../{species => halloween}/assembly.html | 0 hugo/layouts/halloween/baseof.html | 97 +++++++++++++++++++ .../{species => halloween}/browser.html | 0 17 files changed, 97 insertions(+) rename hugo/archetypes/{species => halloween}/_index.md (100%) rename hugo/archetypes/{species => halloween}/assembly/_index.md (100%) rename hugo/archetypes/{species => halloween}/assembly/assembly.yaml (100%) rename hugo/archetypes/{species => halloween}/assembly/contrib.md (100%) rename hugo/archetypes/{species => halloween}/assembly/stats.yaml (100%) rename hugo/archetypes/{species => halloween}/download.md (100%) rename hugo/archetypes/{species => halloween}/taxonomy.json (100%) rename hugo/content/{species => halloween}/foo_bar/_index.md (100%) rename hugo/content/{species => halloween}/foo_bar/assembly/assembly.yaml (100%) rename hugo/content/{species => halloween}/foo_bar/assembly/contrib.md (100%) rename hugo/content/{species => halloween}/foo_bar/assembly/index.md (100%) rename hugo/content/{species => halloween}/foo_bar/assembly/stats.yaml (100%) rename hugo/content/{species => halloween}/foo_bar/download.md (100%) rename hugo/content/{species => halloween}/foo_bar/taxonomy.json (100%) rename hugo/layouts/{species => halloween}/assembly.html (100%) create mode 100644 hugo/layouts/halloween/baseof.html rename hugo/layouts/{species => halloween}/browser.html (100%) diff --git a/hugo/archetypes/species/_index.md b/hugo/archetypes/halloween/_index.md similarity index 100% rename from hugo/archetypes/species/_index.md rename to hugo/archetypes/halloween/_index.md diff --git a/hugo/archetypes/species/assembly/_index.md b/hugo/archetypes/halloween/assembly/_index.md similarity index 100% rename from hugo/archetypes/species/assembly/_index.md rename to hugo/archetypes/halloween/assembly/_index.md diff --git a/hugo/archetypes/species/assembly/assembly.yaml b/hugo/archetypes/halloween/assembly/assembly.yaml similarity index 100% rename from hugo/archetypes/species/assembly/assembly.yaml rename to hugo/archetypes/halloween/assembly/assembly.yaml diff --git a/hugo/archetypes/species/assembly/contrib.md b/hugo/archetypes/halloween/assembly/contrib.md similarity index 100% rename from hugo/archetypes/species/assembly/contrib.md rename to hugo/archetypes/halloween/assembly/contrib.md diff --git a/hugo/archetypes/species/assembly/stats.yaml b/hugo/archetypes/halloween/assembly/stats.yaml similarity index 100% rename from hugo/archetypes/species/assembly/stats.yaml rename to hugo/archetypes/halloween/assembly/stats.yaml diff --git a/hugo/archetypes/species/download.md b/hugo/archetypes/halloween/download.md similarity index 100% rename from hugo/archetypes/species/download.md rename to hugo/archetypes/halloween/download.md diff --git a/hugo/archetypes/species/taxonomy.json b/hugo/archetypes/halloween/taxonomy.json similarity index 100% rename from hugo/archetypes/species/taxonomy.json rename to hugo/archetypes/halloween/taxonomy.json diff --git a/hugo/content/species/foo_bar/_index.md b/hugo/content/halloween/foo_bar/_index.md similarity index 100% rename from hugo/content/species/foo_bar/_index.md rename to hugo/content/halloween/foo_bar/_index.md diff --git a/hugo/content/species/foo_bar/assembly/assembly.yaml b/hugo/content/halloween/foo_bar/assembly/assembly.yaml similarity index 100% rename from hugo/content/species/foo_bar/assembly/assembly.yaml rename to hugo/content/halloween/foo_bar/assembly/assembly.yaml diff --git a/hugo/content/species/foo_bar/assembly/contrib.md b/hugo/content/halloween/foo_bar/assembly/contrib.md similarity index 100% rename from hugo/content/species/foo_bar/assembly/contrib.md rename to hugo/content/halloween/foo_bar/assembly/contrib.md diff --git a/hugo/content/species/foo_bar/assembly/index.md b/hugo/content/halloween/foo_bar/assembly/index.md similarity index 100% rename from hugo/content/species/foo_bar/assembly/index.md rename to hugo/content/halloween/foo_bar/assembly/index.md diff --git a/hugo/content/species/foo_bar/assembly/stats.yaml b/hugo/content/halloween/foo_bar/assembly/stats.yaml similarity index 100% rename from hugo/content/species/foo_bar/assembly/stats.yaml rename to hugo/content/halloween/foo_bar/assembly/stats.yaml diff --git a/hugo/content/species/foo_bar/download.md b/hugo/content/halloween/foo_bar/download.md similarity index 100% rename from hugo/content/species/foo_bar/download.md rename to hugo/content/halloween/foo_bar/download.md diff --git a/hugo/content/species/foo_bar/taxonomy.json b/hugo/content/halloween/foo_bar/taxonomy.json similarity index 100% rename from hugo/content/species/foo_bar/taxonomy.json rename to hugo/content/halloween/foo_bar/taxonomy.json diff --git a/hugo/layouts/species/assembly.html b/hugo/layouts/halloween/assembly.html similarity index 100% rename from hugo/layouts/species/assembly.html rename to hugo/layouts/halloween/assembly.html diff --git a/hugo/layouts/halloween/baseof.html b/hugo/layouts/halloween/baseof.html new file mode 100644 index 00000000..865edeed --- /dev/null +++ b/hugo/layouts/halloween/baseof.html @@ -0,0 +1,97 @@ + + + + + + + {{ printf "%s | %s" (or .Params.banner_title .Title) .Site.Title }} + + {{ $description := partial "create_description.html" . }} + + + + + + + + + + + {{ template "_internal/opengraph.html" . }} + {{ template "_internal/twitter_cards.html" . }} + + + + + + + + {{ block "early_connections" . }} {{ end }} + + + + + + + + + + + + {{ $cssResource := resources.Get "css/styles.css" | resources.Minify | resources.Fingerprint }} + + + + + + + {{ block "script_includes" . }} {{ end }} + + + + + + {{- partial "navbar.html" . -}} + + {{ if eq .Kind "home" }} + {{- partial "hero.html" . -}} + {{ else }} + {{- partial "banner.html" . -}} + {{ end }} + + {{ $isGenomePage := eq .RelPermalink "/genome-browser/" }} + {{ if and (not $isGenomePage) (not .IsHome) }} + {{- partial "breadcrumbs.html" . -}} + {{ end }} + + {{- block "header" . }}{{- end }} +
+ + {{ if $isGenomePage }} +
+ {{ else }} +
+ {{ end }} + + {{ if .Params.toc }} +
+
{{- partial "toc.html" . -}}
+
{{- block "main" . }}{{- end }}
+
+ {{ else }} + {{- block "main" . }}{{- end }} + {{ end }} +
+
+ + {{ if not $isGenomePage }} +
+ {{- partial "footer.html" . -}} + {{ end }} + + diff --git a/hugo/layouts/species/browser.html b/hugo/layouts/halloween/browser.html similarity index 100% rename from hugo/layouts/species/browser.html rename to hugo/layouts/halloween/browser.html From 2170e580a674fc0f23f2895bd3fcf1fc0a527bf1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 10:36:47 +0200 Subject: [PATCH 05/59] Specify cover image as page resource --- hugo/content/halloween/foo_bar/_index.md | 30 ++- hugo/content/halloween/foo_bar/pumpkin.jpg | Bin 0 -> 29752 bytes hugo/layouts/halloween/species_assembly.html | 189 +++++++++++++++++++ hugo/layouts/halloween/species_download.html | 107 +++++++++++ hugo/layouts/halloween/species_intro.html | 174 +++++++++++++++++ 5 files changed, 482 insertions(+), 18 deletions(-) create mode 100644 hugo/content/halloween/foo_bar/pumpkin.jpg create mode 100644 hugo/layouts/halloween/species_assembly.html create mode 100644 hugo/layouts/halloween/species_download.html create mode 100644 hugo/layouts/halloween/species_intro.html diff --git a/hugo/content/halloween/foo_bar/_index.md b/hugo/content/halloween/foo_bar/_index.md index 7d08497c..9fbd287d 100644 --- a/hugo/content/halloween/foo_bar/_index.md +++ b/hugo/content/halloween/foo_bar/_index.md @@ -1,39 +1,33 @@ --- -# Required params below -title: "*Foo barus*" -subtitle: "Pacifc herring" +title: Jacobus lanternibus +subtitle: "Jack-o'-lantern" +lastmod: 2024-10-26T10:00:00+0200 + +resources: + - title: "Fiery pumpkin" + name: cover_image + src: pumpkin.jpg + params: + attribution: demonic domain, CC BY-SATAN + link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg -last_updated: "15/05/2024" - -# TODO Place image in bundle and use metadata for uniform naming -# TODO Extract non-standard fields under params key cover_image: "/img/species/clupea_harengus.webp" img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" - -# The params below were auto-generated, you should not need to edit them... -# unless you were warned by the add-new-species.py script. layout: "species_intro" -banner_title: "Species overview" +banner_title: "Halloween species overview" weight: 1 science_name: "Clupea harengus" lineage_data_path: "clupea_harengus/taxonomy" gbif_taxon_id: "8351946" goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" - - -# Optional params below, -# remove them if you don't want them or they are not relevant. iucn_category: "Least Concern" iucn_link: "https://www.iucnredlist.org/species/155123/4717767" swe_red_list: "Viable" swe_red_list_link: "https://artfakta.se/taxa/206089/" - -# These 3 params define the initial view for the map -# latitude and longitude are for the map center. latitude: 60 longitude: -40 initialZoom: 1 diff --git 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zBmwP7_I>)uzZK?Z_gL7=iajYUJI_ohYLXE=fG({xsurv=g)%D6ZI}%I0Gh;4#5b zN@okmUVgMuQzfZ!lMvmWK2c9MXK?vPG*M9`Z4HGtXCvhlsdRI|0*WbE+M3i)wz{@J z0G=vP?IUEKNTP}?bfyiFj&qt+JHZ44k7_8S(WS)l*EuSu@TVjqMj(a9(uyl7ww{H> zj}}OC!jHm`S*n6^I3AQyP^9~jEy#ta&m<9_N*>uk=mvc#qJ<~i6CE5%2HXM%Jk;xM zx!@@LD59H_v8_2WcwkUQRZrnpV7HD(#>E&Olu=koYI-y_FI#Exxg!cc3X$}DHGDr4IX=L8IUQAG)AXHn=x&QX8>bL~u)R#FHfpK2(owx>15i>Dvm zKZOr?_~@UN6jj)XGAVD_6CqHarB-c4*pO95Jp~k1#T+<^H1s1nqlUpyK&L*aMn87B zKJ-ytG@%zAQOnN7Gpv9TfRcS_mnDLNHh_C#iYqy*PeDpf#b=$9B!zC>D!Xb72>}!G OqKeuo`m>r(L;u-t5k(9D literal 0 HcmV?d00001 diff --git a/hugo/layouts/halloween/species_assembly.html b/hugo/layouts/halloween/species_assembly.html new file mode 100644 index 00000000..fa75c204 --- /dev/null +++ b/hugo/layouts/halloween/species_assembly.html @@ -0,0 +1,189 @@ +{{ define "early_connections" }} + + + +{{ end }} + + +{{ define "script_includes" }} + +{{ partial "add_datatables_jquery.html" . }} + +{{ end }} + + + +{{ define "main" }} + +{{ partial "species_title.html" . }} + +{{ partial "species_nav.html" . }} + + +{{ $stats_file := (split .Params.stats_data_path "/") }} +{{ $stats_contents := index .Site.Data $stats_file }} + + +{{ $.Scratch.Add "accession" "" }} +{{ range .Params.key_info }} + {{ if isset . "Accession" }} + {{ $.Scratch.Set "accession" .Accession }} + {{ end }} +{{ end }} +{{ $accession := $.Scratch.Get "accession" }} + +{{ $ena_link := print "https://www.ebi.ac.uk/ena/browser/view/" $accession }} +{{ $ncbi_link := print "https://www.ncbi.nlm.nih.gov/datasets/genome/" $accession }} + + + +{{ $content := split .Content "|||||| Content divider - do not remove ||||||" }} +{{ $contentp1 := index $content 0 }} +{{ $contentp2 := index $content 1 }} + + +
+ +
+
+

Description

+
    + {{ range .Params.key_info }} + {{ range $key, $value := . }} +
  • {{ $key }}: {{ $value }}
    • + {{ end }} + {{ end }} +
+
+
+
+ + + +
+ +
+ +
+ + +
+
+ {{ $contentp1 | safeHTML }} +
+
+ +
+ + +
+

Assembly Statistics

+ + {{ if .Params.stats_data_path }} +
+ + + + + + + + + + + {{ range $idx, $statistic := $stats_contents.assembly }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+ {{ else }} +

No assembly data has been provided for this species

+ {{ end }} +
+ + +
+

Annotation Statistics

+ + {{ if .Params.stats_data_path }} +
+ + + + + + + + + + + {{ range $idx, $statistic := $stats_contents.annotation }} + {{ range $stat_name, $value := $statistic }} + + + + + {{ end }} + {{ end }} + + +
StatisticValue
{{ $stat_name }} {{ $value }}
+
+ {{ else }} +

No annotation data has been provided for this species

+ {{ end }} +
+ +
+
+ + +
+
+ {{ $contentp2 | safeHTML }} +
+
+ +{{ partial "last_updated.html" . }} + + +{{ end }} + +{{ define "scripts" }} + + + +{{ end }} diff --git a/hugo/layouts/halloween/species_download.html b/hugo/layouts/halloween/species_download.html new file mode 100644 index 00000000..65172973 --- /dev/null +++ b/hugo/layouts/halloween/species_download.html @@ -0,0 +1,107 @@ +{{ define "early_connections" }} + + + +{{ end }} + + +{{ define "script_includes" }} + +{{ partial "add_datatables_jquery.html" . }} + +{{ end }} + + + +{{ define "main" }} + +{{ partial "species_title.html" . }} + +{{ partial "species_nav.html" . }} + +
+ +
+
+

Data availability

+

+ The table below lists the data files currently displayed on the Genome Portal. + In the Links column, you can find action buttons to download the data file, + go to the website of the source repository from where the data was fetched, + and (if applicable) the associated scientific article(s) to the data. + You can use the toggle on the top right of the table to switch between the default and the expanded table view. +

+
+
+ + + {{ $speciesName := index (split .RelPermalink "/") 1 }} + + {{ $tableDataPath := printf "%s/data_tracks.json" $speciesName }} + {{ $tableDataResource := resources.Get $tableDataPath }} + {{ $tableData := $tableDataResource | transform.Unmarshal }} + + {{ $staticDirPath := printf "/%s/data_tracks" $speciesName }} + {{ $staticDirFile := printf "%s/data_tracks.json" $speciesName }} + + {{ (resources.Get $tableDataPath | resources.Copy $staticDirFile).Publish }} + + + {{ $aliasFileURL := "" }} + {{ if .Params.alias_file_url }} + {{ $aliasFileURL = .Params.alias_file_url }} + {{ end }} + + +
+
+ + +
+ +
+ {{ partial "download_table" (dict "tableType" "long" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} +
+ +
+ {{ partial "download_table" (dict "tableType" "short" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} +
+
+ +
+ +{{ partial "last_updated.html" . }} + + + +{{ end }} diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html new file mode 100644 index 00000000..a4d2d0e4 --- /dev/null +++ b/hugo/layouts/halloween/species_intro.html @@ -0,0 +1,174 @@ +{{ define "early_connections" }} + + + +{{ end }} + + +{{ define "script_includes" }} + + + + + +{{ end }} + + +{{ define "main" }} + +{{ partial "species_title.html" . }} + +{{ partial "species_nav.html" . }} + + +
+ + +
+ +
+
+ {{ with .Resources.Get "cover_image"}} + {{ .Title }} + {{ $title := printf "%s - %s" .Title .Params.Attribution }} + {{ if .Params.Link }} + +
{{ $title }}
+ + {{ else }} +

+ {{ $title }} +

+ {{ end }} + {{ end }} +
+
+ +
+ {{ partial "distrib_map.html" . }} +
+
+ + +
+ + +
+

Taxonomy

+ + {{ $lineage_file := (split .Params.lineage_data_path "/") }} + {{ $unsorted_dict := index .Site.Data $lineage_file }} + + + {{ $lineage_slice := slice }} + {{ range $rank, $value := $unsorted_dict }} + {{ $lineage_slice = $lineage_slice | append (dict "rank" $rank "value" $value) }} + {{ end }} + {{ $sorted_lineage := sort $lineage_slice "value.display_order" "desc" }} + + + {{ range $rank, $item := $sorted_lineage }} +
+
+ {{ if eq $item.rank "Superkingdom" }} + Domain: + {{ else }} + {{ $item.rank }}: + {{ end }} + {{if or (eq $item.rank "Genus") (eq $item.rank "Species") }} + {{ $item.value.science_name }} + {{ else }} + {{ $item.value.science_name }} + {{ end }} +
+ +
+
+ {{ end }} + +
+
+ NCBI Taxonomy ID: + + {{ $species_dict := index $unsorted_dict "Species" }} + {{ $tax_id := index $species_dict "tax_id" }} + {{ $ncbi_link := index $species_dict "ncbi_link" }} + + {{$tax_id}} + +
+
+
+ +
+ {{ if or .Params.iucn_category .Params.swe_red_list }} +

Vulnerability

+

+ {{ if .Params.iucn_category }} + IUCN Category: + {{ .Params.iucn_category }} +
+ {{ end }} + + {{ if .Params.swe_red_list }} + Swedish Red List: + {{ .Params.swe_red_list }} +
+ {{ end }} +

+ {{ end }} + + +

External links

+ +
+ {{ if .Params.gbif_taxon_id }} + + + + + + + + {{ end }} + + {{ if .Params.goat_webpage }} + + + + {{ end }} + +
+ +
+ + + +
+ +
+ +
+
+ {{ .Content }} +
+
+ + {{ partial "last_updated.html" . }} + +
+{{ end }} From afd4ed1ba07be2876dc290254b7f58caf73d5807 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 10:53:50 +0200 Subject: [PATCH 06/59] Use lastmod property in last_updated partial --- hugo/layouts/partials/last_updated.html | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/hugo/layouts/partials/last_updated.html b/hugo/layouts/partials/last_updated.html index d74d42ed..674abf06 100644 --- a/hugo/layouts/partials/last_updated.html +++ b/hugo/layouts/partials/last_updated.html @@ -1,10 +1,5 @@ -{{ $lastUpdated := .Params.last_updated }} -{{ if not (or .IsHome .IsSection) }} - {{ $lastUpdated = .Parent.Params.last_updated }} -{{ end }} -

- Page last updated: {{ $lastUpdated }} + Page last updated: {{ .Lastmod | time.Format ":date_long"}}

From 9da233aec0d72c19f8cf22ed64bf086e0a396ae6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 10:57:42 +0200 Subject: [PATCH 07/59] fixup! Specify cover image as page resource --- hugo/content/halloween/foo_bar/_index.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/hugo/content/halloween/foo_bar/_index.md b/hugo/content/halloween/foo_bar/_index.md index 9fbd287d..864daa63 100644 --- a/hugo/content/halloween/foo_bar/_index.md +++ b/hugo/content/halloween/foo_bar/_index.md @@ -11,10 +11,6 @@ resources: attribution: demonic domain, CC BY-SATAN link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg -cover_image: "/img/species/clupea_harengus.webp" -img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" -img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" - layout: "species_intro" banner_title: "Halloween species overview" weight: 1 From 5f588499a15eb62a66b5309ba1563c178668f43b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 11:15:17 +0200 Subject: [PATCH 08/59] Properly name pumpkin directory --- hugo/content/halloween/foo_bar/_index.md | 46 -------------- .../halloween/foo_bar/assembly/assembly.yaml | 15 ----- .../halloween/foo_bar/assembly/contrib.md | 14 ----- .../halloween/foo_bar/assembly/index.md | 6 -- .../halloween/foo_bar/assembly/stats.yaml | 24 -------- hugo/content/halloween/foo_bar/download.md | 6 -- hugo/content/halloween/foo_bar/pumpkin.jpg | Bin 29752 -> 0 bytes hugo/content/halloween/foo_bar/taxonomy.json | 58 ------------------ 8 files changed, 169 deletions(-) delete mode 100644 hugo/content/halloween/foo_bar/_index.md delete mode 100644 hugo/content/halloween/foo_bar/assembly/assembly.yaml delete mode 100644 hugo/content/halloween/foo_bar/assembly/contrib.md delete mode 100644 hugo/content/halloween/foo_bar/assembly/index.md delete mode 100644 hugo/content/halloween/foo_bar/assembly/stats.yaml delete mode 100644 hugo/content/halloween/foo_bar/download.md delete mode 100644 hugo/content/halloween/foo_bar/pumpkin.jpg delete mode 100644 hugo/content/halloween/foo_bar/taxonomy.json diff --git a/hugo/content/halloween/foo_bar/_index.md b/hugo/content/halloween/foo_bar/_index.md deleted file mode 100644 index 864daa63..00000000 --- a/hugo/content/halloween/foo_bar/_index.md +++ /dev/null @@ -1,46 +0,0 @@ ---- -title: Jacobus lanternibus -subtitle: "Jack-o'-lantern" -lastmod: 2024-10-26T10:00:00+0200 - -resources: - - title: "Fiery pumpkin" - name: cover_image - src: pumpkin.jpg - params: - attribution: demonic domain, CC BY-SATAN - link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg - -layout: "species_intro" -banner_title: "Halloween species overview" -weight: 1 -science_name: "Clupea harengus" -lineage_data_path: "clupea_harengus/taxonomy" - -gbif_taxon_id: "8351946" -goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" -iucn_category: "Least Concern" -iucn_link: "https://www.iucnredlist.org/species/155123/4717767" - -swe_red_list: "Viable" -swe_red_list_link: "https://artfakta.se/taxa/206089/" -latitude: 60 -longitude: -40 -initialZoom: 1 ---- - -### Description - -Write some content here in markdown for the introduction tab of the species page. - -#### Genome reference - -[EDIT] - -#### References - -- [EDIT] - -#### Changelog - -- DD/MM/YYYY - Species first published on the Portal diff --git a/hugo/content/halloween/foo_bar/assembly/assembly.yaml b/hugo/content/halloween/foo_bar/assembly/assembly.yaml deleted file mode 100644 index 3bd79ccd..00000000 --- a/hugo/content/halloween/foo_bar/assembly/assembly.yaml +++ /dev/null @@ -1,15 +0,0 @@ -name: - label: "Assembly Name" - value: "Foobarus" -type: - label: "Assembly Type" - value: "" -level: - label: "Assembly Level" - value: "" -representation: - label: "Assembly Representation" - value: "" -accession: - label: "Accession" - value: "GCA_XXX" diff --git a/hugo/content/halloween/foo_bar/assembly/contrib.md b/hugo/content/halloween/foo_bar/assembly/contrib.md deleted file mode 100644 index 97e53c71..00000000 --- a/hugo/content/halloween/foo_bar/assembly/contrib.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -build: - list: never - publishResources: false - render: never ---- - -### Contributor(s) - -### Publication(s) - -### Funding - -### Acknowledgements diff --git a/hugo/content/halloween/foo_bar/assembly/index.md b/hugo/content/halloween/foo_bar/assembly/index.md deleted file mode 100644 index 59c22e0a..00000000 --- a/hugo/content/halloween/foo_bar/assembly/index.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Genome assembly" -layout: assembly ---- - -### Methods diff --git a/hugo/content/halloween/foo_bar/assembly/stats.yaml b/hugo/content/halloween/foo_bar/assembly/stats.yaml deleted file mode 100644 index 0b6aa3d3..00000000 --- a/hugo/content/halloween/foo_bar/assembly/stats.yaml +++ /dev/null @@ -1,24 +0,0 @@ -assembly: - - "Assembly length (Mbp)": [EDIT] - - "GC %": [EDIT] - - "Contig #": [EDIT] - - "Contig N50 (Mbp)": [EDIT] - - "Contig L50": [EDIT] - - "Contig N90 (Mbp)": [EDIT] - - "Contig L90": [EDIT] - - "Scaffold #": [EDIT] - - "Scaffold N50 (Mbp)": [EDIT] - - "Scaffold L50": [EDIT] - - "Scaffold N90 (Mbp)": [EDIT] - - "Scaffold L90": [EDIT] - - "Scaffolds >= 10 kb": [EDIT] - - "BUSCO % [EDIT]": "[EDIT]" - -annotation: - - "Gene #": [EDIT] - - "Transcript #": [EDIT] - - "Avg exons per transcript": [EDIT] - - "Avg gene length (bp)": [EDIT] - - "Avg transcript length (bp)": [EDIT] - - "Avg exon length (bp)": [EDIT] - - "Avg intron length (bp)": [EDIT] diff --git a/hugo/content/halloween/foo_bar/download.md b/hugo/content/halloween/foo_bar/download.md deleted file mode 100644 index be355e9c..00000000 --- a/hugo/content/halloween/foo_bar/download.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -title: "Download" -layout: "species_download" -url: "clupea_harengus/download" -weight: 3 ---- diff --git a/hugo/content/halloween/foo_bar/pumpkin.jpg b/hugo/content/halloween/foo_bar/pumpkin.jpg deleted file mode 100644 index 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"display_order": 1 - }, - "Genus": { - "science_name": "Clupea", - "tax_id": "7949", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", - "display_order": 2 - }, - "Family": { - "science_name": "Clupeidae", - "tax_id": "55118", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", - "display_order": 3 - }, - "Order": { - "science_name": "Clupeiformes", - "tax_id": "32446", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", - "display_order": 4 - }, - "Class": { - "science_name": "Actinopteri", - "tax_id": "186623", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", - "display_order": 5 - }, - "Phylum": { - "science_name": "Chordata", - "tax_id": "7711", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", - "display_order": 6 - }, - "Kingdom": { - "science_name": "Metazoa", - "tax_id": "33208", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", - "display_order": 7 - }, - "Superkingdom": { - "science_name": "Eukaryota", - "tax_id": "2759", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", - "display_order": 8 - } -} From b97143251d3e29104f5677c6ab2e15a6364cb441 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 11:15:48 +0200 Subject: [PATCH 09/59] Use concise form of crossorigin HTML attribute --- hugo/layouts/halloween/species_intro.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index a4d2d0e4..675fb402 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -8,10 +8,10 @@ {{ define "script_includes" }} + integrity="sha256-p4NxAoJBhIIN+hmNHrzRCf9tD/miZyoHS5obTRR9BMY=" crossorigin/> + integrity="sha256-20nQCchB9co0qIjJZRGuk2/Z9VM+kNiyxNV1lvTlZBo=" crossorigin defer> {{ end }} From 15140fc7534a294947d1af945123d97afa515a0c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 11:16:25 +0200 Subject: [PATCH 10/59] Show debug information in development environment --- hugo/layouts/halloween/baseof.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/hugo/layouts/halloween/baseof.html b/hugo/layouts/halloween/baseof.html index 865edeed..cca47405 100644 --- a/hugo/layouts/halloween/baseof.html +++ b/hugo/layouts/halloween/baseof.html @@ -93,5 +93,8 @@
{{- partial "footer.html" . -}} {{ end }} + {{ if hugo.IsDevelopment }} + 
 {{ debug.Dump . }}
+ {{ end }} From a2f2634fb7f78abd9b7b66fba3259796485123c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 11:17:50 +0200 Subject: [PATCH 11/59] Add forgotten content directory --- .../halloween/jacobus_lanternibus/_index.md | 46 ++++++++++++++ .../assembly/assembly.yaml | 15 +++++ .../jacobus_lanternibus/assembly/contrib.md | 14 +++++ .../jacobus_lanternibus/assembly/index.md | 6 ++ .../jacobus_lanternibus/assembly/stats.yaml | 24 ++++++++ .../halloween/jacobus_lanternibus/download.md | 6 ++ .../jacobus_lanternibus/intro/index.md | 3 + .../halloween/jacobus_lanternibus/pumpkin.jpg | Bin 0 -> 29752 bytes .../jacobus_lanternibus/taxonomy.json | 58 ++++++++++++++++++ 9 files changed, 172 insertions(+) create mode 100644 hugo/content/halloween/jacobus_lanternibus/_index.md create mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml create mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md create mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/index.md create mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml create mode 100644 hugo/content/halloween/jacobus_lanternibus/download.md create mode 100644 hugo/content/halloween/jacobus_lanternibus/intro/index.md create mode 100644 hugo/content/halloween/jacobus_lanternibus/pumpkin.jpg create mode 100644 hugo/content/halloween/jacobus_lanternibus/taxonomy.json diff --git a/hugo/content/halloween/jacobus_lanternibus/_index.md b/hugo/content/halloween/jacobus_lanternibus/_index.md new file mode 100644 index 00000000..864daa63 --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/_index.md @@ -0,0 +1,46 @@ +--- +title: Jacobus lanternibus +subtitle: "Jack-o'-lantern" +lastmod: 2024-10-26T10:00:00+0200 + +resources: + - title: "Fiery pumpkin" + name: cover_image + src: pumpkin.jpg + params: + attribution: demonic domain, CC BY-SATAN + link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg + +layout: "species_intro" +banner_title: "Halloween species overview" +weight: 1 +science_name: "Clupea harengus" +lineage_data_path: "clupea_harengus/taxonomy" + +gbif_taxon_id: "8351946" +goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" +iucn_category: "Least Concern" +iucn_link: "https://www.iucnredlist.org/species/155123/4717767" + +swe_red_list: "Viable" +swe_red_list_link: "https://artfakta.se/taxa/206089/" +latitude: 60 +longitude: -40 +initialZoom: 1 +--- + +### Description + +Write some content here in markdown for the introduction tab of the species page. + +#### Genome reference + +[EDIT] + +#### References + +- [EDIT] + +#### Changelog + +- DD/MM/YYYY - Species first published on the Portal diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml new file mode 100644 index 00000000..3bd79ccd --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml @@ -0,0 +1,15 @@ +name: + label: "Assembly Name" + value: "Foobarus" +type: + label: "Assembly Type" + value: "" +level: + label: "Assembly Level" + value: "" +representation: + label: "Assembly Representation" + value: "" +accession: + label: "Accession" + value: "GCA_XXX" diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md b/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md new file mode 100644 index 00000000..97e53c71 --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md @@ -0,0 +1,14 @@ +--- +build: + list: never + publishResources: false + render: never +--- + +### Contributor(s) + +### Publication(s) + +### Funding + +### Acknowledgements diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md new file mode 100644 index 00000000..59c22e0a --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md @@ -0,0 +1,6 @@ +--- +title: "Genome assembly" +layout: assembly +--- + +### Methods diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml new file mode 100644 index 00000000..0b6aa3d3 --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml @@ -0,0 +1,24 @@ +assembly: + - "Assembly length (Mbp)": [EDIT] + - "GC %": [EDIT] + - "Contig #": [EDIT] + - "Contig N50 (Mbp)": [EDIT] + - "Contig L50": [EDIT] + - "Contig N90 (Mbp)": [EDIT] + - "Contig L90": [EDIT] + - "Scaffold #": [EDIT] + - "Scaffold N50 (Mbp)": [EDIT] + - "Scaffold L50": [EDIT] + - "Scaffold N90 (Mbp)": [EDIT] + - "Scaffold L90": [EDIT] + - "Scaffolds >= 10 kb": [EDIT] + - "BUSCO % [EDIT]": "[EDIT]" + +annotation: + - "Gene #": [EDIT] + - "Transcript #": [EDIT] + - "Avg exons per transcript": [EDIT] + - "Avg gene length (bp)": [EDIT] + - "Avg transcript length (bp)": [EDIT] + - "Avg exon length (bp)": [EDIT] + - "Avg intron length (bp)": [EDIT] diff --git a/hugo/content/halloween/jacobus_lanternibus/download.md b/hugo/content/halloween/jacobus_lanternibus/download.md new file mode 100644 index 00000000..be355e9c --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/download.md @@ -0,0 +1,6 @@ +--- +title: "Download" +layout: "species_download" +url: "clupea_harengus/download" +weight: 3 +--- diff --git a/hugo/content/halloween/jacobus_lanternibus/intro/index.md b/hugo/content/halloween/jacobus_lanternibus/intro/index.md new file mode 100644 index 00000000..ca03031f --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/intro/index.md @@ -0,0 +1,3 @@ +--- +headless: true +--- diff --git a/hugo/content/halloween/jacobus_lanternibus/pumpkin.jpg b/hugo/content/halloween/jacobus_lanternibus/pumpkin.jpg new file mode 100644 index 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"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7950", + "display_order": 1 + }, + "Genus": { + "science_name": "Clupea", + "tax_id": "7949", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", + "display_order": 2 + }, + "Family": { + "science_name": "Clupeidae", + "tax_id": "55118", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", + "display_order": 3 + }, + "Order": { + "science_name": "Clupeiformes", + "tax_id": "32446", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", + "display_order": 4 + }, + "Class": { + "science_name": "Actinopteri", + "tax_id": "186623", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", + "display_order": 5 + }, + "Phylum": { + "science_name": "Chordata", + "tax_id": "7711", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", + "display_order": 6 + }, + "Kingdom": { + "science_name": "Metazoa", + "tax_id": "33208", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", + "display_order": 7 + }, + "Superkingdom": { + "science_name": "Eukaryota", + "tax_id": "2759", + "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", + "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", + "display_order": 8 + } +} From 8d753d7f1538d4bea4bea90ce63b84848cf49044 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 26 Oct 2024 14:51:36 +0200 Subject: [PATCH 12/59] Use XML taxonomy as resource --- .../jacobus_lanternibus/taxonomy.xml | 36 +++++++++++++++++++ hugo/layouts/halloween/species_intro.html | 9 +++++ .../partials/halloween/GetTaxonomyRanks.html | 11 ++++++ 3 files changed, 56 insertions(+) create mode 100644 hugo/content/halloween/jacobus_lanternibus/taxonomy.xml create mode 100644 hugo/layouts/partials/halloween/GetTaxonomyRanks.html diff --git a/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml b/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml new file mode 100644 index 00000000..ed33ef9d --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml @@ -0,0 +1,36 @@ + + + + \ No newline at end of file diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index 675fb402..9f79a27a 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -58,6 +58,15 @@

Taxonomy

+ {{ with .Resources.Get "taxonomy.xml" | transform.Unmarshal }} + {{ with partial "halloween/GetTaxonomyRanks.html" .taxon.lineage.taxon }} + 
 {{ debug.Dump . }}
+ {{ end }} + {{ else }} + {{ errorf "Unable to get taxonomy file" }} + {{ end }} + + {{ $lineage_file := (split .Params.lineage_data_path "/") }} {{ $unsorted_dict := index .Site.Data $lineage_file }} diff --git a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html new file mode 100644 index 00000000..c8d9095e --- /dev/null +++ b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html @@ -0,0 +1,11 @@ +{{ $byrank := dict }} +{{ range . }} + {{ $rank := index . "-rank" }} + {{ $scientificName := index . "-scientificName" }} + {{ $taxId := index . "-taxId" }} + {{ with $rank }} + {{ $data := dict "scientificName" $scientificName "taxId" $taxId }} + {{ $byrank = merge $byrank (dict $rank $data) }} + {{ end }} +{{ end }} +{{ return $byrank }} From db7345a415a717338420098febbffd3f806441ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 28 Oct 2024 10:09:55 +0100 Subject: [PATCH 13/59] Correct typo in .gitignore --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index cc87a647..ca72736d 100644 --- a/.gitignore +++ b/.gitignore @@ -38,7 +38,7 @@ __pycache__/ targets.mk # Emacs -.dirs-local.el +.dir-locals.el # JBrowse bundle hugo/static/browser \ No newline at end of file From 07ae29367c8878bd0bab420db09c1e71858552da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 28 Oct 2024 11:27:27 +0100 Subject: [PATCH 14/59] Generate lineage using a partial --- hugo/layouts/halloween/species_intro.html | 248 +++++++----------- .../partials/halloween/GetTaxonomyRanks.html | 5 +- hugo/layouts/partials/halloween/lineage.html | 43 +++ 3 files changed, 148 insertions(+), 148 deletions(-) create mode 100644 hugo/layouts/partials/halloween/lineage.html diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index 9f79a27a..3cd34014 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -1,183 +1,139 @@ {{ define "early_connections" }} - + {{ end }} {{ define "script_includes" }} - + - + {{ end }} {{ define "main" }} -{{ partial "species_title.html" . }} + {{ partial "species_title.html" . }} -{{ partial "species_nav.html" . }} + {{ partial "species_nav.html" . }} -
+
- -
+ +
-
-
- {{ with .Resources.Get "cover_image"}} - {{ .Title }} - {{ $title := printf "%s - %s" .Title .Params.Attribution }} - {{ if .Params.Link }} - -
{{ $title }}
- - {{ else }} -

- {{ $title }} -

- {{ end }} - {{ end }} -
-
- -
- {{ partial "distrib_map.html" . }} -
-
- - -
- - -
-

Taxonomy

- - {{ with .Resources.Get "taxonomy.xml" | transform.Unmarshal }} - {{ with partial "halloween/GetTaxonomyRanks.html" .taxon.lineage.taxon }} - 
 {{ debug.Dump . }}
- {{ end }} - {{ else }} - {{ errorf "Unable to get taxonomy file" }} - {{ end }} - - - {{ $lineage_file := (split .Params.lineage_data_path "/") }} - {{ $unsorted_dict := index .Site.Data $lineage_file }} - - - {{ $lineage_slice := slice }} - {{ range $rank, $value := $unsorted_dict }} - {{ $lineage_slice = $lineage_slice | append (dict "rank" $rank "value" $value) }} - {{ end }} - {{ $sorted_lineage := sort $lineage_slice "value.display_order" "desc" }} - - - {{ range $rank, $item := $sorted_lineage }} -
-
- {{ if eq $item.rank "Superkingdom" }} - Domain: - {{ else }} - {{ $item.rank }}: - {{ end }} - {{if or (eq $item.rank "Genus") (eq $item.rank "Species") }} - {{ $item.value.science_name }} - {{ else }} - {{ $item.value.science_name }} - {{ end }} -
- -
-
- {{ end }} - -
-
- NCBI Taxonomy ID: - - {{ $species_dict := index $unsorted_dict "Species" }} - {{ $tax_id := index $species_dict "tax_id" }} - {{ $ncbi_link := index $species_dict "ncbi_link" }} - - {{$tax_id}} - -
-
-
- -
- {{ if or .Params.iucn_category .Params.swe_red_list }} -

Vulnerability

-

- {{ if .Params.iucn_category }} - IUCN Category: - {{ .Params.iucn_category }} -
- {{ end }} +

+
+ {{ with .Resources.Get "cover_image"}} + {{ .Title }} + {{ $title := printf "%s - %s" .Title .Params.Attribution }} + {{ if .Params.Link }} + +
{{ $title }}
+ + {{ else }} +

+ {{ $title }} +

+ {{ end }} + {{ end }} +
+
- {{ if .Params.swe_red_list }} - Swedish Red List: - {{ .Params.swe_red_list }} -
- {{ end }} -

- {{ end }} +
+ {{ partial "distrib_map.html" . }} +
+
-

External links

+
-
- {{ if .Params.gbif_taxon_id }} - - - + +
+

Taxonomy

+ {{ with .Resources.Get "taxonomy.xml" | transform.Unmarshal }} + {{ with partial "halloween/GetTaxonomyRanks.html" . }} + {{ partial "halloween/lineage.html" . }} + {{ end }} + {{ else }} + {{ errorf "Unable to get taxonomy file" }} + {{ end }} - -
+ +
+ {{ if or .Params.iucn_category .Params.swe_red_list }} +

Vulnerability

+

+ {{ if .Params.iucn_category }} + IUCN Category: + {{ .Params.iucn_category }}
- Occurrence data in GBIF - - - {{ end }} - - {{ if .Params.goat_webpage }} - - - - {{ end }} + {{ end }} +

+ {{ end }} -
-
+

External links

+ +
+ {{ if .Params.gbif_taxon_id }} + + + + + + + + {{ end }} + + {{ if .Params.goat_webpage }} + + + + {{ end }} + +
+ +
-
+
-
+
-
-
- {{ .Content }} -
-
+
+
+ {{ .Content }} +
+
- {{ partial "last_updated.html" . }} + {{ partial "last_updated.html" . }} -
+
{{ end }} diff --git a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html index c8d9095e..ddaa2941 100644 --- a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html +++ b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html @@ -1,5 +1,6 @@ -{{ $byrank := dict }} -{{ range . }} +{{ $species := dict "scientificName" (index .taxon "-scientificName") "taxId" (index .taxon "-taxId") }} +{{ $byrank := dict "species" $species }} +{{ range .taxon.lineage.taxon }} {{ $rank := index . "-rank" }} {{ $scientificName := index . "-scientificName" }} {{ $taxId := index . "-taxId" }} diff --git a/hugo/layouts/partials/halloween/lineage.html b/hugo/layouts/partials/halloween/lineage.html new file mode 100644 index 00000000..14fa6727 --- /dev/null +++ b/hugo/layouts/partials/halloween/lineage.html @@ -0,0 +1,43 @@ +{{ $ena_url := "https://www.ebi.ac.uk/ena/browser/view/Taxon:" }} +{{ $ncbi_url := "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" }} + +{{ $order := slice +"superkingdom" +"kingdom" +"phylum" +"class" +"order" +"family" +"genus" +"species" +}} + +{{ $labels := dict "superkingdom" "Domain"}} + +{{ $fmt := dict "genus" "%s" "species" "%s" }} + +{{ range $order }} + {{ $rank := . }} + {{ with index $ $rank }} +
+
+ {{ or (index $labels $rank) $rank | strings.FirstUpper }}: + + {{ printf (or (index $fmt $rank) "%s") .scientificName | safe.HTML }} + +
+ +
+
+ {{ else }} + {{ warnf "Missing lineage entry %s for %s" . $.species.scientificName }} + {{ end }} +{{ end }} +
+
+ NCBI Taxonomy ID: + + {{ .species.taxId }} + +
+
From 1ff6d605119239c4ddff19f5074d52a554af1412 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 28 Oct 2024 11:41:24 +0100 Subject: [PATCH 15/59] Comment taxonomy templates --- hugo/layouts/partials/halloween/GetTaxonomyRanks.html | 8 ++++++++ hugo/layouts/partials/halloween/lineage.html | 6 +++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html index ddaa2941..7d5883f6 100644 --- a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html +++ b/hugo/layouts/partials/halloween/GetTaxonomyRanks.html @@ -1,3 +1,11 @@ +{{/* +Given a dictionary representation of taxonomy.xml, return lineage entries indexed by rank. +Example output: +{ + "species": { "scientificName": "Jacobus lanternibus", "taxId": 666 }, + "superkingdom": { "scientificName": "Eukaryota", "taxId": 2759 }, +} +*/}} {{ $species := dict "scientificName" (index .taxon "-scientificName") "taxId" (index .taxon "-taxId") }} {{ $byrank := dict "species" $species }} {{ range .taxon.lineage.taxon }} diff --git a/hugo/layouts/partials/halloween/lineage.html b/hugo/layouts/partials/halloween/lineage.html index 14fa6727..3423da6b 100644 --- a/hugo/layouts/partials/halloween/lineage.html +++ b/hugo/layouts/partials/halloween/lineage.html @@ -12,8 +12,10 @@ "species" }} +{{/* Ranks that need special labels */}} {{ $labels := dict "superkingdom" "Domain"}} +{{/* Ranks that need special name formatting */}} {{ $fmt := dict "genus" "%s" "species" "%s" }} {{ range $order }} @@ -21,8 +23,10 @@ {{ with index $ $rank }}
+ {{/* Uppercased rank or custom label */}} {{ or (index $labels $rank) $rank | strings.FirstUpper }}: + {{/* Scientific name with optional formatting */}} {{ printf (or (index $fmt $rank) "%s") .scientificName | safe.HTML }}
@@ -36,7 +40,7 @@
NCBI Taxonomy ID: - + {{ .species.taxId }}
From 1160dd85b38915662bd2e61a24ad5f8e2de5c83e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 28 Oct 2024 11:46:45 +0100 Subject: [PATCH 16/59] Remove obsolete references --- .../halloween/jacobus_lanternibus/_index.md | 4 +- .../jacobus_lanternibus/taxonomy.json | 58 ------------------- 2 files changed, 1 insertion(+), 61 deletions(-) delete mode 100644 hugo/content/halloween/jacobus_lanternibus/taxonomy.json diff --git a/hugo/content/halloween/jacobus_lanternibus/_index.md b/hugo/content/halloween/jacobus_lanternibus/_index.md index 864daa63..c88fde10 100644 --- a/hugo/content/halloween/jacobus_lanternibus/_index.md +++ b/hugo/content/halloween/jacobus_lanternibus/_index.md @@ -8,14 +8,12 @@ resources: name: cover_image src: pumpkin.jpg params: - attribution: demonic domain, CC BY-SATAN + attribution: demonic domain, CC BY-SA-TA-N link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg layout: "species_intro" banner_title: "Halloween species overview" weight: 1 -science_name: "Clupea harengus" -lineage_data_path: "clupea_harengus/taxonomy" gbif_taxon_id: "8351946" goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" diff --git a/hugo/content/halloween/jacobus_lanternibus/taxonomy.json b/hugo/content/halloween/jacobus_lanternibus/taxonomy.json deleted file mode 100644 index d64f3d63..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/taxonomy.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "Species": { - "science_name": "Clupea harengus", - "tax_id": "7950", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7950", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7950", - "display_order": 1 - }, - "Genus": { - "science_name": "Clupea", - "tax_id": "7949", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", - "display_order": 2 - }, - "Family": { - "science_name": "Clupeidae", - "tax_id": "55118", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", - "display_order": 3 - }, - "Order": { - "science_name": "Clupeiformes", - "tax_id": "32446", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", - "display_order": 4 - }, - "Class": { - "science_name": "Actinopteri", - "tax_id": "186623", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", - "display_order": 5 - }, - "Phylum": { - "science_name": "Chordata", - "tax_id": "7711", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", - "display_order": 6 - }, - "Kingdom": { - "science_name": "Metazoa", - "tax_id": "33208", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", - "display_order": 7 - }, - "Superkingdom": { - "science_name": "Eukaryota", - "tax_id": "2759", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", - "display_order": 8 - } -} From defc5f1f6d0731a9cb3d2f69619f988513274c5b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Tue, 29 Oct 2024 10:54:02 +0100 Subject: [PATCH 17/59] Create download page bundle --- .../download/data_tracks.json | 268 ++++++++++++++++++ .../{download.md => download/index.md} | 2 +- hugo/layouts/halloween/species_download.html | 19 +- .../partials/halloween/download_table.html | 128 +++++++++ 4 files changed, 403 insertions(+), 14 deletions(-) create mode 100644 hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json rename hugo/content/halloween/jacobus_lanternibus/{download.md => download/index.md} (63%) create mode 100644 hugo/layouts/partials/halloween/download_table.html diff --git a/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json b/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json new file mode 100644 index 00000000..69d763d7 --- /dev/null +++ b/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json @@ -0,0 +1,268 @@ +[ + { + "dataTrackName": "Genome", + "description": "Reference genome sequence", + "fileName": "CAMGYJ01.fasta.gz", + "links": [ + {"Download": "https://ftp.ebi.ac.uk/pub/databases/ena/wgs/public/cam/CAMGYJ01.fasta.gz"}, + {"Website": "https://www.ebi.ac.uk/ena/browser/view/GCA_946122785.1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "GCA_946122785.1", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Protein-coding genes", + "description": "Functional annotation of protein-coding genes", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/45076090"}, + {"Website": "https://doi.org/10.17044/scilifelab.24340378.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.24340378.v1", + "fileName": "ltenue_v1_genes.gff.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Repeats", + "description": "Annotation of the repetitive regions", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/48879751"}, + {"Website": "https://doi.org/10.17044/scilifelab.24343000.v2"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.24340378.v1", + "fileName": "L_tenue_v1_rep.bed.gz", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 06", + "description": "Whole genome Tajima's D estimates for individuals of population 06 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006876"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop06_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 08", + "description": "Whole genome Tajima's D estimates for individuals of population 08 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006879"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop08_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 17", + "description": "Whole genome Tajima's D estimates for individuals of population 17 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006882"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop17_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 21", + "description": "Whole genome Tajima's D estimates for individuals of population 21 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006888"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop21_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 23", + "description": "Whole genome Tajima's D estimates for individuals of population 23 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006891"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop23_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 26", + "description": "Whole genome Tajima's D estimates for individuals of population 26 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49007380"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop26_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 32", + "description": "Whole genome Tajima's D estimates for individuals of population 32 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006918"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop32_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Tajima's D, population 34", + "description": "Whole genome Tajima's D estimates for individuals of population 34 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006924"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937304.v1", + "fileName": "Lten_pop34_TD.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 06", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 06 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006264"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop06_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 08", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 08 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006267"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop08_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 17", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 17 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006270"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop17_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 21", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 21 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006273"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop21_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 23", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 23 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006282"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop23_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 26", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 26 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006285"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop26_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 32", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 32 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006297"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop32_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + }, + { + "dataTrackName": "Nucleotide diversity (Ï€), population 34", + "description": "Whole genome nucleotide diversity (Ï€) estimates for individuals of population 34 of L. tenue per 100 kb windows.", + "links": [ + {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006300"}, + {"Website": "https://doi.org/10.17044/scilifelab.26937271.v1"}, + {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} + ], + "accessionOrDOI": "10.17044/scilifelab.26937271.v1", + "fileName": "Lten_pop34_Pi.bed.zip", + "principalInvestigator": "Tanja Slotte", + "principalInvestigatorAffiliation": "Stockholm University", + "firstDateOnPortal": "15 October 2024" + } +] diff --git a/hugo/content/halloween/jacobus_lanternibus/download.md b/hugo/content/halloween/jacobus_lanternibus/download/index.md similarity index 63% rename from hugo/content/halloween/jacobus_lanternibus/download.md rename to hugo/content/halloween/jacobus_lanternibus/download/index.md index be355e9c..26e08224 100644 --- a/hugo/content/halloween/jacobus_lanternibus/download.md +++ b/hugo/content/halloween/jacobus_lanternibus/download/index.md @@ -1,6 +1,6 @@ --- title: "Download" layout: "species_download" -url: "clupea_harengus/download" +url: "jacobus_lanternibus/download" weight: 3 --- diff --git a/hugo/layouts/halloween/species_download.html b/hugo/layouts/halloween/species_download.html index 65172973..1136f81c 100644 --- a/hugo/layouts/halloween/species_download.html +++ b/hugo/layouts/halloween/species_download.html @@ -37,17 +37,10 @@

Data availability

- {{ $speciesName := index (split .RelPermalink "/") 1 }} - - {{ $tableDataPath := printf "%s/data_tracks.json" $speciesName }} - {{ $tableDataResource := resources.Get $tableDataPath }} - {{ $tableData := $tableDataResource | transform.Unmarshal }} - - {{ $staticDirPath := printf "/%s/data_tracks" $speciesName }} - {{ $staticDirFile := printf "%s/data_tracks.json" $speciesName }} - - {{ (resources.Get $tableDataPath | resources.Copy $staticDirFile).Publish }} + This means we don't need to store a copy of the data_tracks.json file inside the static dir. --> + {{ $resource := .Resources.Get "data_tracks.json" }} + {{ $tableData := $resource | transform.Unmarshal }} + {{ $staticDirPath := $resource.RelPermalink }} {{ $aliasFileURL := "" }} @@ -63,11 +56,11 @@

Data availability

- {{ partial "download_table" (dict "tableType" "long" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} + {{ partial "halloween/download_table" (dict "tableType" "long" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}}
- {{ partial "download_table" (dict "tableType" "short" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} + {{ partial "halloween/download_table" (dict "tableType" "short" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}}
diff --git a/hugo/layouts/partials/halloween/download_table.html b/hugo/layouts/partials/halloween/download_table.html new file mode 100644 index 00000000..9e904d18 --- /dev/null +++ b/hugo/layouts/partials/halloween/download_table.html @@ -0,0 +1,128 @@ +{{ $tableType := .tableType }} +{{ $tableData := .tableData }} +{{ $staticDirPath := .staticDirPath }} +{{ $aliasFileURL := .aliasFileURL }} + +
+ + + + + + + {{ if eq $tableType "long"}} + + + {{ end }} + + + {{ if eq $tableType "long"}} + + {{ end }} + + + + {{ range $tableData }} + + + + + + {{ if eq $tableType "long"}} + + + {{ end }} + + + + + {{ if eq $tableType "long"}} + + {{ end }} + + + {{ end }} + +
Data track nameDescriptionLinksAccession/DOIFile namePrincipal investigatorPrincipal investigator affiliationFirst date on portal
{{ .dataTrackName }}{{ .description }} +
+ {{ range .links }} + {{ range $linkType, $url := . }} + + {{ if eq $linkType "Download"}} + + Download id + Download + + + {{ else if eq $linkType "Website"}} + + Website icon + Website + + + {{ else if eq $linkType "Article"}} + + Article icon + Article + + + {{ end }} + + {{ end }} + {{ end }} +
+ 		+ {{ $accessionUrl := "" }} + {{ range .links}} + {{ if .Website }} + {{ $accessionUrl = .Website }} + {{ end }} + {{ end }} + {{ if $accessionUrl }} + {{ .accessionOrDOI }} + {{ else }} + {{ .accessionOrDOI }} + {{ end }} + {{ .fileName }}{{ .principalInvestigator }}{{ .principalInvestigatorAffiliation }}{{ .firstDateOnPortal }}
+
+ +
+
+ + + Download Icon + Download the table contents as a JSON file. + + +
+ + {{ if ne $aliasFileURL "" }} +
+ + + File icon + Open (in a new tab) the refNameAlias text file used in JBrowse to set the aliases for reference sequence names (e.g., to define that "chr1" is an alias for "1"). + + +
+ {{ end }} +
+ + + Open book icon + Open the Glossary (in a new tab). + + +
+
+ + From ac8fd6f5a786fa7664e919175bdb2a182f550ed1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 31 Oct 2024 10:14:34 +0100 Subject: [PATCH 18/59] Remove unused data tables event listener --- hugo/layouts/halloween/assembly.html | 22 --- hugo/layouts/halloween/species_assembly.html | 189 ------------------- 2 files changed, 211 deletions(-) delete mode 100644 hugo/layouts/halloween/species_assembly.html diff --git a/hugo/layouts/halloween/assembly.html b/hugo/layouts/halloween/assembly.html index c1574139..3d155652 100644 --- a/hugo/layouts/halloween/assembly.html +++ b/hugo/layouts/halloween/assembly.html @@ -126,25 +126,3 @@

Annotation Statistics

{{ end }} - -{{ define "scripts" }} - - - -{{ end }} diff --git a/hugo/layouts/halloween/species_assembly.html b/hugo/layouts/halloween/species_assembly.html deleted file mode 100644 index fa75c204..00000000 --- a/hugo/layouts/halloween/species_assembly.html +++ /dev/null @@ -1,189 +0,0 @@ -{{ define "early_connections" }} - - - -{{ end }} - - -{{ define "script_includes" }} - -{{ partial "add_datatables_jquery.html" . }} - -{{ end }} - - - -{{ define "main" }} - -{{ partial "species_title.html" . }} - -{{ partial "species_nav.html" . }} - - -{{ $stats_file := (split .Params.stats_data_path "/") }} -{{ $stats_contents := index .Site.Data $stats_file }} - - -{{ $.Scratch.Add "accession" "" }} -{{ range .Params.key_info }} - {{ if isset . "Accession" }} - {{ $.Scratch.Set "accession" .Accession }} - {{ end }} -{{ end }} -{{ $accession := $.Scratch.Get "accession" }} - -{{ $ena_link := print "https://www.ebi.ac.uk/ena/browser/view/" $accession }} -{{ $ncbi_link := print "https://www.ncbi.nlm.nih.gov/datasets/genome/" $accession }} - - - -{{ $content := split .Content "|||||| Content divider - do not remove ||||||" }} -{{ $contentp1 := index $content 0 }} -{{ $contentp2 := index $content 1 }} - - -
- -
-
-

Description

-
    - {{ range .Params.key_info }} - {{ range $key, $value := . }} -
  • {{ $key }}: {{ $value }}
    • - {{ end }} - {{ end }} -
-
-
-
- - - -
- -
- -
- - -
-
- {{ $contentp1 | safeHTML }} -
-
- -
- - -
-

Assembly Statistics

- - {{ if .Params.stats_data_path }} -
- - - - - - - - - - - {{ range $idx, $statistic := $stats_contents.assembly }} - {{ range $stat_name, $value := $statistic }} - - - - - {{ end }} - {{ end }} - - -
StatisticValue
{{ $stat_name }} {{ $value }}
-
- {{ else }} -

No assembly data has been provided for this species

- {{ end }} -
- - -
-

Annotation Statistics

- - {{ if .Params.stats_data_path }} -
- - - - - - - - - - - {{ range $idx, $statistic := $stats_contents.annotation }} - {{ range $stat_name, $value := $statistic }} - - - - - {{ end }} - {{ end }} - - -
StatisticValue
{{ $stat_name }} {{ $value }}
-
- {{ else }} -

No annotation data has been provided for this species

- {{ end }} -
- -
-
- - -
-
- {{ $contentp2 | safeHTML }} -
-
- -{{ partial "last_updated.html" . }} - - -{{ end }} - -{{ define "scripts" }} - - - -{{ end }} From 0de94d99be60dc0c833be93bbc9cdace375f3e66 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 31 Oct 2024 10:32:32 +0100 Subject: [PATCH 19/59] Remove labels assmbly description configuration --- .../assembly/assembly.yaml | 20 +++++-------------- hugo/layouts/halloween/assembly.html | 11 +++------- 2 files changed, 8 insertions(+), 23 deletions(-) diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml index 3bd79ccd..b14a1695 100644 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml @@ -1,15 +1,5 @@ -name: - label: "Assembly Name" - value: "Foobarus" -type: - label: "Assembly Type" - value: "" -level: - label: "Assembly Level" - value: "" -representation: - label: "Assembly Representation" - value: "" -accession: - label: "Accession" - value: "GCA_XXX" +name: "Jaco_Lant" +type: "Spectroid" +level: "Underwordly" +repr: "Partially obscure" +accession: "GCA_666" diff --git a/hugo/layouts/halloween/assembly.html b/hugo/layouts/halloween/assembly.html index 3d155652..de61216c 100644 --- a/hugo/layouts/halloween/assembly.html +++ b/hugo/layouts/halloween/assembly.html @@ -10,16 +10,11 @@

Description

-
    - {{ range slice "name" "type" "level" "representation" "accession" }} - {{ $entry := index $metadata . }} -
  • {{ $entry.label }}: {{ $entry.value }}
    • - {{ end }} -
+ {{ partial "halloween/assembly_description.html" $metadata }}
- +
- +
- {{ else }} - No metadata was provided for this assembly. - {{ end }} -
-
- {{ .Content }} +
+
+ {{ .Content }} +
-
-
- {{ with .Resources.Get "assembly.yaml" | transform.Unmarshal }} +

Assembly Statistics

@@ -53,21 +48,22 @@

Assembly Statistics

Annotation Statistics

{{ partial "halloween/annotation_stats.html" .annotation }} - {{ else }} -

No assembly and annotation statistics have been provided for this species

- {{ end }} -
+
-
+
-
-
- {{ with .Resources.Get "contrib.md" }} - {{ .Content }} - {{ end }} -
-
+
+
+ {{ with .Resources.Get "contrib.md" }} + {{ .Content }} + {{ end }} +
+
+ {{ else }} + {{ warnf "Missing assembby statistics for %s" .Path }} +

No statistics were provided for this assembly

+ {{ end}} {{ partial "last_updated.html" . }} From 4f6165f48437b6561a20f7aca032e26520ce5053 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 31 Oct 2024 11:36:51 +0100 Subject: [PATCH 25/59] Restore contributions section --- .../jacobus_lanternibus/assembly/contrib.md | 8 ++++++++ hugo/layouts/halloween/assembly.html | 16 ++++++++-------- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md b/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md index 97e53c71..0f19ad6c 100644 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md @@ -7,8 +7,16 @@ build: ### Contributor(s) +Restless souls. + ### Publication(s) +- [How far will a pumpkin fly +?](https://www.nbcnews.com/id/wbna21197135) +- [The great pumpkin](https://www.smithsonianmag.com/science-nature/the-great-pumpkin-74423844/?no-ist=&page=1) + ### Funding +Mephisto Pact Treasury Foundation + ### Acknowledgements diff --git a/hugo/layouts/halloween/assembly.html b/hugo/layouts/halloween/assembly.html index 1096b44c..b4690fdf 100644 --- a/hugo/layouts/halloween/assembly.html +++ b/hugo/layouts/halloween/assembly.html @@ -53,19 +53,19 @@

Annotation Statistics

-
-
- {{ with .Resources.Get "contrib.md" }} - {{ .Content }} - {{ end }} -
-
{{ else }} {{ warnf "Missing assembby statistics for %s" .Path }}

No statistics were provided for this assembly

{{ end}} - {{ partial "last_updated.html" . }} +
+
+ {{ with .Resources.Get "contrib.md" }} + {{ .Content }} + {{ end }} +
+
+ {{ partial "last_updated.html" . }} {{ end }} From fabeaefae72d5501319a7639f941260a4d0e6ccb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 31 Oct 2024 11:57:44 +0100 Subject: [PATCH 26/59] Minor tweaks --- .../halloween/jacobus_lanternibus/_index.md | 34 ++++++++----------- 1 file changed, 15 insertions(+), 19 deletions(-) diff --git a/hugo/content/halloween/jacobus_lanternibus/_index.md b/hugo/content/halloween/jacobus_lanternibus/_index.md index c88fde10..2ad0c6e9 100644 --- a/hugo/content/halloween/jacobus_lanternibus/_index.md +++ b/hugo/content/halloween/jacobus_lanternibus/_index.md @@ -1,30 +1,30 @@ --- -title: Jacobus lanternibus +title: Jacobus Lanternibus subtitle: "Jack-o'-lantern" lastmod: 2024-10-26T10:00:00+0200 resources: - - title: "Fiery pumpkin" + - title: Fiery pumpkin name: cover_image src: pumpkin.jpg params: - attribution: demonic domain, CC BY-SA-TA-N + attribution: pandemonic domain, CC BY-SA-TA-N link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg layout: "species_intro" -banner_title: "Halloween species overview" weight: 1 -gbif_taxon_id: "8351946" -goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" -iucn_category: "Least Concern" -iucn_link: "https://www.iucnredlist.org/species/155123/4717767" - -swe_red_list: "Viable" -swe_red_list_link: "https://artfakta.se/taxa/206089/" -latitude: 60 -longitude: -40 -initialZoom: 1 +params: + banner_title: "Halloween species overview" + gbif_taxon_id: 2874508 + goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" + iucn_category: "Least Concern" + iucn_link: "https://www.iucnredlist.org/species/155123/4717767" + swe_red_list: "Viable" + swe_red_list_link: "https://artfakta.se/taxa/206089/" + latitude: 60 + longitude: -40 + initialZoom: 1.5 --- ### Description @@ -33,12 +33,8 @@ Write some content here in markdown for the introduction tab of the species page #### Genome reference -[EDIT] - #### References -- [EDIT] - #### Changelog -- DD/MM/YYYY - Species first published on the Portal +- 31/10/2024 - Species first published on the Portal From 13b6b45ba67932ca759294d8061e77bd98575f37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 31 Oct 2024 13:53:51 +0100 Subject: [PATCH 27/59] Add basic archetype --- hugo/archetypes/halloween/_index.md | 66 ++++++++----------- .../halloween/assembly/assembly.yaml | 44 ++++++++----- hugo/archetypes/halloween/assembly/contrib.md | 13 ++-- .../assembly/{_index.md => index.md} | 1 + .../halloween/download/data_tracks.json | 16 +++++ .../{download.md => download/index.md} | 2 +- hugo/archetypes/halloween/intro/index.md | 3 + hugo/archetypes/halloween/taxonomy.json | 58 ---------------- hugo/archetypes/halloween/taxonomy.xml | 36 ++++++++++ hugo/layouts/halloween/species_intro.html | 2 +- 10 files changed, 124 insertions(+), 117 deletions(-) rename hugo/archetypes/halloween/assembly/{_index.md => index.md} (73%) create mode 100644 hugo/archetypes/halloween/download/data_tracks.json rename hugo/archetypes/halloween/{download.md => download/index.md} (63%) create mode 100644 hugo/archetypes/halloween/intro/index.md delete mode 100644 hugo/archetypes/halloween/taxonomy.json create mode 100644 hugo/archetypes/halloween/taxonomy.xml diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 7506ad6a..b7b6f893 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,41 +1,35 @@ --- -# Required params below -title: "*Clupea harengus*" -subtitle: "Atlantic herring" +title: '{{ replace .File.ContentBaseName `_` ` ` | title }}' +subtitle: Species common name +lastmod: {{ time.Format "31/01/2014" .Date }} + +resources: + - title: '{{ replace .File.ContentBaseName `_` ` ` | title }}' + name: cover_image + # Use relative path for a local image + src: "https://placehold.co/600x400" + params: + attribution: CC-BY-SA + link: "https://placehold.co/600x400" -last_updated: "15/05/2024" - -cover_image: "/img/species/clupea_harengus.webp" -img_attrib_text: "Clupea harengus by Gervais et Boulart, public domain" -img_attrib_link: "https://en.wikipedia.org/wiki/File:Clupea_harengus_Gervais.jpg" - - -# The params below were auto-generated, you should not need to edit them... -# unless you were warned by the add-new-species.py script. layout: "species_intro" -banner_title: "Species overview" -url: "clupea_harengus" weight: 1 -science_name: "Clupea harengus" -lineage_data_path: "clupea_harengus/taxonomy" - -gbif_taxon_id: "8351946" -goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" - -# Optional params below, -# remove them if you don't want them or they are not relevant. -iucn_category: "Least Concern" -iucn_link: "https://www.iucnredlist.org/species/155123/4717767" - -swe_red_list: "Viable" -swe_red_list_link: "https://artfakta.se/taxa/206089/" - -# These 3 params define the initial view for the map -# latitude and longitude are for the map center. -latitude: 60 -longitude: -40 -initialZoom: 1 +params: + banner_title: "Species overview" + goat_webpage: "https://goat.genomehubs.org" + + # Map + gbif_taxon_id: 2874508 + latitude: 60 + longitude: -40 + initialZoom: 1.5 + + # Optional + iucn_category: + iucn_link: + swe_red_list: + swe_red_list_link: --- ### Description @@ -44,12 +38,8 @@ Write some content here in markdown for the introduction tab of the species page #### Genome reference -[EDIT] - #### References -- [EDIT] - #### Changelog -- DD/MM/YYYY - Species first published on the Portal +- 31/10/2024 - Species first published on the Portal diff --git a/hugo/archetypes/halloween/assembly/assembly.yaml b/hugo/archetypes/halloween/assembly/assembly.yaml index 1a49687b..27999d94 100644 --- a/hugo/archetypes/halloween/assembly/assembly.yaml +++ b/hugo/archetypes/halloween/assembly/assembly.yaml @@ -1,15 +1,29 @@ -name: - label: "Assembly Name" - value: "" -type: - label: "Assembly Type" - value: "" -level: - label: "Assembly Level" - value: "" -representation: - label: "Assembly Representation" - value: "" -accession: - label: "Assembly Accession" - value: "" +description: + name: "Jaco_Lant" + type: "Spectroid" + level: "Underwordly" + repr: "Partially obscure" + accession: "GCA_666" +stats: + length: + gc: + contig: + contig_n50: + contig_l50: + contig_n90: + contig_l90: + scaffold: + scaffold_n50: + scaffold_l50: + scaffold_n90: + scaffold_l90: + scaffold_gt_10: + busco: +annotation: + gene_cnt: + transcript_cnt: + exons_avg: + gene_length_avg: + transcript_length_avg: + exon_length_avg: + intron_length_avg: diff --git a/hugo/archetypes/halloween/assembly/contrib.md b/hugo/archetypes/halloween/assembly/contrib.md index c76ea97a..0f19ad6c 100644 --- a/hugo/archetypes/halloween/assembly/contrib.md +++ b/hugo/archetypes/halloween/assembly/contrib.md @@ -1,17 +1,22 @@ --- build: - list: never - publishResources: false - render: never + list: never + publishResources: false + render: never --- - + ### Contributor(s) +Restless souls. ### Publication(s) +- [How far will a pumpkin fly +?](https://www.nbcnews.com/id/wbna21197135) +- [The great pumpkin](https://www.smithsonianmag.com/science-nature/the-great-pumpkin-74423844/?no-ist=&page=1) ### Funding +Mephisto Pact Treasury Foundation ### Acknowledgements diff --git a/hugo/archetypes/halloween/assembly/_index.md b/hugo/archetypes/halloween/assembly/index.md similarity index 73% rename from hugo/archetypes/halloween/assembly/_index.md rename to hugo/archetypes/halloween/assembly/index.md index 7630469e..59c22e0a 100644 --- a/hugo/archetypes/halloween/assembly/_index.md +++ b/hugo/archetypes/halloween/assembly/index.md @@ -1,5 +1,6 @@ --- title: "Genome assembly" +layout: assembly --- ### Methods diff --git a/hugo/archetypes/halloween/download/data_tracks.json b/hugo/archetypes/halloween/download/data_tracks.json new file mode 100644 index 00000000..1ba0765d --- /dev/null +++ b/hugo/archetypes/halloween/download/data_tracks.json @@ -0,0 +1,16 @@ +[ + { + "dataTrackName": "Genome", + "description": "Reference genome sequence", + "fileName": "placeholder.fasta.gz", + "links": [ + {"Download": "#"}, + {"Website": "#"}, + {"Article": "#"} + ], + "accessionOrDOI": "GCA_1234", + "principalInvestigator": "Someone", + "principalInvestigatorAffiliation": "Some university", + "firstDateOnPortal": "15 October 2024" + } +] diff --git a/hugo/archetypes/halloween/download.md b/hugo/archetypes/halloween/download/index.md similarity index 63% rename from hugo/archetypes/halloween/download.md rename to hugo/archetypes/halloween/download/index.md index be355e9c..26e08224 100644 --- a/hugo/archetypes/halloween/download.md +++ b/hugo/archetypes/halloween/download/index.md @@ -1,6 +1,6 @@ --- title: "Download" layout: "species_download" -url: "clupea_harengus/download" +url: "jacobus_lanternibus/download" weight: 3 --- diff --git a/hugo/archetypes/halloween/intro/index.md b/hugo/archetypes/halloween/intro/index.md new file mode 100644 index 00000000..ca03031f --- /dev/null +++ b/hugo/archetypes/halloween/intro/index.md @@ -0,0 +1,3 @@ +--- +headless: true +--- diff --git a/hugo/archetypes/halloween/taxonomy.json b/hugo/archetypes/halloween/taxonomy.json deleted file mode 100644 index d64f3d63..00000000 --- a/hugo/archetypes/halloween/taxonomy.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "Species": { - "science_name": "Clupea harengus", - "tax_id": "7950", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7950", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7950", - "display_order": 1 - }, - "Genus": { - "science_name": "Clupea", - "tax_id": "7949", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7949", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7949", - "display_order": 2 - }, - "Family": { - "science_name": "Clupeidae", - "tax_id": "55118", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:55118", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=55118", - "display_order": 3 - }, - "Order": { - "science_name": "Clupeiformes", - "tax_id": "32446", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:32446", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32446", - "display_order": 4 - }, - "Class": { - "science_name": "Actinopteri", - "tax_id": "186623", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:186623", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186623", - "display_order": 5 - }, - "Phylum": { - "science_name": "Chordata", - "tax_id": "7711", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:7711", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7711", - "display_order": 6 - }, - "Kingdom": { - "science_name": "Metazoa", - "tax_id": "33208", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:33208", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33208", - "display_order": 7 - }, - "Superkingdom": { - "science_name": "Eukaryota", - "tax_id": "2759", - "ena_link": "https://www.ebi.ac.uk/ena/browser/view/Taxon:2759", - "ncbi_link": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2759", - "display_order": 8 - } -} diff --git a/hugo/archetypes/halloween/taxonomy.xml b/hugo/archetypes/halloween/taxonomy.xml new file mode 100644 index 00000000..3a5d0b2f --- /dev/null +++ b/hugo/archetypes/halloween/taxonomy.xml @@ -0,0 +1,36 @@ + + + + diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index 3cd34014..ac496d91 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -62,7 +62,7 @@

Taxonomy

{{ partial "halloween/lineage.html" . }} {{ end }} {{ else }} - {{ errorf "Unable to get taxonomy file" }} + {{ errorf "Missing taxonomy file: %s/taxonomy.json" $.Path }} {{ end }}
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b/hugo/layouts/halloween/species_intro.html index ac496d91..416fd246 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -39,7 +39,7 @@ {{ else }}

- {{ $title }} + {{ .Title }}

{{ end }} {{ end }} From 4252a4bfc81fc2de7a07fbcfd7f35b4cd396a756 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 16 Nov 2024 13:54:58 +0100 Subject: [PATCH 29/59] Extensible assembly fields --- .../_default/hugo.yaml} | 0 hugo/config/_default/params.yaml | 30 +++++++++ hugo/config/production/hugo.yaml | 1 + .../assembly/assembly.yaml | 44 ++++++------- .../jacobus_lanternibus/assembly/index.md | 5 ++ hugo/layouts/halloween/assembly.html | 22 +++++-- .../partials/halloween/annotation_stats.html | 31 --------- .../halloween/assembly_description.html | 31 ++++----- .../partials/halloween/assembly_stats.html | 63 +++++++++---------- 9 files changed, 122 insertions(+), 105 deletions(-) rename hugo/{config.yaml => config/_default/hugo.yaml} (100%) create mode 100644 hugo/config/_default/params.yaml create mode 100644 hugo/config/production/hugo.yaml delete mode 100644 hugo/layouts/partials/halloween/annotation_stats.html diff --git a/hugo/config.yaml b/hugo/config/_default/hugo.yaml similarity index 100% rename from hugo/config.yaml rename to hugo/config/_default/hugo.yaml diff --git a/hugo/config/_default/params.yaml b/hugo/config/_default/params.yaml new file mode 100644 index 00000000..9c622975 --- /dev/null +++ b/hugo/config/_default/params.yaml @@ -0,0 +1,30 @@ +assembly_fields: + description: + - ["name", "Assembly Name"] + - ["type", "Assembly Type"] + - ["level", "Assembly Level"] + - ["repr", "Assembly Representation"] + - ["accession"] + stats: + - ["length", "Assembly length (Mbp)"] + - ["gc", "GC %"] + - ["contig", "Contig #" ] + - ["contig_n50", "Contig N50 (Mbp)" ] + - ["contig_l50"] + - ["contig_n90", "Contig N90 (Mbp)" ] + - ["contig_l90"] + - ["scaffold", "Scaffold #"] + - ["scaffold_n50", "Scaffold N50 (Mbp)"] + - ["scaffold_l50"] + - ["scaffold_n90", "Scaffold N90 (Mbp)"] + - ["scaffold_l90"] + - ["scaffold_gt_10", "Scaffolds >= 10 kb"] + - ["busco", "BUSCO %"] + annotation: + - ["gene_cnt", "Gene #"] + - ["transcript_cnt", "Transcript #"] + - ["exons_avg", "Avg exons per transcript"] + - ["gene_length_avg","Avg gene length (bp)"] + - ["transcript_length_avg", "Avg transcript length (bp)"] + - ["exon_length_avg", "Avg exon length (bp)"] + - ["intron_length_avg", "Avg intron length (bp)"] diff --git a/hugo/config/production/hugo.yaml b/hugo/config/production/hugo.yaml new file mode 100644 index 00000000..94144a66 --- /dev/null +++ b/hugo/config/production/hugo.yaml @@ -0,0 +1 @@ +panicOnWarning: true diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml index 27999d94..c113ff16 100644 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml @@ -4,26 +4,28 @@ description: level: "Underwordly" repr: "Partially obscure" accession: "GCA_666" + extra_1: 666 + extra_2: 999 stats: - length: - gc: - contig: - contig_n50: - contig_l50: - contig_n90: - contig_l90: - scaffold: - scaffold_n50: - scaffold_l50: - scaffold_n90: - scaffold_l90: - scaffold_gt_10: - busco: + length: 1 + gc: 2 + contig: 3 + contig_n50: 4 + contig_l50: 5 + contig_n90: 6 + contig_l90: 7 + scaffold: 8 + scaffold_n50: 9 + scaffold_l50: 10 + scaffold_n90: 11 + scaffold_l90: 12 + scaffold_gt_10: 13 + busco: 34 annotation: - gene_cnt: - transcript_cnt: - exons_avg: - gene_length_avg: - transcript_length_avg: - exon_length_avg: - intron_length_avg: + gene_cnt: 14 + transcript_cnt: 15 + exons_avg: 16 + gene_length_avg: 17 + transcript_length_avg: 18 + exon_length_avg: 19 + intron_length_avg: 20 diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md index 59c22e0a..d6db17cc 100644 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md @@ -1,6 +1,11 @@ --- title: "Genome assembly" layout: assembly +params: + assembly_fields: + description: + - ["extra_1", "Additional field"] + - ["extra_2", "Another Additional field"] --- ### Methods diff --git a/hugo/layouts/halloween/assembly.html b/hugo/layouts/halloween/assembly.html index b4690fdf..a83621ca 100644 --- a/hugo/layouts/halloween/assembly.html +++ b/hugo/layouts/halloween/assembly.html @@ -4,12 +4,25 @@ {{ partial "species_nav.html" . }} + {{ $fields := dict + "default" .Site.Params.assembly_fields + "extra" (or .Params.assembly_fields dict) + }} + {{ with .Resources.Get "assembly.yaml" | transform.Unmarshal }} + {{/* Common context for partials rendering assembly description tables */}} + {{ $context := dict + "path" $.Page.Path + "fields" $fields + "values" . + }} +

Description

- {{ partial "halloween/assembly_description.html" .description }} + {{ $context = (merge $context (dict "section" "description")) }} + {{ partial "halloween/assembly_description.html" $context }}
@@ -41,18 +54,19 @@

Description

Assembly Statistics

- {{ partial "halloween/assembly_stats.html" .stats }} + {{ $context = merge $context (dict "section" "stats") }} + {{ partial "halloween/assembly_stats.html" $context }}

Annotation Statistics

- {{ partial "halloween/annotation_stats.html" .annotation }} + {{ $context = merge $context (dict "section" "annotation") }} + {{ partial "halloween/assembly_stats.html" $context }}
- {{ else }} {{ warnf "Missing assembby statistics for %s" .Path }}

No statistics were provided for this assembly

diff --git a/hugo/layouts/partials/halloween/annotation_stats.html b/hugo/layouts/partials/halloween/annotation_stats.html deleted file mode 100644 index 1e38b33c..00000000 --- a/hugo/layouts/partials/halloween/annotation_stats.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $labels := dict -"gene_cnt" "Gene #" -"transcript_cnt" "Transcript #" -"exons_avg" "Avg exons per transcript" -"gene_length_avg" "Avg gene length (bp)" -"transcript_length_avg" "Avg transcript length (bp)" -"exon_length_avg" "Avg exon length (bp)" -"intron_length_avg" "Avg intron length (bp)" -}} - -
- - - - - - - - - - - {{ range $key, $label := $labels }} - - - - - {{ end }} - - -
StatisticValue
{{ $label }} {{ or (index $ $key) "Not provided" }}
-
diff --git a/hugo/layouts/partials/halloween/assembly_description.html b/hugo/layouts/partials/halloween/assembly_description.html index 00337789..2701100c 100644 --- a/hugo/layouts/partials/halloween/assembly_description.html +++ b/hugo/layouts/partials/halloween/assembly_description.html @@ -1,14 +1,17 @@ -{{ $labels := dict -"name" "Assembly Name" -"type" "Assembly Type" -"level" "Assembly Level" -"repr" "Assembly Representation" -"accession" "Accession" -}} - - -
    - {{ range $key, $label := $labels }} -
  • {{ $label }}: {{ index $ $key }}
    • - {{ end }} -
+{{ $fields := append (or (index .fields.extra .section) slice) (index .fields.default .section) }} +{{ $values := index .values .section }} +{{ with $fields }} +
    + {{ range $fields }} + {{ $key := index . 0 }} + {{ $label := or (index . 1) (replace $key "_" " " | title ) }} + {{ with index $values $key }} +
  • {{ $label }}: {{ . }}
    • + {{ else }} + {{ warnidf "missing-assembly-meta" "%s/assembly.yaml lacks key %s" $.path $key }} + {{ end }} + {{ end }} +
+{{ else }} + {{ warnf "No assembly fields declared for section: %s" .section }} +{{ end }} diff --git a/hugo/layouts/partials/halloween/assembly_stats.html b/hugo/layouts/partials/halloween/assembly_stats.html index 05a0af48..07fd27bf 100644 --- a/hugo/layouts/partials/halloween/assembly_stats.html +++ b/hugo/layouts/partials/halloween/assembly_stats.html @@ -1,38 +1,31 @@ -{{ $labels := dict -"length" "Assembly length (Mbp)" -"gc" "GC %" -"contig" "Contig #" -"contig_n50" "Contig N50 (Mbp)" -"contig_l50" "Contig L50" -"contig_n90" "Contig N90 (Mbp)" -"contig_l90" "Contig L90" -"scaffold" "Scaffold #" -"scaffold_n50" "Scaffold N50 (Mbp)" -"scaffold_l50" "Scaffold L50" -"scaffold_n90" "Scaffold N90 (Mbp)" -"scaffold_l90" "Scaffold L90" -"scaffold_gt_10" "Scaffolds >= 10 kb" -"busco" "BUSCO %" -}} +{{ $fields := append (or (index .fields.extra .section) slice) (index .fields.default .section) }} +{{ $values := index .values .section }} +{{ with $fields }} +
+ -
-
- - - - - - - - - - {{ range $key, $label := $labels }} + - - + + - {{ end }} - - -
StatisticValue
{{ $label }} {{ or (index $ $key) "Not provided" }} StatisticValue
-
+ + + {{ range $fields }} + {{ $key := index . 0 }} + {{ $label := or (index . 1) (replace $key "_" " " | title ) }} + {{ with index $values $key | string }} + + {{ $label }} + {{ . }} + + {{ else }} + {{ warnidf "missing-assembly-stat" "%s/assembly.yaml: %s undefined" $.path $key }} + {{ end }} + {{ end }} + + +
+{{ else }} + {{ warnf "No assembly fields declared for section: %s" .section }} +{{ end }} From 8e5d859fb2bea888a38e5abeef44da008eb97fd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Sat, 16 Nov 2024 15:08:55 +0100 Subject: [PATCH 30/59] Use templates for templates --- scripts/add_new_species.py | 69 ++++++++++++++++++++--------------- scripts/templates/_index.md | 12 +++--- scripts/templates/assembly.md | 6 +-- scripts/templates/download.md | 2 +- 4 files changed, 49 insertions(+), 40 deletions(-) diff --git a/scripts/add_new_species.py b/scripts/add_new_species.py index bed46e2f..3989108d 100644 --- a/scripts/add_new_species.py +++ b/scripts/add_new_species.py @@ -7,8 +7,12 @@ """ import argparse +import logging +import re import shutil +from collections import defaultdict from pathlib import Path +from string import Template import requests from get_taxonomy import EbiRestException, get_taxonomy @@ -73,42 +77,47 @@ def create_dirs(dir_name: str) -> tuple[Path, Path, Path]: return content_dir_path, data_dir_path, assets_dir_path +def slugify(name): + return re.sub(r"\s+", "_", name) + + +def get_template_context(species_name: str, tax_id: str | None = None) -> dict: + ctxt = defaultdict( + lambda: "[EDIT]", + species_name=species_name, + slug=slugify(species_name), + ) + try: + ctxt["gbif_taxon_key"] = get_gbif_taxon_key(species_name) + except (requests.HTTPError, KeyError): + logging.warn("Failed to get GBIF key for species: %s", species_name) + if tax_id: + ctxt["goat_link"] = make_goat_weblink(species_name=species_name, tax_id=tax_id) + return ctxt + + +def render(template_str, context): + return Template(template_str).substitute(context) + + +def load_template(template_name): + try: + return (TEMPLATE_DIR / template_name).read_text() + except IOError: + raise ValueError(f"Template not found: {template_name}") from None + + def add_content_files(species_name: str, content_dir_path: Path, tax_id: str) -> None: """ Add the species name to the template content files, then write them to disk. """ - dir_name = species_name.replace(" ", "_").lower() + ctxt = get_template_context(species_name, tax_id) for file_name in CONTENT_FILES: - with open(TEMPLATE_DIR / file_name, "r") as file_in: - template = file_in.read() - - template = template.replace("SPECIES_NAME", species_name) - template = template.replace("SPECIES_FOLDER", dir_name) - - if file_name == INDEX_FILE: - try: - gbif_taxon_key = get_gbif_taxon_key(species_name=species_name) - template = template.replace("GBIF_TAXON_ID", gbif_taxon_key) - except (requests.exceptions.HTTPError, KeyError): - print( - f"""WARNING: Failed to get GBIF key for species: {args.species_name}. - Not to worry, - you can instead add it manually to the _index.md file in the species directory.""" - ) - template = template.replace("GBIF_TAXON_ID", "[EDIT]") - - if tax_id: - goat_link = make_goat_weblink(species_name=species_name, tax_id=tax_id) - template = template.replace("GOAT_WEBPAGE", goat_link) - else: - template = template.replace("GOAT_WEBPAGE", "[EDIT]") - - output_file_path = content_dir_path / file_name - - with open(output_file_path, "w") as file_out: - file_out.write(template) - print(f"File created: {output_file_path.resolve()}") + template_str = load_template(file_name) + content = render(template_str, ctxt) + (out_file := content_dir_path / file_name).write_text(content) + logging.info("File created: %s", out_file.resolve()) def add_stats_file(data_dir_path: Path) -> None: diff --git a/scripts/templates/_index.md b/scripts/templates/_index.md index 46104286..c13f2671 100644 --- a/scripts/templates/_index.md +++ b/scripts/templates/_index.md @@ -14,13 +14,13 @@ img_attrib_link: "[EDIT] - if there is no hyperlink available for this file, the # unless you were warned by the add-new-species.py script. layout: "species_intro" banner_title: "Species overview" -url: "SPECIES_FOLDER" +url: "${slug}" weight: 1 -science_name: "SPECIES_NAME" -lineage_data_path: "SPECIES_FOLDER/taxonomy" +science_name: "${species_name}" +lineage_data_path: "${slug}/taxonomy" -gbif_taxon_id: "GBIF_TAXON_ID" -goat_webpage: "GOAT_WEBPAGE" +gbif_taxon_id: "${gbif_taxon_id}" +goat_webpage: "${goat_webpage}" # Optional params below, @@ -50,4 +50,4 @@ Write content here in markdown for the introduction tab of the species page. #### Changelog -- [TODO - Add date] - Species first published on the Portal \ No newline at end of file +- [TODO - Add date] - Species first published on the Portal diff --git a/scripts/templates/assembly.md b/scripts/templates/assembly.md index d79bc4bc..c5c34f8c 100644 --- a/scripts/templates/assembly.md +++ b/scripts/templates/assembly.md @@ -11,11 +11,11 @@ key_info: # unless you were warned by the add-new-species.py script. title: "Genome assembly" layout: "species_assembly" -url: "SPECIES_FOLDER/assembly" +url: "${slug}/assembly" weight: 2 -stats_data_path: "SPECIES_FOLDER/species_stats" -lineage_data_path: "SPECIES_FOLDER/taxonomy" +stats_data_path: "${slug}/species_stats" +lineage_data_path: "${slug}/taxonomy" --- |||||| Content divider - do not remove |||||| diff --git a/scripts/templates/download.md b/scripts/templates/download.md index fa952a34..35f05707 100644 --- a/scripts/templates/download.md +++ b/scripts/templates/download.md @@ -3,6 +3,6 @@ alias_file_url: "[EDIT]" # The below parameters were generated automatically and do not need to be changed. title: "Download" layout: "species_download" -url: "SPECIES_FOLDER/download" +url: "${slug}/download" weight: 3 --- From 37ed418464f95a4d59fa51c00473557fcdd5630d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 18 Nov 2024 12:02:05 +0100 Subject: [PATCH 31/59] Allow optional fields defined globally --- hugo/config/_default/params.yaml | 76 ++++++++++++------- .../jacobus_lanternibus/assembly/index.md | 6 +- .../halloween/assembly_description.html | 9 ++- .../partials/halloween/assembly_stats.html | 9 ++- 4 files changed, 64 insertions(+), 36 deletions(-) diff --git a/hugo/config/_default/params.yaml b/hugo/config/_default/params.yaml index 9c622975..0a25fd5f 100644 --- a/hugo/config/_default/params.yaml +++ b/hugo/config/_default/params.yaml @@ -1,30 +1,54 @@ assembly_fields: description: - - ["name", "Assembly Name"] - - ["type", "Assembly Type"] - - ["level", "Assembly Level"] - - ["repr", "Assembly Representation"] - - ["accession"] + - key: name + label: Assembly Name + - key: type + label: Assembly Type + - key: level + label: Assembly Level + - key: repr + label: Assembly Representation + - key: accession stats: - - ["length", "Assembly length (Mbp)"] - - ["gc", "GC %"] - - ["contig", "Contig #" ] - - ["contig_n50", "Contig N50 (Mbp)" ] - - ["contig_l50"] - - ["contig_n90", "Contig N90 (Mbp)" ] - - ["contig_l90"] - - ["scaffold", "Scaffold #"] - - ["scaffold_n50", "Scaffold N50 (Mbp)"] - - ["scaffold_l50"] - - ["scaffold_n90", "Scaffold N90 (Mbp)"] - - ["scaffold_l90"] - - ["scaffold_gt_10", "Scaffolds >= 10 kb"] - - ["busco", "BUSCO %"] + - key: length + label: "Assembly length (Mbp)" + - key: gc + label: "GC %" + - key: contig + label: "Contig #" + - key: contig_n50 + label: "Contig N50 (Mbp)" + - key: contig_l50 + - key: contig_n90 + label: "Contig N90 (Mbp)" + - key: contig_l90 + - key: scaffold + label: "Scaffold #" + - key: scaffold_n50 + label: "Scaffold N50 (Mbp)" + - key: scaffold_l50 + - key: scaffold_n90 + label: Scaffold N90 (Mbp) + - key: scaffold_l90 + - key: scaffold_gt_10 + label: "Scaffolds >= 10 kb" + - key: busco + label: BUSCO % annotation: - - ["gene_cnt", "Gene #"] - - ["transcript_cnt", "Transcript #"] - - ["exons_avg", "Avg exons per transcript"] - - ["gene_length_avg","Avg gene length (bp)"] - - ["transcript_length_avg", "Avg transcript length (bp)"] - - ["exon_length_avg", "Avg exon length (bp)"] - - ["intron_length_avg", "Avg intron length (bp)"] + - key: gene_cnt + label: "Gene #" + - key: transcript_cnt + label: "Transcript #" + - key: exons_avg + label: Avg exons per transcript + - key: gene_length_avg + label: Avg gene length (bp) + - key: transcript_length_avg + label: Avg transcript length (bp) + - key: exon_length_avg + label: Avg exon length (bp) + - key: intron_length_avg + label: Avg intron length (bp) + - key: busco + label: BUSCO % + optional: true diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md index d6db17cc..af456f47 100644 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md +++ b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md @@ -4,8 +4,10 @@ layout: assembly params: assembly_fields: description: - - ["extra_1", "Additional field"] - - ["extra_2", "Another Additional field"] + - key: extra_1 + label: Additional field + - key: extra_2 + label: Another Additional field --- ### Methods diff --git a/hugo/layouts/partials/halloween/assembly_description.html b/hugo/layouts/partials/halloween/assembly_description.html index 2701100c..69f13877 100644 --- a/hugo/layouts/partials/halloween/assembly_description.html +++ b/hugo/layouts/partials/halloween/assembly_description.html @@ -3,12 +3,13 @@ {{ with $fields }}
    {{ range $fields }} - {{ $key := index . 0 }} - {{ $label := or (index . 1) (replace $key "_" " " | title ) }} - {{ with index $values $key }} + {{ $label := .label | default (replace .key "_" " " | title ) }} + {{ with index $values .key }}
  • {{ $label }}: {{ . }}
    • {{ else }} - {{ warnidf "missing-assembly-meta" "%s/assembly.yaml lacks key %s" $.path $key }} + {{ if not .optional }} + {{ warnidf "missing-assembly-meta" "%s/assembly.yaml: %s undefined" $.path .key }} + {{ end }} {{ end }} {{ end }}
diff --git a/hugo/layouts/partials/halloween/assembly_stats.html b/hugo/layouts/partials/halloween/assembly_stats.html index 07fd27bf..c2f7a8ea 100644 --- a/hugo/layouts/partials/halloween/assembly_stats.html +++ b/hugo/layouts/partials/halloween/assembly_stats.html @@ -12,15 +12,16 @@ {{ range $fields }} - {{ $key := index . 0 }} - {{ $label := or (index . 1) (replace $key "_" " " | title ) }} - {{ with index $values $key | string }} + {{ $label := .key | default (replace .key "_" " " | title ) }} + {{ with index $values .key | string }} {{ $label }} {{ . }} {{ else }} - {{ warnidf "missing-assembly-stat" "%s/assembly.yaml: %s undefined" $.path $key }} + {{ if not .optional }} + {{ warnidf "missing-assembly-stat" "%s/assembly.yaml: %s undefined" $.path .key }} + {{ end}} {{ end }} {{ end }} From 5e6a61b67f0b02a51ca12b129e9ac010d95cc267 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Mon, 18 Nov 2024 16:08:45 +0100 Subject: [PATCH 32/59] Inline taxonomic lineage in archetype --- hugo/archetypes/halloween/_index.md | 7 +++++-- hugo/layouts/partials/halloween/FetchTaxId.html | 3 +++ hugo/layouts/partials/halloween/LineageConfig | 3 +++ 3 files changed, 11 insertions(+), 2 deletions(-) create mode 100644 hugo/layouts/partials/halloween/FetchTaxId.html create mode 100644 hugo/layouts/partials/halloween/LineageConfig diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 7c27d0ca..ceac4226 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,7 +1,8 @@ +{{ $scientificName := replace .File.ContentBaseName `_` ` ` | title }} --- date: {{ .Date }} -title: '{{ replace .File.ContentBaseName `_` ` ` | title }}' -subtitle: Species common name +title: {{ $scientificName }} +subtitle: lastmod: {{ .Date }} resources: @@ -15,7 +16,9 @@ resources: layout: "species_intro" weight: 1 +{{ $taxId := partial "halloween/FetchTaxId" $scientificName }} params: + lineage: {{ partial "halloween/LineageConfig" $taxId }} banner_title: "Species overview" goat_webpage: "https://goat.genomehubs.org" diff --git a/hugo/layouts/partials/halloween/FetchTaxId.html b/hugo/layouts/partials/halloween/FetchTaxId.html new file mode 100644 index 00000000..8f30fca4 --- /dev/null +++ b/hugo/layouts/partials/halloween/FetchTaxId.html @@ -0,0 +1,3 @@ +{{ $url := replace . " " "%20" | printf "https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/%s" }} +{{ $data := resources.GetRemote $url | transform.Unmarshal }} +{{ return index $data 0 "taxId" }} diff --git a/hugo/layouts/partials/halloween/LineageConfig b/hugo/layouts/partials/halloween/LineageConfig new file mode 100644 index 00000000..a4c82ad9 --- /dev/null +++ b/hugo/layouts/partials/halloween/LineageConfig @@ -0,0 +1,3 @@ +{{- $taxId := . -}} +{{- $taxonomy := resources.GetRemote (printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId) | transform.Unmarshal -}} +{{- partial "halloween/GetTaxonomyRanks" $taxonomy | encoding.Jsonify (dict "prefix" " " "indent" " ") -}} From 8a126530080c2d22c3574fa24a3313ebb435c9d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Tue, 19 Nov 2024 10:59:42 +0100 Subject: [PATCH 33/59] Add error handling to partials fetching ENA taxonomic information --- hugo/archetypes/halloween/_index.md | 3 +- .../archetypes/halloween/lineage.default.yaml | 35 +++++++++++++++++++ .../partials/halloween/FetchTaxId.html | 13 +++++-- hugo/layouts/partials/halloween/LineageConfig | 3 -- .../partials/halloween/LineageConfig.html | 10 ++++++ 5 files changed, 57 insertions(+), 7 deletions(-) create mode 100644 hugo/archetypes/halloween/lineage.default.yaml delete mode 100644 hugo/layouts/partials/halloween/LineageConfig create mode 100644 hugo/layouts/partials/halloween/LineageConfig.html diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index ceac4226..91e113ae 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,12 +1,11 @@ {{ $scientificName := replace .File.ContentBaseName `_` ` ` | title }} ---- date: {{ .Date }} title: {{ $scientificName }} subtitle: lastmod: {{ .Date }} resources: - - title: '{{ replace .File.ContentBaseName `_` ` ` | title }}' + - title: '{{ $scientificName }}' name: cover_image src: "placeholder.png" params: diff --git a/hugo/archetypes/halloween/lineage.default.yaml b/hugo/archetypes/halloween/lineage.default.yaml new file mode 100644 index 00000000..e70836a1 --- /dev/null +++ b/hugo/archetypes/halloween/lineage.default.yaml @@ -0,0 +1,35 @@ +# Example lineage configuration. +# This format is expeced by the .Params.lineage front matter key in `_index.md` +clade: + scientificName: Embryophyta + taxId: "3193" +class: + scientificName: Magnoliopsida + taxId: "3398" +family: + scientificName: Cucurbitaceae + taxId: "3650" +genus: + scientificName: Cucurbita + taxId: "3660" +kingdom: + scientificName: Viridiplantae + taxId: "33090" +order: + scientificName: Cucurbitales + taxId: "71239" +phylum: + scientificName: Streptophyta + taxId: "35493" +species: + scientificName: Cucurbita pepo + taxId: "3663" +subphylum: + scientificName: Streptophytina + taxId: "131221" +superkingdom: + scientificName: Eukaryota + taxId: "2759" +tribe: + scientificName: Cucurbiteae + taxId: "1003878" diff --git a/hugo/layouts/partials/halloween/FetchTaxId.html b/hugo/layouts/partials/halloween/FetchTaxId.html index 8f30fca4..0111ff42 100644 --- a/hugo/layouts/partials/halloween/FetchTaxId.html +++ b/hugo/layouts/partials/halloween/FetchTaxId.html @@ -1,3 +1,12 @@ {{ $url := replace . " " "%20" | printf "https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/%s" }} -{{ $data := resources.GetRemote $url | transform.Unmarshal }} -{{ return index $data 0 "taxId" }} +{{ $taxId := "" }} +{{ with resources.GetRemote $url }} + {{ with .Err }} + {{ errorf "Error fetch ENA taxon ID for species %s: %s" $ . }} + {{ else }} + {{ $taxId = index (transform.Unmarshal .) 0 "taxId" }} + {{ return $taxId }} + {{ end }} +{{ else }} + {{ warnf "Could not find ENA taxon ID for species %s." $ }} +{{ end }} diff --git a/hugo/layouts/partials/halloween/LineageConfig b/hugo/layouts/partials/halloween/LineageConfig deleted file mode 100644 index a4c82ad9..00000000 --- a/hugo/layouts/partials/halloween/LineageConfig +++ /dev/null @@ -1,3 +0,0 @@ -{{- $taxId := . -}} -{{- $taxonomy := resources.GetRemote (printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId) | transform.Unmarshal -}} -{{- partial "halloween/GetTaxonomyRanks" $taxonomy | encoding.Jsonify (dict "prefix" " " "indent" " ") -}} diff --git a/hugo/layouts/partials/halloween/LineageConfig.html b/hugo/layouts/partials/halloween/LineageConfig.html new file mode 100644 index 00000000..c24f243e --- /dev/null +++ b/hugo/layouts/partials/halloween/LineageConfig.html @@ -0,0 +1,10 @@ +{{- $taxId := . -}} +{{- with resources.GetRemote (printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId) -}} + {{ with .Err }} + {{ errorf "Error fetching lineage of taxon %s: %s. Consider editing .Params.lineage" $taxId . }} + {{ else }} + {{- transform.Unmarshal . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") -}} + {{ end }} +{{- else -}} + {{ warnf "Missing lineage information. Consider editing .Params.lineage" $taxId . }} +{{- end -}} From ece065935306a5e776a8d4e6a0a83e22805cfc55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Tue, 19 Nov 2024 11:34:41 +0100 Subject: [PATCH 34/59] Restore dashing header --- hugo/archetypes/halloween/_index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 91e113ae..7144250e 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,4 +1,5 @@ {{ $scientificName := replace .File.ContentBaseName `_` ` ` | title }} +--- date: {{ .Date }} title: {{ $scientificName }} subtitle: From b3246938866e6a95b46a2dedd9b9d69d1a289969 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Tue, 19 Nov 2024 11:35:51 +0100 Subject: [PATCH 35/59] Define lineage fields in site parameters --- hugo/config/_default/params.yaml | 12 +++++++ hugo/layouts/halloween/species_intro.html | 8 ++--- hugo/layouts/partials/halloween/lineage.html | 34 ++++++-------------- 3 files changed, 24 insertions(+), 30 deletions(-) diff --git a/hugo/config/_default/params.yaml b/hugo/config/_default/params.yaml index 0a25fd5f..5b70b839 100644 --- a/hugo/config/_default/params.yaml +++ b/hugo/config/_default/params.yaml @@ -52,3 +52,15 @@ assembly_fields: - key: busco label: BUSCO % optional: true +taxonomy_ranks: + - key: "superkingdom" + label: "Domain" + - key: "kingdom" + - key: "phylum" + - key: "class" + - key: "order" + - key: "family" + - key: "genus" + format: "%s" + - key: "species" + format: "%s" diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index 416fd246..de557673 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -57,12 +57,10 @@

Taxonomy

- {{ with .Resources.Get "taxonomy.xml" | transform.Unmarshal }} - {{ with partial "halloween/GetTaxonomyRanks.html" . }} - {{ partial "halloween/lineage.html" . }} - {{ end }} + {{ with .Params.lineage }} + {{ partial "halloween/lineage.html" . }} {{ else }} - {{ errorf "Missing taxonomy file: %s/taxonomy.json" $.Path }} + {{ warnidf "missing-taxonomy" "Missing taxonmomy lineage for %s" $.Path }} {{ end }}
diff --git a/hugo/layouts/partials/halloween/lineage.html b/hugo/layouts/partials/halloween/lineage.html index 3423da6b..cb578a77 100644 --- a/hugo/layouts/partials/halloween/lineage.html +++ b/hugo/layouts/partials/halloween/lineage.html @@ -1,40 +1,24 @@ {{ $ena_url := "https://www.ebi.ac.uk/ena/browser/view/Taxon:" }} {{ $ncbi_url := "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" }} - -{{ $order := slice -"superkingdom" -"kingdom" -"phylum" -"class" -"order" -"family" -"genus" -"species" -}} - -{{/* Ranks that need special labels */}} -{{ $labels := dict "superkingdom" "Domain"}} - -{{/* Ranks that need special name formatting */}} -{{ $fmt := dict "genus" "%s" "species" "%s" }} - -{{ range $order }} - {{ $rank := . }} +{{ range site.Params.taxonomy_ranks }} + {{ $rank := .key }} + {{/* Uppercased rank or custom label */}} + {{ $label := .label | default $rank | strings.FirstUpper }} + {{/* Optional formatting for the scientific name */}} + {{ $fmt := .format | default "%s" }} {{ with index $ $rank }}
- {{/* Uppercased rank or custom label */}} - {{ or (index $labels $rank) $rank | strings.FirstUpper }}: + {{ $label }}: - {{/* Scientific name with optional formatting */}} - {{ printf (or (index $fmt $rank) "%s") .scientificName | safe.HTML }} + {{ printf $fmt .scientificName | safe.HTML }}
{{ else }} - {{ warnf "Missing lineage entry %s for %s" . $.species.scientificName }} + {{ warnf "Missing lineage entry %s for %s" $rank $.species.scientificName }} {{ end }} {{ end }}
From 9fbd5205aefbd5951adf5fc70497ddf551b38135 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Tue, 19 Nov 2024 11:36:11 +0100 Subject: [PATCH 36/59] Remove taxonomy.xml --- hugo/archetypes/halloween/taxonomy.xml | 36 --------------- .../halloween/jacobus_lanternibus/_index.md | 46 +++++++++++++++++++ .../jacobus_lanternibus/taxonomy.xml | 36 --------------- 3 files changed, 46 insertions(+), 72 deletions(-) delete mode 100644 hugo/archetypes/halloween/taxonomy.xml delete mode 100644 hugo/content/halloween/jacobus_lanternibus/taxonomy.xml diff --git a/hugo/archetypes/halloween/taxonomy.xml b/hugo/archetypes/halloween/taxonomy.xml deleted file mode 100644 index 3a5d0b2f..00000000 --- a/hugo/archetypes/halloween/taxonomy.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - diff --git a/hugo/content/halloween/jacobus_lanternibus/_index.md b/hugo/content/halloween/jacobus_lanternibus/_index.md index 2ad0c6e9..da84d50f 100644 --- a/hugo/content/halloween/jacobus_lanternibus/_index.md +++ b/hugo/content/halloween/jacobus_lanternibus/_index.md @@ -15,6 +15,52 @@ layout: "species_intro" weight: 1 params: + lineage: { + "clade": { + "scientificName": "Embryophyta", + "taxId": "3193" + }, + "class": { + "scientificName": "Magnoliopsida", + "taxId": "3398" + }, + "family": { + "scientificName": "Cucurbitaceae", + "taxId": "3650" + }, + "genus": { + "scientificName": "Cucurbita", + "taxId": "3660" + }, + "kingdom": { + "scientificName": "Viridiplantae", + "taxId": "33090" + }, + "order": { + "scientificName": "Cucurbitales", + "taxId": "71239" + }, + "phylum": { + "scientificName": "Streptophyta", + "taxId": "35493" + }, + "species": { + "scientificName": "Cucurbita pepo", + "taxId": "3663" + }, + "subphylum": { + "scientificName": "Streptophytina", + "taxId": "131221" + }, + "superkingdom": { + "scientificName": "Eukaryota", + "taxId": "2759" + }, + "tribe": { + "scientificName": "Cucurbiteae", + "taxId": "1003878" + } + } banner_title: "Halloween species overview" gbif_taxon_id: 2874508 goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" diff --git a/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml b/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml deleted file mode 100644 index ed33ef9d..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/taxonomy.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - \ No newline at end of file From 2a4b49b9f6ef2d1a899bd97c82cb912a6a814993 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 10:34:27 +0100 Subject: [PATCH 37/59] Introduce helper partial to fetch remote data --- .../partials/halloween/FetchTaxId.html | 13 ++++------ .../partials/halloween/LineageConfig.html | 9 +++---- .../partials/halloween/get-remote-data.html | 25 +++++++++++++++++++ 3 files changed, 33 insertions(+), 14 deletions(-) create mode 100644 hugo/layouts/partials/halloween/get-remote-data.html diff --git a/hugo/layouts/partials/halloween/FetchTaxId.html b/hugo/layouts/partials/halloween/FetchTaxId.html index 0111ff42..f3af2240 100644 --- a/hugo/layouts/partials/halloween/FetchTaxId.html +++ b/hugo/layouts/partials/halloween/FetchTaxId.html @@ -1,12 +1,9 @@ {{ $url := replace . " " "%20" | printf "https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/%s" }} +{{ $data := partial "halloween/get-remote-data.html" $url }} {{ $taxId := "" }} -{{ with resources.GetRemote $url }} - {{ with .Err }} - {{ errorf "Error fetch ENA taxon ID for species %s: %s" $ . }} - {{ else }} - {{ $taxId = index (transform.Unmarshal .) 0 "taxId" }} - {{ return $taxId }} - {{ end }} +{{ with index $data 0 "taxId" }} + {{ $taxId = . }} {{ else }} - {{ warnf "Could not find ENA taxon ID for species %s." $ }} + {{ warnf "Could not find ENA taxon ID for species: %s" $ }} {{ end }} +{{ return $taxId }} diff --git a/hugo/layouts/partials/halloween/LineageConfig.html b/hugo/layouts/partials/halloween/LineageConfig.html index c24f243e..5a6489bb 100644 --- a/hugo/layouts/partials/halloween/LineageConfig.html +++ b/hugo/layouts/partials/halloween/LineageConfig.html @@ -1,10 +1,7 @@ {{- $taxId := . -}} -{{- with resources.GetRemote (printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId) -}} - {{ with .Err }} - {{ errorf "Error fetching lineage of taxon %s: %s. Consider editing .Params.lineage" $taxId . }} - {{ else }} - {{- transform.Unmarshal . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") -}} - {{ end }} +{{- $url := printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId -}} +{{- with partial "halloween/get-remote-data.html" $url -}} + {{ . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} {{- else -}} {{ warnf "Missing lineage information. Consider editing .Params.lineage" $taxId . }} {{- end -}} diff --git a/hugo/layouts/partials/halloween/get-remote-data.html b/hugo/layouts/partials/halloween/get-remote-data.html new file mode 100644 index 00000000..6061e97c --- /dev/null +++ b/hugo/layouts/partials/halloween/get-remote-data.html @@ -0,0 +1,25 @@ +{{/* +Copied from: https://github.com/gohugoio/gohugoioTheme/layouts/partials/utilities/get-remote-data.html + +Parses the serialized data from the given URL and returns a map or an array. + +Supports CSV, JSON, TOML, YAML, and XML. + +@param {string} . The URL from which to retrieve the serialized data. +@returns {any} + +@example {{ partial "get-remote-data.html" "https://example.org/foo.json" }} +*/}} + +{{ $url := . }} +{{ $data := dict }} +{{ with resources.GetRemote $url }} + {{ with .Err }} + {{ errorf "%s" . }} + {{ else }} + {{ $data = .Content | transform.Unmarshal }} + {{ end }} +{{ else }} + {{ errorf "Unable to get remote resource %q" $url }} +{{ end }} +{{ return $data }} From 66da5a8ab60324268ce2cb632fae9040375ebeb6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 10:34:55 +0100 Subject: [PATCH 38/59] Uppercase only firts letter of scientific name --- hugo/archetypes/halloween/_index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 7144250e..a241dcd0 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,4 +1,4 @@ -{{ $scientificName := replace .File.ContentBaseName `_` ` ` | title }} +{{ $scientificName := replace .File.ContentBaseName `_` ` ` | strings.FirstUpper }} --- date: {{ .Date }} title: {{ $scientificName }} From 34ad61f40c24700de9051705f6e5ffb7e104442d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 11:16:14 +0100 Subject: [PATCH 39/59] Allow to define taxonomic ranks at species level --- hugo/archetypes/halloween/_index.md | 5 ++++- hugo/layouts/halloween/species_intro.html | 9 +++++++-- hugo/layouts/partials/halloween/LineageConfig.html | 2 +- hugo/layouts/partials/halloween/lineage.html | 13 ++++++++----- 4 files changed, 20 insertions(+), 9 deletions(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index a241dcd0..93f69e6e 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -17,8 +17,11 @@ layout: "species_intro" weight: 1 {{ $taxId := partial "halloween/FetchTaxId" $scientificName }} +lineage: {{ partial "halloween/LineageConfig" $taxId }} +# Use this setting to override the default taxonomy ranks to display. +# See config/_default/params.yaml for the syntax to use. +taxonomy_ranks: params: - lineage: {{ partial "halloween/LineageConfig" $taxId }} banner_title: "Species overview" goat_webpage: "https://goat.genomehubs.org" diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/halloween/species_intro.html index de557673..a77224b9 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/halloween/species_intro.html @@ -58,9 +58,14 @@

Taxonomy

{{ with .Params.lineage }} - {{ partial "halloween/lineage.html" . }} + {{ $context := dict + "path" $.Path + "lineage" . + "taxonomy_ranks" (or $.Page.Params.taxonomy_ranks $.Site.Params.taxonomy_ranks) + }} + {{ partial "halloween/lineage.html" $context }} {{ else }} - {{ warnidf "missing-taxonomy" "Missing taxonmomy lineage for %s" $.Path }} + {{ warnidf "missing-taxonomy" "Missing taxonmomy lineage for %s" .Path }} {{ end }}
diff --git a/hugo/layouts/partials/halloween/LineageConfig.html b/hugo/layouts/partials/halloween/LineageConfig.html index 5a6489bb..2f7da22a 100644 --- a/hugo/layouts/partials/halloween/LineageConfig.html +++ b/hugo/layouts/partials/halloween/LineageConfig.html @@ -1,7 +1,7 @@ {{- $taxId := . -}} {{- $url := printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId -}} {{- with partial "halloween/get-remote-data.html" $url -}} - {{ . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} + {{ . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} {{- else -}} {{ warnf "Missing lineage information. Consider editing .Params.lineage" $taxId . }} {{- end -}} diff --git a/hugo/layouts/partials/halloween/lineage.html b/hugo/layouts/partials/halloween/lineage.html index cb578a77..8d85615b 100644 --- a/hugo/layouts/partials/halloween/lineage.html +++ b/hugo/layouts/partials/halloween/lineage.html @@ -1,12 +1,15 @@ +{{ $path := .path }} +{{ $lineage := .lineage }} +{{ $ranks := .taxonomy_ranks }} {{ $ena_url := "https://www.ebi.ac.uk/ena/browser/view/Taxon:" }} {{ $ncbi_url := "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" }} -{{ range site.Params.taxonomy_ranks }} +{{ range $ranks }} {{ $rank := .key }} {{/* Uppercased rank or custom label */}} {{ $label := .label | default $rank | strings.FirstUpper }} {{/* Optional formatting for the scientific name */}} {{ $fmt := .format | default "%s" }} - {{ with index $ $rank }} + {{ with index $lineage $rank }}
{{ $label }}: @@ -18,14 +21,14 @@
{{ else }} - {{ warnf "Missing lineage entry %s for %s" $rank $.species.scientificName }} + {{ warnf "%s: missing lineage entry %s" $path $rank }} {{ end }} {{ end }}
NCBI Taxonomy ID: - - {{ .species.taxId }} + + {{ $lineage.species.taxId }}
From fb74f20f535b142a8a2009f9cab41df064c3e030 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 11:41:16 +0100 Subject: [PATCH 40/59] GBIF usage key and Goat link support --- hugo/archetypes/halloween/_index.md | 11 +++++++---- hugo/layouts/partials/halloween/GetGbifKey.html | 9 +++++++++ .../halloween/{FetchTaxId.html => GetTaxId.html} | 0 hugo/layouts/partials/halloween/LineageConfig.html | 2 +- .../{GetTaxonomyRanks.html => TaxonomyRanks.html} | 0 5 files changed, 17 insertions(+), 5 deletions(-) create mode 100644 hugo/layouts/partials/halloween/GetGbifKey.html rename hugo/layouts/partials/halloween/{FetchTaxId.html => GetTaxId.html} (100%) rename hugo/layouts/partials/halloween/{GetTaxonomyRanks.html => TaxonomyRanks.html} (100%) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 93f69e6e..4b419286 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -1,4 +1,4 @@ -{{ $scientificName := replace .File.ContentBaseName `_` ` ` | strings.FirstUpper }} +{{- $scientificName := replace .File.ContentBaseName `_` ` ` | strings.FirstUpper -}} --- date: {{ .Date }} title: {{ $scientificName }} @@ -16,17 +16,20 @@ resources: layout: "species_intro" weight: 1 -{{ $taxId := partial "halloween/FetchTaxId" $scientificName }} +{{ $taxId := partial "halloween/GetTaxId" $scientificName }} lineage: {{ partial "halloween/LineageConfig" $taxId }} # Use this setting to override the default taxonomy ranks to display. # See config/_default/params.yaml for the syntax to use. taxonomy_ranks: params: banner_title: "Species overview" - goat_webpage: "https://goat.genomehubs.org" + goat_webpage: "{{ printf + "https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi" + $taxId + }}" # Map - gbif_taxon_id: 2874508 + gbif_taxon_id: {{ partial "halloween/GetGbifKey.html" $scientificName }} latitude: 60 longitude: -40 initialZoom: 1.5 diff --git a/hugo/layouts/partials/halloween/GetGbifKey.html b/hugo/layouts/partials/halloween/GetGbifKey.html new file mode 100644 index 00000000..3cafd5c5 --- /dev/null +++ b/hugo/layouts/partials/halloween/GetGbifKey.html @@ -0,0 +1,9 @@ +{{ $url := replace . " " "%20" | lower | printf "https://api.gbif.org/v1/species/match?name=%s" }} +{{ $data := partial "halloween/get-remote-data.html" $url }} +{{ $key := "" }} +{{ with $data.usageKey | string }} + {{ $key = . }} +{{ else }} + {{ warnf "%s: could not find GBIF taxon key" $ }} +{{ end }} +{{ return $key }} diff --git a/hugo/layouts/partials/halloween/FetchTaxId.html b/hugo/layouts/partials/halloween/GetTaxId.html similarity index 100% rename from hugo/layouts/partials/halloween/FetchTaxId.html rename to hugo/layouts/partials/halloween/GetTaxId.html diff --git a/hugo/layouts/partials/halloween/LineageConfig.html b/hugo/layouts/partials/halloween/LineageConfig.html index 2f7da22a..cdf88d48 100644 --- a/hugo/layouts/partials/halloween/LineageConfig.html +++ b/hugo/layouts/partials/halloween/LineageConfig.html @@ -1,7 +1,7 @@ {{- $taxId := . -}} {{- $url := printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId -}} {{- with partial "halloween/get-remote-data.html" $url -}} - {{ . | partial "halloween/GetTaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} + {{ . | partial "halloween/TaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} {{- else -}} {{ warnf "Missing lineage information. Consider editing .Params.lineage" $taxId . }} {{- end -}} diff --git a/hugo/layouts/partials/halloween/GetTaxonomyRanks.html b/hugo/layouts/partials/halloween/TaxonomyRanks.html similarity index 100% rename from hugo/layouts/partials/halloween/GetTaxonomyRanks.html rename to hugo/layouts/partials/halloween/TaxonomyRanks.html From 4d0732e3b2f4b65a2f0d9764fc1abbed5bcd687b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 11:44:25 +0100 Subject: [PATCH 41/59] Cleanup archetype content --- .../halloween/assembly/assembly.yaml | 10 ++++---- hugo/archetypes/halloween/assembly/contrib.md | 8 ------- hugo/archetypes/halloween/assembly/stats.yaml | 24 ------------------- 3 files changed, 5 insertions(+), 37 deletions(-) delete mode 100644 hugo/archetypes/halloween/assembly/stats.yaml diff --git a/hugo/archetypes/halloween/assembly/assembly.yaml b/hugo/archetypes/halloween/assembly/assembly.yaml index 27999d94..c438d3e1 100644 --- a/hugo/archetypes/halloween/assembly/assembly.yaml +++ b/hugo/archetypes/halloween/assembly/assembly.yaml @@ -1,9 +1,9 @@ description: - name: "Jaco_Lant" - type: "Spectroid" - level: "Underwordly" - repr: "Partially obscure" - accession: "GCA_666" + name: + type: + level: + repr: + accession: stats: length: gc: diff --git a/hugo/archetypes/halloween/assembly/contrib.md b/hugo/archetypes/halloween/assembly/contrib.md index 0f19ad6c..97e53c71 100644 --- a/hugo/archetypes/halloween/assembly/contrib.md +++ b/hugo/archetypes/halloween/assembly/contrib.md @@ -7,16 +7,8 @@ build: ### Contributor(s) -Restless souls. - ### Publication(s) -- [How far will a pumpkin fly -?](https://www.nbcnews.com/id/wbna21197135) -- [The great pumpkin](https://www.smithsonianmag.com/science-nature/the-great-pumpkin-74423844/?no-ist=&page=1) - ### Funding -Mephisto Pact Treasury Foundation - ### Acknowledgements diff --git a/hugo/archetypes/halloween/assembly/stats.yaml b/hugo/archetypes/halloween/assembly/stats.yaml deleted file mode 100644 index 0b6aa3d3..00000000 --- a/hugo/archetypes/halloween/assembly/stats.yaml +++ /dev/null @@ -1,24 +0,0 @@ -assembly: - - "Assembly length (Mbp)": [EDIT] - - "GC %": [EDIT] - - "Contig #": [EDIT] - - "Contig N50 (Mbp)": [EDIT] - - "Contig L50": [EDIT] - - "Contig N90 (Mbp)": [EDIT] - - "Contig L90": [EDIT] - - "Scaffold #": [EDIT] - - "Scaffold N50 (Mbp)": [EDIT] - - "Scaffold L50": [EDIT] - - "Scaffold N90 (Mbp)": [EDIT] - - "Scaffold L90": [EDIT] - - "Scaffolds >= 10 kb": [EDIT] - - "BUSCO % [EDIT]": "[EDIT]" - -annotation: - - "Gene #": [EDIT] - - "Transcript #": [EDIT] - - "Avg exons per transcript": [EDIT] - - "Avg gene length (bp)": [EDIT] - - "Avg transcript length (bp)": [EDIT] - - "Avg exon length (bp)": [EDIT] - - "Avg intron length (bp)": [EDIT] From 9a2810c0d8e0cf995258c830ba41d90c56fd1951 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 15:04:53 +0100 Subject: [PATCH 42/59] Fix default map coordinates --- hugo/archetypes/halloween/_index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 4b419286..40eaead7 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -30,9 +30,9 @@ params: # Map gbif_taxon_id: {{ partial "halloween/GetGbifKey.html" $scientificName }} - latitude: 60 - longitude: -40 - initialZoom: 1.5 + latitude: 0 + longitude: 0 + initialZoom: 1 # Optional iucn_category: From c1cde56d9ed75b9a15edf6c00f227ea9ee2656f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 15:05:30 +0100 Subject: [PATCH 43/59] Use simple quotes to appease syntax highlighter --- hugo/archetypes/halloween/_index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index 40eaead7..fadccc67 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -24,7 +24,7 @@ taxonomy_ranks: params: banner_title: "Species overview" goat_webpage: "{{ printf - "https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi" + 'https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi' $taxId }}" From 460248924cb9dfdabbbf17146fc0043dbf9d6ebb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 15:06:01 +0100 Subject: [PATCH 44/59] Remove unnecessary intro bundle --- hugo/archetypes/halloween/intro/index.md | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 hugo/archetypes/halloween/intro/index.md diff --git a/hugo/archetypes/halloween/intro/index.md b/hugo/archetypes/halloween/intro/index.md deleted file mode 100644 index ca03031f..00000000 --- a/hugo/archetypes/halloween/intro/index.md +++ /dev/null @@ -1,3 +0,0 @@ ---- -headless: true ---- From 53efb4371d8d35334765f90981d51800b2d91c82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 15:09:44 +0100 Subject: [PATCH 45/59] fixup! Use simple quotes to appease syntax highlighter --- hugo/archetypes/halloween/_index.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index fadccc67..b8655807 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -23,10 +23,10 @@ lineage: {{ partial "halloween/LineageConfig" $taxId }} taxonomy_ranks: params: banner_title: "Species overview" - goat_webpage: "{{ printf - 'https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi' + goat_webpage: '{{ printf + "https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi" $taxId - }}" + }}' # Map gbif_taxon_id: {{ partial "halloween/GetGbifKey.html" $scientificName }} @@ -43,12 +43,10 @@ params: ### Description -Write some content here in markdown for the introduction tab of the species page. - #### Genome reference #### References #### Changelog -- 31/10/2024 - Species first published on the Portal +- {{ .Date | time.Format "31/10/2024" }} - Species first published on the Portal From d41ab0febcde86aa2a3e87ff31b7055a7df7adda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 15:41:15 +0100 Subject: [PATCH 46/59] Use medium date format to avoid ambiguities --- hugo/archetypes/halloween/_index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/halloween/_index.md index b8655807..104fc84c 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/halloween/_index.md @@ -49,4 +49,4 @@ params: #### Changelog -- {{ .Date | time.Format "31/10/2024" }} - Species first published on the Portal +- {{ .Date | time.Format ":date_medium" }} - Species first published on the Portal From 87147eca906d570604fc259a19d6025146dfccc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 16:03:08 +0100 Subject: [PATCH 47/59] Introduce `species_bundle` namespace (formerly `halloween`) --- .../{halloween => species}/_index.md | 8 +- .../assembly/assembly.yaml | 0 .../assembly/contrib.md | 0 .../{halloween => species}/assembly/index.md | 2 +- .../download/data_tracks.json | 0 .../{halloween => species}/download/index.md | 2 +- .../lineage.default.yaml | 0 .../{halloween => species}/placeholder.png | Bin .../halloween/jacobus_lanternibus/_index.md | 86 ------ .../assembly/assembly.yaml | 31 -- .../jacobus_lanternibus/assembly/contrib.md | 22 -- .../jacobus_lanternibus/assembly/index.md | 13 - .../jacobus_lanternibus/assembly/stats.yaml | 24 -- .../download/data_tracks.json | 268 ------------------ .../jacobus_lanternibus/download/index.md | 6 - .../jacobus_lanternibus/intro/index.md | 3 - .../halloween/jacobus_lanternibus/pumpkin.jpg | Bin 29752 -> 0 bytes .../GetGbifKey.html | 2 +- .../GetTaxId.html | 2 +- .../LineageConfig.html | 4 +- .../TaxonomyRanks.html | 0 .../assembly_description.html | 0 .../assembly_stats.html | 0 .../download_table.html | 0 .../get-remote-data.html | 0 .../lineage.html | 0 .../assembly.html | 6 +- .../{halloween => species_bundle}/baseof.html | 0 .../browser.html | 0 .../species_download.html | 4 +- .../species_intro.html | 2 +- 31 files changed, 16 insertions(+), 469 deletions(-) rename hugo/archetypes/{halloween => species}/_index.md (79%) rename hugo/archetypes/{halloween => species}/assembly/assembly.yaml (100%) rename hugo/archetypes/{halloween => species}/assembly/contrib.md (100%) rename hugo/archetypes/{halloween => species}/assembly/index.md (57%) rename hugo/archetypes/{halloween => species}/download/data_tracks.json (100%) rename hugo/archetypes/{halloween => species}/download/index.md (63%) rename hugo/archetypes/{halloween => species}/lineage.default.yaml (100%) rename hugo/archetypes/{halloween => species}/placeholder.png (100%) delete mode 100644 hugo/content/halloween/jacobus_lanternibus/_index.md delete mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml delete mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md delete mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/index.md delete mode 100644 hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml delete mode 100644 hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json delete mode 100644 hugo/content/halloween/jacobus_lanternibus/download/index.md delete mode 100644 hugo/content/halloween/jacobus_lanternibus/intro/index.md delete mode 100644 hugo/content/halloween/jacobus_lanternibus/pumpkin.jpg rename hugo/layouts/partials/{halloween => species_bundle}/GetGbifKey.html (80%) rename hugo/layouts/partials/{halloween => species_bundle}/GetTaxId.html (81%) rename hugo/layouts/partials/{halloween => species_bundle}/LineageConfig.html (56%) rename hugo/layouts/partials/{halloween => species_bundle}/TaxonomyRanks.html (100%) rename hugo/layouts/partials/{halloween => species_bundle}/assembly_description.html (100%) rename hugo/layouts/partials/{halloween => species_bundle}/assembly_stats.html (100%) rename hugo/layouts/partials/{halloween => species_bundle}/download_table.html (100%) rename hugo/layouts/partials/{halloween => species_bundle}/get-remote-data.html (100%) rename hugo/layouts/partials/{halloween => species_bundle}/lineage.html (100%) rename hugo/layouts/{halloween => species_bundle}/assembly.html (91%) rename hugo/layouts/{halloween => species_bundle}/baseof.html (100%) rename hugo/layouts/{halloween => species_bundle}/browser.html (100%) rename hugo/layouts/{halloween => species_bundle}/species_download.html (90%) rename hugo/layouts/{halloween => species_bundle}/species_intro.html (98%) diff --git a/hugo/archetypes/halloween/_index.md b/hugo/archetypes/species/_index.md similarity index 79% rename from hugo/archetypes/halloween/_index.md rename to hugo/archetypes/species/_index.md index 104fc84c..2793466e 100644 --- a/hugo/archetypes/halloween/_index.md +++ b/hugo/archetypes/species/_index.md @@ -13,11 +13,11 @@ resources: attribution: CC-BY-SA link: "https://placehold.co/600x400/png" -layout: "species_intro" +layout: "species_bundle/species_intro" weight: 1 -{{ $taxId := partial "halloween/GetTaxId" $scientificName }} -lineage: {{ partial "halloween/LineageConfig" $taxId }} +{{ $taxId := partial "species_bundle/GetTaxId" $scientificName }} +lineage: {{ partial "species_bundle/LineageConfig" $taxId }} # Use this setting to override the default taxonomy ranks to display. # See config/_default/params.yaml for the syntax to use. taxonomy_ranks: @@ -29,7 +29,7 @@ params: }}' # Map - gbif_taxon_id: {{ partial "halloween/GetGbifKey.html" $scientificName }} + gbif_taxon_id: {{ partial "species_bundle/GetGbifKey.html" $scientificName }} latitude: 0 longitude: 0 initialZoom: 1 diff --git a/hugo/archetypes/halloween/assembly/assembly.yaml b/hugo/archetypes/species/assembly/assembly.yaml similarity index 100% rename from hugo/archetypes/halloween/assembly/assembly.yaml rename to hugo/archetypes/species/assembly/assembly.yaml diff --git a/hugo/archetypes/halloween/assembly/contrib.md b/hugo/archetypes/species/assembly/contrib.md similarity index 100% rename from hugo/archetypes/halloween/assembly/contrib.md rename to hugo/archetypes/species/assembly/contrib.md diff --git a/hugo/archetypes/halloween/assembly/index.md b/hugo/archetypes/species/assembly/index.md similarity index 57% rename from hugo/archetypes/halloween/assembly/index.md rename to hugo/archetypes/species/assembly/index.md index 59c22e0a..b53f4aef 100644 --- a/hugo/archetypes/halloween/assembly/index.md +++ b/hugo/archetypes/species/assembly/index.md @@ -1,6 +1,6 @@ --- title: "Genome assembly" -layout: assembly +layout: "species_bundle/assembly" --- ### Methods diff --git a/hugo/archetypes/halloween/download/data_tracks.json b/hugo/archetypes/species/download/data_tracks.json similarity index 100% rename from hugo/archetypes/halloween/download/data_tracks.json rename to hugo/archetypes/species/download/data_tracks.json diff --git a/hugo/archetypes/halloween/download/index.md b/hugo/archetypes/species/download/index.md similarity index 63% rename from hugo/archetypes/halloween/download/index.md rename to hugo/archetypes/species/download/index.md index 26e08224..1c41de67 100644 --- a/hugo/archetypes/halloween/download/index.md +++ b/hugo/archetypes/species/download/index.md @@ -1,6 +1,6 @@ --- title: "Download" -layout: "species_download" +layout: "species_bundle/species_download" url: "jacobus_lanternibus/download" weight: 3 --- diff --git a/hugo/archetypes/halloween/lineage.default.yaml b/hugo/archetypes/species/lineage.default.yaml similarity index 100% rename from hugo/archetypes/halloween/lineage.default.yaml rename to hugo/archetypes/species/lineage.default.yaml diff --git a/hugo/archetypes/halloween/placeholder.png b/hugo/archetypes/species/placeholder.png similarity index 100% rename from hugo/archetypes/halloween/placeholder.png rename to hugo/archetypes/species/placeholder.png diff --git a/hugo/content/halloween/jacobus_lanternibus/_index.md b/hugo/content/halloween/jacobus_lanternibus/_index.md deleted file mode 100644 index da84d50f..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/_index.md +++ /dev/null @@ -1,86 +0,0 @@ ---- -title: Jacobus Lanternibus -subtitle: "Jack-o'-lantern" -lastmod: 2024-10-26T10:00:00+0200 - -resources: - - title: Fiery pumpkin - name: cover_image - src: pumpkin.jpg - params: - attribution: pandemonic domain, CC BY-SA-TA-N - link: https://commons.wikimedia.org/wiki/File:Pumpkin2007.jpg - -layout: "species_intro" -weight: 1 - -params: - lineage: { - "clade": { - "scientificName": "Embryophyta", - "taxId": "3193" - }, - "class": { - "scientificName": "Magnoliopsida", - "taxId": "3398" - }, - "family": { - "scientificName": "Cucurbitaceae", - "taxId": "3650" - }, - "genus": { - "scientificName": "Cucurbita", - "taxId": "3660" - }, - "kingdom": { - "scientificName": "Viridiplantae", - "taxId": "33090" - }, - "order": { - "scientificName": "Cucurbitales", - "taxId": "71239" - }, - "phylum": { - "scientificName": "Streptophyta", - "taxId": "35493" - }, - "species": { - "scientificName": "Cucurbita pepo", - "taxId": "3663" - }, - "subphylum": { - "scientificName": "Streptophytina", - "taxId": "131221" - }, - "superkingdom": { - "scientificName": "Eukaryota", - "taxId": "2759" - }, - "tribe": { - "scientificName": "Cucurbiteae", - "taxId": "1003878" - } - } - banner_title: "Halloween species overview" - gbif_taxon_id: 2874508 - goat_webpage: "https://goat.genomehubs.org/record?recordId=213953&result=taxon&taxonomy=ncbi#Parnassius%20mnemosyne" - iucn_category: "Least Concern" - iucn_link: "https://www.iucnredlist.org/species/155123/4717767" - swe_red_list: "Viable" - swe_red_list_link: "https://artfakta.se/taxa/206089/" - latitude: 60 - longitude: -40 - initialZoom: 1.5 ---- - -### Description - -Write some content here in markdown for the introduction tab of the species page. - -#### Genome reference - -#### References - -#### Changelog - -- 31/10/2024 - Species first published on the Portal diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml deleted file mode 100644 index c113ff16..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/assembly.yaml +++ /dev/null @@ -1,31 +0,0 @@ -description: - name: "Jaco_Lant" - type: "Spectroid" - level: "Underwordly" - repr: "Partially obscure" - accession: "GCA_666" - extra_1: 666 - extra_2: 999 -stats: - length: 1 - gc: 2 - contig: 3 - contig_n50: 4 - contig_l50: 5 - contig_n90: 6 - contig_l90: 7 - scaffold: 8 - scaffold_n50: 9 - scaffold_l50: 10 - scaffold_n90: 11 - scaffold_l90: 12 - scaffold_gt_10: 13 - busco: 34 -annotation: - gene_cnt: 14 - transcript_cnt: 15 - exons_avg: 16 - gene_length_avg: 17 - transcript_length_avg: 18 - exon_length_avg: 19 - intron_length_avg: 20 diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md b/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md deleted file mode 100644 index 0f19ad6c..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/contrib.md +++ /dev/null @@ -1,22 +0,0 @@ ---- -build: - list: never - publishResources: false - render: never ---- - -### Contributor(s) - -Restless souls. - -### Publication(s) - -- [How far will a pumpkin fly -?](https://www.nbcnews.com/id/wbna21197135) -- [The great pumpkin](https://www.smithsonianmag.com/science-nature/the-great-pumpkin-74423844/?no-ist=&page=1) - -### Funding - -Mephisto Pact Treasury Foundation - -### Acknowledgements diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md b/hugo/content/halloween/jacobus_lanternibus/assembly/index.md deleted file mode 100644 index af456f47..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/index.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: "Genome assembly" -layout: assembly -params: - assembly_fields: - description: - - key: extra_1 - label: Additional field - - key: extra_2 - label: Another Additional field ---- - -### Methods diff --git a/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml b/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml deleted file mode 100644 index 0b6aa3d3..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/assembly/stats.yaml +++ /dev/null @@ -1,24 +0,0 @@ -assembly: - - "Assembly length (Mbp)": [EDIT] - - "GC %": [EDIT] - - "Contig #": [EDIT] - - "Contig N50 (Mbp)": [EDIT] - - "Contig L50": [EDIT] - - "Contig N90 (Mbp)": [EDIT] - - "Contig L90": [EDIT] - - "Scaffold #": [EDIT] - - "Scaffold N50 (Mbp)": [EDIT] - - "Scaffold L50": [EDIT] - - "Scaffold N90 (Mbp)": [EDIT] - - "Scaffold L90": [EDIT] - - "Scaffolds >= 10 kb": [EDIT] - - "BUSCO % [EDIT]": "[EDIT]" - -annotation: - - "Gene #": [EDIT] - - "Transcript #": [EDIT] - - "Avg exons per transcript": [EDIT] - - "Avg gene length (bp)": [EDIT] - - "Avg transcript length (bp)": [EDIT] - - "Avg exon length (bp)": [EDIT] - - "Avg intron length (bp)": [EDIT] diff --git a/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json b/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json deleted file mode 100644 index 69d763d7..00000000 --- a/hugo/content/halloween/jacobus_lanternibus/download/data_tracks.json +++ /dev/null @@ -1,268 +0,0 @@ -[ - { - "dataTrackName": "Genome", - "description": "Reference genome sequence", - "fileName": "CAMGYJ01.fasta.gz", - "links": [ - {"Download": "https://ftp.ebi.ac.uk/pub/databases/ena/wgs/public/cam/CAMGYJ01.fasta.gz"}, - {"Website": "https://www.ebi.ac.uk/ena/browser/view/GCA_946122785.1"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "GCA_946122785.1", - "principalInvestigator": "Tanja Slotte", - "principalInvestigatorAffiliation": "Stockholm University", - "firstDateOnPortal": "15 October 2024" - }, - { - "dataTrackName": "Protein-coding genes", - "description": "Functional annotation of protein-coding genes", - "links": [ - {"Download": "https://figshare.scilifelab.se/ndownloader/files/45076090"}, - {"Website": "https://doi.org/10.17044/scilifelab.24340378.v1"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "10.17044/scilifelab.24340378.v1", - "fileName": "ltenue_v1_genes.gff.zip", - "principalInvestigator": "Tanja Slotte", - "principalInvestigatorAffiliation": "Stockholm University", - "firstDateOnPortal": "15 October 2024" - }, - { - "dataTrackName": "Repeats", - "description": "Annotation of the repetitive regions", - "links": [ - {"Download": "https://figshare.scilifelab.se/ndownloader/files/48879751"}, - {"Website": "https://doi.org/10.17044/scilifelab.24343000.v2"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "10.17044/scilifelab.24340378.v1", - "fileName": "L_tenue_v1_rep.bed.gz", - "principalInvestigator": "Tanja Slotte", - "principalInvestigatorAffiliation": "Stockholm University", - "firstDateOnPortal": "15 October 2024" - }, - { - "dataTrackName": "Tajima's D, population 06", - "description": "Whole genome Tajima's D estimates for individuals of population 06 of L. tenue per 100 kb windows.", - "links": [ - {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006876"}, - {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "10.17044/scilifelab.26937304.v1", - "fileName": "Lten_pop06_TD.bed.zip", - "principalInvestigator": "Tanja Slotte", - "principalInvestigatorAffiliation": "Stockholm University", - "firstDateOnPortal": "15 October 2024" - }, - { - "dataTrackName": "Tajima's D, population 08", - "description": "Whole genome Tajima's D estimates for individuals of population 08 of L. tenue per 100 kb windows.", - "links": [ - {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006879"}, - {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "10.17044/scilifelab.26937304.v1", - "fileName": "Lten_pop08_TD.bed.zip", - "principalInvestigator": "Tanja Slotte", - "principalInvestigatorAffiliation": "Stockholm University", - "firstDateOnPortal": "15 October 2024" - }, - { - "dataTrackName": "Tajima's D, population 17", - "description": "Whole genome Tajima's D estimates for individuals of population 17 of L. tenue per 100 kb windows.", - "links": [ - {"Download": "https://figshare.scilifelab.se/ndownloader/files/49006882"}, - {"Website": "https://doi.org/10.17044/scilifelab.26937304.v1"}, - {"Article": "https://doi.org/10.1016/j.cub.2022.08.042"} - ], - "accessionOrDOI": "10.17044/scilifelab.26937304.v1", - "fileName": "Lten_pop17_TD.bed.zip", - "principalInvestigator": "Tanja Slotte", - 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zKJ-ytG@%zAQOnN7Gpv9TfRcS_mnDLNHh_C#iYqy*PeDpf#b=$9B!zC>D!Xb72>}!G OqKeuo`m>r(L;u-t5k(9D diff --git a/hugo/layouts/partials/halloween/GetGbifKey.html b/hugo/layouts/partials/species_bundle/GetGbifKey.html similarity index 80% rename from hugo/layouts/partials/halloween/GetGbifKey.html rename to hugo/layouts/partials/species_bundle/GetGbifKey.html index 3cafd5c5..eb3acab4 100644 --- a/hugo/layouts/partials/halloween/GetGbifKey.html +++ b/hugo/layouts/partials/species_bundle/GetGbifKey.html @@ -1,5 +1,5 @@ {{ $url := replace . " " "%20" | lower | printf "https://api.gbif.org/v1/species/match?name=%s" }} -{{ $data := partial "halloween/get-remote-data.html" $url }} +{{ $data := partial "species_bundle/get-remote-data.html" $url }} {{ $key := "" }} {{ with $data.usageKey | string }} {{ $key = . }} diff --git a/hugo/layouts/partials/halloween/GetTaxId.html b/hugo/layouts/partials/species_bundle/GetTaxId.html similarity index 81% rename from hugo/layouts/partials/halloween/GetTaxId.html rename to hugo/layouts/partials/species_bundle/GetTaxId.html index f3af2240..c72afd88 100644 --- a/hugo/layouts/partials/halloween/GetTaxId.html +++ b/hugo/layouts/partials/species_bundle/GetTaxId.html @@ -1,5 +1,5 @@ {{ $url := replace . " " "%20" | printf "https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/%s" }} -{{ $data := partial "halloween/get-remote-data.html" $url }} +{{ $data := partial "species_bundle/get-remote-data.html" $url }} {{ $taxId := "" }} {{ with index $data 0 "taxId" }} {{ $taxId = . }} diff --git a/hugo/layouts/partials/halloween/LineageConfig.html b/hugo/layouts/partials/species_bundle/LineageConfig.html similarity index 56% rename from hugo/layouts/partials/halloween/LineageConfig.html rename to hugo/layouts/partials/species_bundle/LineageConfig.html index cdf88d48..4e70e75b 100644 --- a/hugo/layouts/partials/halloween/LineageConfig.html +++ b/hugo/layouts/partials/species_bundle/LineageConfig.html @@ -1,7 +1,7 @@ {{- $taxId := . -}} {{- $url := printf "https://www.ebi.ac.uk/ena/browser/api/xml/%s" $taxId -}} -{{- with partial "halloween/get-remote-data.html" $url -}} - {{ . | partial "halloween/TaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} +{{- with partial "species_bundle/get-remote-data.html" $url -}} + {{ . | partial "species_bundle/TaxonomyRanks" | jsonify (dict "prefix" " " "indent" " ") }} {{- else -}} {{ warnf "Missing lineage information. Consider editing .Params.lineage" $taxId . }} {{- end -}} diff --git a/hugo/layouts/partials/halloween/TaxonomyRanks.html b/hugo/layouts/partials/species_bundle/TaxonomyRanks.html similarity index 100% rename from hugo/layouts/partials/halloween/TaxonomyRanks.html rename to hugo/layouts/partials/species_bundle/TaxonomyRanks.html diff --git a/hugo/layouts/partials/halloween/assembly_description.html b/hugo/layouts/partials/species_bundle/assembly_description.html similarity index 100% rename from hugo/layouts/partials/halloween/assembly_description.html rename to hugo/layouts/partials/species_bundle/assembly_description.html diff --git a/hugo/layouts/partials/halloween/assembly_stats.html b/hugo/layouts/partials/species_bundle/assembly_stats.html similarity index 100% rename from hugo/layouts/partials/halloween/assembly_stats.html rename to hugo/layouts/partials/species_bundle/assembly_stats.html diff --git a/hugo/layouts/partials/halloween/download_table.html b/hugo/layouts/partials/species_bundle/download_table.html similarity index 100% rename from hugo/layouts/partials/halloween/download_table.html rename to hugo/layouts/partials/species_bundle/download_table.html diff --git a/hugo/layouts/partials/halloween/get-remote-data.html b/hugo/layouts/partials/species_bundle/get-remote-data.html similarity index 100% rename from hugo/layouts/partials/halloween/get-remote-data.html rename to hugo/layouts/partials/species_bundle/get-remote-data.html diff --git a/hugo/layouts/partials/halloween/lineage.html b/hugo/layouts/partials/species_bundle/lineage.html similarity index 100% rename from hugo/layouts/partials/halloween/lineage.html rename to hugo/layouts/partials/species_bundle/lineage.html diff --git a/hugo/layouts/halloween/assembly.html b/hugo/layouts/species_bundle/assembly.html similarity index 91% rename from hugo/layouts/halloween/assembly.html rename to hugo/layouts/species_bundle/assembly.html index a83621ca..25610166 100644 --- a/hugo/layouts/halloween/assembly.html +++ b/hugo/layouts/species_bundle/assembly.html @@ -22,7 +22,7 @@

Description

{{ $context = (merge $context (dict "section" "description")) }} - {{ partial "halloween/assembly_description.html" $context }} + {{ partial "species_bundle/assembly_description.html" $context }}
@@ -55,14 +55,14 @@

Description

Assembly Statistics

{{ $context = merge $context (dict "section" "stats") }} - {{ partial "halloween/assembly_stats.html" $context }} + {{ partial "species_bundle/assembly_stats.html" $context }}

Annotation Statistics

{{ $context = merge $context (dict "section" "annotation") }} - {{ partial "halloween/assembly_stats.html" $context }} + {{ partial "species_bundle/assembly_stats.html" $context }}
diff --git a/hugo/layouts/halloween/baseof.html b/hugo/layouts/species_bundle/baseof.html similarity index 100% rename from hugo/layouts/halloween/baseof.html rename to hugo/layouts/species_bundle/baseof.html diff --git a/hugo/layouts/halloween/browser.html b/hugo/layouts/species_bundle/browser.html similarity index 100% rename from hugo/layouts/halloween/browser.html rename to hugo/layouts/species_bundle/browser.html diff --git a/hugo/layouts/halloween/species_download.html b/hugo/layouts/species_bundle/species_download.html similarity index 90% rename from hugo/layouts/halloween/species_download.html rename to hugo/layouts/species_bundle/species_download.html index 1136f81c..5c0ce612 100644 --- a/hugo/layouts/halloween/species_download.html +++ b/hugo/layouts/species_bundle/species_download.html @@ -56,11 +56,11 @@

Data availability

- {{ partial "halloween/download_table" (dict "tableType" "long" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} + {{ partial "species_bundle/download_table" (dict "tableType" "long" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}}
- {{ partial "halloween/download_table" (dict "tableType" "short" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}} + {{ partial "species_bundle/download_table" (dict "tableType" "short" "staticDirPath" $staticDirPath "tableData" $tableData "aliasFileURL" $aliasFileURL )}}
diff --git a/hugo/layouts/halloween/species_intro.html b/hugo/layouts/species_bundle/species_intro.html similarity index 98% rename from hugo/layouts/halloween/species_intro.html rename to hugo/layouts/species_bundle/species_intro.html index a77224b9..ff3bf9e2 100644 --- a/hugo/layouts/halloween/species_intro.html +++ b/hugo/layouts/species_bundle/species_intro.html @@ -63,7 +63,7 @@

Taxonomy

"lineage" . "taxonomy_ranks" (or $.Page.Params.taxonomy_ranks $.Site.Params.taxonomy_ranks) }} - {{ partial "halloween/lineage.html" $context }} + {{ partial "species_bundle/lineage.html" $context }} {{ else }} {{ warnidf "missing-taxonomy" "Missing taxonmomy lineage for %s" .Path }} {{ end }} From 25537e93529f33f329f6a91cdf3e79bd0ae3dbb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 16:40:14 +0100 Subject: [PATCH 48/59] Explicit content type --- hugo/archetypes/species/_index.md | 7 ++++--- hugo/archetypes/species/assembly/index.md | 4 +++- hugo/archetypes/species/download/index.md | 5 +++-- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/hugo/archetypes/species/_index.md b/hugo/archetypes/species/_index.md index 2793466e..97b31132 100644 --- a/hugo/archetypes/species/_index.md +++ b/hugo/archetypes/species/_index.md @@ -5,6 +5,10 @@ title: {{ $scientificName }} subtitle: lastmod: {{ .Date }} +type: species_bundle +layout: "species_intro" +weight: 1 + resources: - title: '{{ $scientificName }}' name: cover_image @@ -13,9 +17,6 @@ resources: attribution: CC-BY-SA link: "https://placehold.co/600x400/png" -layout: "species_bundle/species_intro" -weight: 1 - {{ $taxId := partial "species_bundle/GetTaxId" $scientificName }} lineage: {{ partial "species_bundle/LineageConfig" $taxId }} # Use this setting to override the default taxonomy ranks to display. diff --git a/hugo/archetypes/species/assembly/index.md b/hugo/archetypes/species/assembly/index.md index b53f4aef..cd1d1951 100644 --- a/hugo/archetypes/species/assembly/index.md +++ b/hugo/archetypes/species/assembly/index.md @@ -1,6 +1,8 @@ --- title: "Genome assembly" -layout: "species_bundle/assembly" +type: species_bundle +layout: "assembly" +lastmod: {{ .Date }} --- ### Methods diff --git a/hugo/archetypes/species/download/index.md b/hugo/archetypes/species/download/index.md index 1c41de67..fcbd11d0 100644 --- a/hugo/archetypes/species/download/index.md +++ b/hugo/archetypes/species/download/index.md @@ -1,6 +1,7 @@ --- title: "Download" -layout: "species_bundle/species_download" -url: "jacobus_lanternibus/download" +type: species_bundle +layout: "species_download" weight: 3 +lastmod: {{ .Date }} --- From c65dc670b772c9280886042244ed16c671e859d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 16:40:32 +0100 Subject: [PATCH 49/59] Manage URL in site configuration --- hugo/config/_default/hugo.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/hugo/config/_default/hugo.yaml b/hugo/config/_default/hugo.yaml index b43718a4..0902c90b 100644 --- a/hugo/config/_default/hugo.yaml +++ b/hugo/config/_default/hugo.yaml @@ -12,6 +12,12 @@ markup: endLevel: 4 ordered: false +permalinks: + section: + species: /:sections[1:] + page: + species: /:sections[1:]/:slug + menus: main: - name: Home From 0fcaf2b57113ae5e1b62a75f062fe20aae5f639f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Wed, 20 Nov 2024 16:46:33 +0100 Subject: [PATCH 50/59] Bona fide pumpkin example --- hugo/content/species/cucurbita_pepo/_index.md | 94 ++++++++++++++++++ .../cucurbita_pepo/assembly/assembly.yaml | 29 ++++++ .../cucurbita_pepo/assembly/contrib.md | 14 +++ .../species/cucurbita_pepo/assembly/index.md | 8 ++ .../cucurbita_pepo/download/data_tracks.json | 16 +++ .../species/cucurbita_pepo/download/index.md | 7 ++ .../cucurbita_pepo/lineage.default.yaml | 35 +++++++ hugo/content/species/cucurbita_pepo/pepo.jpg | Bin 0 -> 80329 bytes 8 files changed, 203 insertions(+) create mode 100644 hugo/content/species/cucurbita_pepo/_index.md create mode 100644 hugo/content/species/cucurbita_pepo/assembly/assembly.yaml create mode 100644 hugo/content/species/cucurbita_pepo/assembly/contrib.md create mode 100644 hugo/content/species/cucurbita_pepo/assembly/index.md create mode 100644 hugo/content/species/cucurbita_pepo/download/data_tracks.json create mode 100644 hugo/content/species/cucurbita_pepo/download/index.md create mode 100644 hugo/content/species/cucurbita_pepo/lineage.default.yaml create mode 100644 hugo/content/species/cucurbita_pepo/pepo.jpg diff --git a/hugo/content/species/cucurbita_pepo/_index.md b/hugo/content/species/cucurbita_pepo/_index.md new file mode 100644 index 00000000..36b4b57a --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/_index.md @@ -0,0 +1,94 @@ +--- +date: 2024-11-20T16:23:21+01:00 +title: Cucurbita pepo +subtitle: +lastmod: 2024-11-20T16:23:21+01:00 +draft: true +type: species_bundle +layout: "species_intro" +weight: 1 + +resources: +- title: 'Cucurbita pepo' + name: cover_image + src: "pepo.jpg" + params: + attribution: CC-BY-SA + link: "https://placehold.co/600x400/png" + + +lineage: { + "clade": { + "scientificName": "Embryophyta", + "taxId": "3193" + }, + "class": { + "scientificName": "Magnoliopsida", + "taxId": "3398" + }, + "family": { + "scientificName": "Cucurbitaceae", + "taxId": "3650" + }, + "genus": { + "scientificName": "Cucurbita", + "taxId": "3660" + }, + "kingdom": { + "scientificName": "Viridiplantae", + "taxId": "33090" + }, + "order": { + "scientificName": "Cucurbitales", + "taxId": "71239" + }, + "phylum": { + "scientificName": "Streptophyta", + "taxId": "35493" + }, + "species": { + "scientificName": "Cucurbita pepo", + "taxId": "3663" + }, + "subphylum": { + "scientificName": "Streptophytina", + "taxId": "131221" + }, + "superkingdom": { + "scientificName": "Eukaryota", + "taxId": "2759" + }, + "tribe": { + "scientificName": "Cucurbiteae", + "taxId": "1003878" + } + } +# Use this setting to override the default taxonomy ranks to display. +# See config/_default/params.yaml for the syntax to use. +taxonomy_ranks: +params: + banner_title: "Species overview" + goat_webpage: 'https://goat.genomehubs.org/record?recordId=3663&result=taxon&taxonomy=ncbi' + + # Map + gbif_taxon_id: 2874508 + latitude: 0 + longitude: 0 + initialZoom: 1 + + # Optional + iucn_category: + iucn_link: + swe_red_list: + swe_red_list_link: +--- + +### Description + +#### Genome reference + +#### References + +#### Changelog + +- Nov 20, 2024 - Species first published on the Portal diff --git a/hugo/content/species/cucurbita_pepo/assembly/assembly.yaml b/hugo/content/species/cucurbita_pepo/assembly/assembly.yaml new file mode 100644 index 00000000..c438d3e1 --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/assembly/assembly.yaml @@ -0,0 +1,29 @@ +description: + name: + type: + level: + repr: + accession: +stats: + length: + gc: + contig: + contig_n50: + contig_l50: + contig_n90: + contig_l90: + scaffold: + scaffold_n50: + scaffold_l50: + scaffold_n90: + scaffold_l90: + scaffold_gt_10: + busco: +annotation: + gene_cnt: + transcript_cnt: + exons_avg: + gene_length_avg: + transcript_length_avg: + exon_length_avg: + intron_length_avg: diff --git a/hugo/content/species/cucurbita_pepo/assembly/contrib.md b/hugo/content/species/cucurbita_pepo/assembly/contrib.md new file mode 100644 index 00000000..97e53c71 --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/assembly/contrib.md @@ -0,0 +1,14 @@ +--- +build: + list: never + publishResources: false + render: never +--- + +### Contributor(s) + +### Publication(s) + +### Funding + +### Acknowledgements diff --git a/hugo/content/species/cucurbita_pepo/assembly/index.md b/hugo/content/species/cucurbita_pepo/assembly/index.md new file mode 100644 index 00000000..730cbbf6 --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/assembly/index.md @@ -0,0 +1,8 @@ +--- +title: "Genome assembly" +type: species_bundle +layout: "assembly" +lastmod: 2024-11-20T16:23:21+01:00 +--- + +### Methods diff --git a/hugo/content/species/cucurbita_pepo/download/data_tracks.json b/hugo/content/species/cucurbita_pepo/download/data_tracks.json new file mode 100644 index 00000000..1ba0765d --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/download/data_tracks.json @@ -0,0 +1,16 @@ +[ + { + "dataTrackName": "Genome", + "description": "Reference genome sequence", + "fileName": "placeholder.fasta.gz", + "links": [ + {"Download": "#"}, + {"Website": "#"}, + {"Article": "#"} + ], + "accessionOrDOI": "GCA_1234", + "principalInvestigator": "Someone", + "principalInvestigatorAffiliation": "Some university", + "firstDateOnPortal": "15 October 2024" + } +] diff --git a/hugo/content/species/cucurbita_pepo/download/index.md b/hugo/content/species/cucurbita_pepo/download/index.md new file mode 100644 index 00000000..1a68a790 --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/download/index.md @@ -0,0 +1,7 @@ +--- +title: "Download" +type: species_bundle +layout: "species_download" +weight: 3 +lastmod: 2024-11-20T16:23:21+01:00 +--- diff --git a/hugo/content/species/cucurbita_pepo/lineage.default.yaml b/hugo/content/species/cucurbita_pepo/lineage.default.yaml new file mode 100644 index 00000000..e70836a1 --- /dev/null +++ b/hugo/content/species/cucurbita_pepo/lineage.default.yaml @@ -0,0 +1,35 @@ +# Example lineage configuration. +# This format is expeced by the .Params.lineage front matter key in `_index.md` +clade: + scientificName: Embryophyta + taxId: "3193" +class: + scientificName: Magnoliopsida + taxId: "3398" +family: + scientificName: Cucurbitaceae + taxId: "3650" +genus: + scientificName: Cucurbita + taxId: "3660" +kingdom: + scientificName: Viridiplantae + taxId: "33090" +order: + scientificName: Cucurbitales + taxId: "71239" +phylum: + scientificName: Streptophyta + taxId: "35493" +species: + scientificName: Cucurbita pepo + taxId: "3663" +subphylum: + scientificName: Streptophytina + taxId: "131221" +superkingdom: + scientificName: Eukaryota + taxId: "2759" +tribe: + scientificName: Cucurbiteae + taxId: "1003878" diff --git a/hugo/content/species/cucurbita_pepo/pepo.jpg b/hugo/content/species/cucurbita_pepo/pepo.jpg new file mode 100644 index 0000000000000000000000000000000000000000..a6fef634dce3426b6f5f0f1dea2e83cd48034fb3 GIT binary patch literal 80329 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zQ&?n-0g6)CK9qsCbNuPpR}|n6dO!#rY1qawOP=4Y18h(@8K4a3o|M)EkC%gVfDBQLQWKt(a(@joeNsnL3kCl3JMsiLl0393dZy@Azj?{wTw;93aln{9| z0uOF!gn)bIfsX6I#Wy=?J^C7HZ*f3ea5*@jj+B5?v)Y*Y3I|G4$i^v(a85c>?>ICu zj^iJNFt;2EL&zIxI&x?Wj~M{cKetK;N)Apr7^SelWN}NJnm}_w#xdTcWAZBAmo~}3 z=nYZb#X2cA$gSvUtr;_1(XrN+;~>*n%|#rl(E>1dq<0nAj}}@A&IqVnk6K22uN4b8 z0;v)tha?~6QM810 Date: Thu, 21 Nov 2024 11:07:30 +0100 Subject: [PATCH 51/59] Cascade draft status --- hugo/archetypes/species/_index.md | 4 ++++ hugo/content/species/cucurbita_pepo/_index.md | 3 +++ 2 files changed, 7 insertions(+) diff --git a/hugo/archetypes/species/_index.md b/hugo/archetypes/species/_index.md index 97b31132..10bdc6dd 100644 --- a/hugo/archetypes/species/_index.md +++ b/hugo/archetypes/species/_index.md @@ -5,6 +5,10 @@ title: {{ $scientificName }} subtitle: lastmod: {{ .Date }} +draft: true +cascade: + params: + draft: true type: species_bundle layout: "species_intro" weight: 1 diff --git a/hugo/content/species/cucurbita_pepo/_index.md b/hugo/content/species/cucurbita_pepo/_index.md index 36b4b57a..b60409c1 100644 --- a/hugo/content/species/cucurbita_pepo/_index.md +++ b/hugo/content/species/cucurbita_pepo/_index.md @@ -4,6 +4,9 @@ title: Cucurbita pepo subtitle: lastmod: 2024-11-20T16:23:21+01:00 draft: true +cascade: + params: + draft: true type: species_bundle layout: "species_intro" weight: 1 From fd1fe9ee5ddf67664530cc23be6f90a40d8db773 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 11:11:30 +0100 Subject: [PATCH 52/59] Rename layouts --- hugo/archetypes/species/_index.md | 2 +- hugo/archetypes/species/assembly/index.md | 2 +- hugo/archetypes/species/download/index.md | 2 +- hugo/content/species/cucurbita_pepo/_index.md | 2 +- hugo/content/species/cucurbita_pepo/assembly/index.md | 4 ++-- hugo/content/species/cucurbita_pepo/download/index.md | 4 ++-- .../species_bundle/{species_download.html => download.html} | 0 .../layouts/species_bundle/{species_intro.html => intro.html} | 0 8 files changed, 8 insertions(+), 8 deletions(-) rename hugo/layouts/species_bundle/{species_download.html => download.html} (100%) rename hugo/layouts/species_bundle/{species_intro.html => intro.html} (100%) diff --git a/hugo/archetypes/species/_index.md b/hugo/archetypes/species/_index.md index 10bdc6dd..473e3eaa 100644 --- a/hugo/archetypes/species/_index.md +++ b/hugo/archetypes/species/_index.md @@ -10,7 +10,7 @@ cascade: params: draft: true type: species_bundle -layout: "species_intro" +layout: intro weight: 1 resources: diff --git a/hugo/archetypes/species/assembly/index.md b/hugo/archetypes/species/assembly/index.md index cd1d1951..1531b6b6 100644 --- a/hugo/archetypes/species/assembly/index.md +++ b/hugo/archetypes/species/assembly/index.md @@ -1,7 +1,7 @@ --- title: "Genome assembly" type: species_bundle -layout: "assembly" +layout: assembly lastmod: {{ .Date }} --- diff --git a/hugo/archetypes/species/download/index.md b/hugo/archetypes/species/download/index.md index fcbd11d0..d7df21ce 100644 --- a/hugo/archetypes/species/download/index.md +++ b/hugo/archetypes/species/download/index.md @@ -1,7 +1,7 @@ --- title: "Download" type: species_bundle -layout: "species_download" +layout: download weight: 3 lastmod: {{ .Date }} --- diff --git a/hugo/content/species/cucurbita_pepo/_index.md b/hugo/content/species/cucurbita_pepo/_index.md index b60409c1..2f1ef7fd 100644 --- a/hugo/content/species/cucurbita_pepo/_index.md +++ b/hugo/content/species/cucurbita_pepo/_index.md @@ -8,7 +8,7 @@ cascade: params: draft: true type: species_bundle -layout: "species_intro" +layout: "intro" weight: 1 resources: diff --git a/hugo/content/species/cucurbita_pepo/assembly/index.md b/hugo/content/species/cucurbita_pepo/assembly/index.md index 730cbbf6..a786f30d 100644 --- a/hugo/content/species/cucurbita_pepo/assembly/index.md +++ b/hugo/content/species/cucurbita_pepo/assembly/index.md @@ -1,8 +1,8 @@ --- title: "Genome assembly" type: species_bundle -layout: "assembly" -lastmod: 2024-11-20T16:23:21+01:00 +layout: assembly +lastmod: 2024-11-21T10:58:49+01:00 --- ### Methods diff --git a/hugo/content/species/cucurbita_pepo/download/index.md b/hugo/content/species/cucurbita_pepo/download/index.md index 1a68a790..60449764 100644 --- a/hugo/content/species/cucurbita_pepo/download/index.md +++ b/hugo/content/species/cucurbita_pepo/download/index.md @@ -1,7 +1,7 @@ --- title: "Download" type: species_bundle -layout: "species_download" +layout: download weight: 3 -lastmod: 2024-11-20T16:23:21+01:00 +lastmod: 2024-11-21T10:58:49+01:00 --- diff --git a/hugo/layouts/species_bundle/species_download.html b/hugo/layouts/species_bundle/download.html similarity index 100% rename from hugo/layouts/species_bundle/species_download.html rename to hugo/layouts/species_bundle/download.html diff --git a/hugo/layouts/species_bundle/species_intro.html b/hugo/layouts/species_bundle/intro.html similarity index 100% rename from hugo/layouts/species_bundle/species_intro.html rename to hugo/layouts/species_bundle/intro.html From c298ee33e11ae75e8046d7ac44138c19687d8360 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 11:16:43 +0100 Subject: [PATCH 53/59] Remove unused layouts --- hugo/layouts/species_bundle/baseof.html | 100 ----------------------- hugo/layouts/species_bundle/browser.html | 60 -------------- 2 files changed, 160 deletions(-) delete mode 100644 hugo/layouts/species_bundle/baseof.html delete mode 100644 hugo/layouts/species_bundle/browser.html diff --git a/hugo/layouts/species_bundle/baseof.html b/hugo/layouts/species_bundle/baseof.html deleted file mode 100644 index cca47405..00000000 --- a/hugo/layouts/species_bundle/baseof.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - - - - {{ printf "%s | %s" (or .Params.banner_title .Title) .Site.Title }} - - {{ $description := partial "create_description.html" . }} - - - - - - - - - - - {{ template "_internal/opengraph.html" . }} - {{ template "_internal/twitter_cards.html" . }} - - - - - - - - {{ block "early_connections" . }} {{ end }} - - - - - - - - - - - - {{ $cssResource := resources.Get "css/styles.css" | resources.Minify | resources.Fingerprint }} - - - - - - - {{ block "script_includes" . }} {{ end }} - - - - - - {{- partial "navbar.html" . -}} - - {{ if eq .Kind "home" }} - {{- partial "hero.html" . -}} - {{ else }} - {{- partial "banner.html" . -}} - {{ end }} - - {{ $isGenomePage := eq .RelPermalink "/genome-browser/" }} - {{ if and (not $isGenomePage) (not .IsHome) }} - {{- partial "breadcrumbs.html" . -}} - {{ end }} - - {{- block "header" . }}{{- end }} -

- - {{ if $isGenomePage }} -
- {{ else }} -
- {{ end }} - - {{ if .Params.toc }} -
-
{{- partial "toc.html" . -}}
-
{{- block "main" . }}{{- end }}
-
- {{ else }} - {{- block "main" . }}{{- end }} - {{ end }} -
-
- - {{ if not $isGenomePage }} -
- {{- partial "footer.html" . -}} - {{ end }} - {{ if hugo.IsDevelopment }} - 
 {{ debug.Dump . }}
- {{ end }} - - diff --git a/hugo/layouts/species_bundle/browser.html b/hugo/layouts/species_bundle/browser.html deleted file mode 100644 index ae2abb84..00000000 --- a/hugo/layouts/species_bundle/browser.html +++ /dev/null @@ -1,60 +0,0 @@ -{{ define "main" }} - -
-
-
-
- - - -
- -{{ if hugo.IsDevelopment }} - -{{ end }} - - - - -{{ end }} From b5f300e5e3c1bd86596c8f196bbd5fa7e293c60b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 11:24:28 +0100 Subject: [PATCH 54/59] Revert add_new_species --- scripts/add_new_species.py | 69 +++++++++++++++++--------------------- 1 file changed, 30 insertions(+), 39 deletions(-) diff --git a/scripts/add_new_species.py b/scripts/add_new_species.py index 3989108d..bed46e2f 100644 --- a/scripts/add_new_species.py +++ b/scripts/add_new_species.py @@ -7,12 +7,8 @@ """ import argparse -import logging -import re import shutil -from collections import defaultdict from pathlib import Path -from string import Template import requests from get_taxonomy import EbiRestException, get_taxonomy @@ -77,47 +73,42 @@ def create_dirs(dir_name: str) -> tuple[Path, Path, Path]: return content_dir_path, data_dir_path, assets_dir_path -def slugify(name): - return re.sub(r"\s+", "_", name) - - -def get_template_context(species_name: str, tax_id: str | None = None) -> dict: - ctxt = defaultdict( - lambda: "[EDIT]", - species_name=species_name, - slug=slugify(species_name), - ) - try: - ctxt["gbif_taxon_key"] = get_gbif_taxon_key(species_name) - except (requests.HTTPError, KeyError): - logging.warn("Failed to get GBIF key for species: %s", species_name) - if tax_id: - ctxt["goat_link"] = make_goat_weblink(species_name=species_name, tax_id=tax_id) - return ctxt - - -def render(template_str, context): - return Template(template_str).substitute(context) - - -def load_template(template_name): - try: - return (TEMPLATE_DIR / template_name).read_text() - except IOError: - raise ValueError(f"Template not found: {template_name}") from None - - def add_content_files(species_name: str, content_dir_path: Path, tax_id: str) -> None: """ Add the species name to the template content files, then write them to disk. """ - ctxt = get_template_context(species_name, tax_id) + dir_name = species_name.replace(" ", "_").lower() for file_name in CONTENT_FILES: - template_str = load_template(file_name) - content = render(template_str, ctxt) - (out_file := content_dir_path / file_name).write_text(content) - logging.info("File created: %s", out_file.resolve()) + with open(TEMPLATE_DIR / file_name, "r") as file_in: + template = file_in.read() + + template = template.replace("SPECIES_NAME", species_name) + template = template.replace("SPECIES_FOLDER", dir_name) + + if file_name == INDEX_FILE: + try: + gbif_taxon_key = get_gbif_taxon_key(species_name=species_name) + template = template.replace("GBIF_TAXON_ID", gbif_taxon_key) + except (requests.exceptions.HTTPError, KeyError): + print( + f"""WARNING: Failed to get GBIF key for species: {args.species_name}. + Not to worry, + you can instead add it manually to the _index.md file in the species directory.""" + ) + template = template.replace("GBIF_TAXON_ID", "[EDIT]") + + if tax_id: + goat_link = make_goat_weblink(species_name=species_name, tax_id=tax_id) + template = template.replace("GOAT_WEBPAGE", goat_link) + else: + template = template.replace("GOAT_WEBPAGE", "[EDIT]") + + output_file_path = content_dir_path / file_name + + with open(output_file_path, "w") as file_out: + file_out.write(template) + print(f"File created: {output_file_path.resolve()}") def add_stats_file(data_dir_path: Path) -> None: From 46fc111deac504da30bf14e7ec3b973edeae733a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 11:38:35 +0100 Subject: [PATCH 55/59] Revert add_new_specie templates --- scripts/templates/_index.md | 12 ++++++------ scripts/templates/assembly.md | 6 +++--- scripts/templates/download.md | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/scripts/templates/_index.md b/scripts/templates/_index.md index 2e1a9092..6d828d96 100644 --- a/scripts/templates/_index.md +++ b/scripts/templates/_index.md @@ -14,13 +14,13 @@ img_attrib_link: "[EDIT] - if there is no hyperlink available for this file, the # unless you were warned by the add-new-species.py script. layout: "species_intro" banner_title: "Species overview" -url: "${slug}" +url: "SPECIES_FOLDER" weight: 1 -science_name: "${species_name}" -lineage_data_path: "${slug}/taxonomy" +science_name: "SPECIES_NAME" +lineage_data_path: "SPECIES_FOLDER/taxonomy" -gbif_taxon_id: "${gbif_taxon_id}" -goat_webpage: "${goat_webpage}" +gbif_taxon_id: "GBIF_TAXON_ID" +goat_webpage: "GOAT_WEBPAGE" # Optional params below, @@ -53,4 +53,4 @@ If you have used the pages for this species in the Genome Portal, please refer t #### Changelog -- [TODO - Add date] - Species first published on the Portal +- [TODO - Add date] - Species first published on the Portal \ No newline at end of file diff --git a/scripts/templates/assembly.md b/scripts/templates/assembly.md index 6fef44f9..6a61cc37 100644 --- a/scripts/templates/assembly.md +++ b/scripts/templates/assembly.md @@ -11,11 +11,11 @@ key_info: # unless you were warned by the add-new-species.py script. title: "Genome assembly" layout: "species_assembly" -url: "${slug}/assembly" +url: "SPECIES_FOLDER/assembly" weight: 2 -stats_data_path: "${slug}/species_stats" -lineage_data_path: "${slug}/taxonomy" +stats_data_path: "SPECIES_FOLDER/species_stats" +lineage_data_path: "SPECIES_FOLDER/taxonomy" --- ### Contributor(s) diff --git a/scripts/templates/download.md b/scripts/templates/download.md index 35f05707..fa952a34 100644 --- a/scripts/templates/download.md +++ b/scripts/templates/download.md @@ -3,6 +3,6 @@ alias_file_url: "[EDIT]" # The below parameters were generated automatically and do not need to be changed. title: "Download" layout: "species_download" -url: "${slug}/download" +url: "SPECIES_FOLDER/download" weight: 3 --- From 85c710b55e0b0e3f4782cbdf258e7e3e4bba8b45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 11:43:57 +0100 Subject: [PATCH 56/59] Revert out-of-topic changes --- hugo/content/species/_index.md | 4 ++-- hugo/layouts/partials/last_updated.html | 7 ++++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/hugo/content/species/_index.md b/hugo/content/species/_index.md index 7d50b2ff..ba412b29 100644 --- a/hugo/content/species/_index.md +++ b/hugo/content/species/_index.md @@ -1,7 +1,7 @@ --- # This prevents the species folder from generating a html file for the path [webaddress]/species/ -build: +_build: render: never list: never publishResources: false ---- +--- \ No newline at end of file diff --git a/hugo/layouts/partials/last_updated.html b/hugo/layouts/partials/last_updated.html index 674abf06..d74d42ed 100644 --- a/hugo/layouts/partials/last_updated.html +++ b/hugo/layouts/partials/last_updated.html @@ -1,5 +1,10 @@ +{{ $lastUpdated := .Params.last_updated }} +{{ if not (or .IsHome .IsSection) }} + {{ $lastUpdated = .Parent.Params.last_updated }} +{{ end }} +

- Page last updated: {{ .Lastmod | time.Format ":date_long"}} + Page last updated: {{ $lastUpdated }}

From aeb558ce3c6a403e846781c1a3ce1f06c6041f4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Thu, 21 Nov 2024 13:24:13 +0100 Subject: [PATCH 57/59] =?UTF-8?q?Genome=20portal=20kit=20=F0=9F=8E=81?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- hugo/{config/_default/hugo.yaml => config.yaml} | 8 +++----- hugo/config/production/hugo.yaml | 1 - hugo/themes/genome-portal-kit/README.md | 8 ++++++++ .../genome-portal-kit}/archetypes/species/_index.md | 0 .../archetypes/species/assembly/assembly.yaml | 0 .../archetypes/species/assembly/contrib.md | 0 .../archetypes/species/assembly/index.md | 0 .../archetypes/species/download/data_tracks.json | 0 .../archetypes/species/download/index.md | 0 .../archetypes/species/lineage.default.yaml | 0 .../archetypes/species/placeholder.png | Bin .../genome-portal-kit/config/_default/hugo.yaml | 3 +++ .../genome-portal-kit}/config/_default/params.yaml | 0 .../layouts/partials/species_bundle/GetGbifKey.html | 0 .../layouts/partials/species_bundle/GetTaxId.html | 0 .../partials/species_bundle/LineageConfig.html | 0 .../partials/species_bundle/TaxonomyRanks.html | 0 .../species_bundle/assembly_description.html | 0 .../partials/species_bundle/assembly_stats.html | 0 .../partials/species_bundle/download_table.html | 0 .../partials/species_bundle/get-remote-data.html | 0 .../layouts/partials/species_bundle/lineage.html | 0 .../layouts/species_bundle/assembly.html | 0 .../layouts/species_bundle/download.html | 0 .../layouts/species_bundle/intro.html | 0 25 files changed, 14 insertions(+), 6 deletions(-) rename hugo/{config/_default/hugo.yaml => config.yaml} (92%) delete mode 100644 hugo/config/production/hugo.yaml create mode 100644 hugo/themes/genome-portal-kit/README.md rename hugo/{ => themes/genome-portal-kit}/archetypes/species/_index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/assembly.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/contrib.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/assembly/index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/download/data_tracks.json (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/download/index.md (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/lineage.default.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/archetypes/species/placeholder.png (100%) create mode 100644 hugo/themes/genome-portal-kit/config/_default/hugo.yaml rename hugo/{ => themes/genome-portal-kit}/config/_default/params.yaml (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/GetGbifKey.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/GetTaxId.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/LineageConfig.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/TaxonomyRanks.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/assembly_description.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/assembly_stats.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/download_table.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/get-remote-data.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/partials/species_bundle/lineage.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/assembly.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/download.html (100%) rename hugo/{ => themes/genome-portal-kit}/layouts/species_bundle/intro.html (100%) diff --git a/hugo/config/_default/hugo.yaml b/hugo/config.yaml similarity index 92% rename from hugo/config/_default/hugo.yaml rename to hugo/config.yaml index 277d04c8..bf7af38b 100644 --- a/hugo/config/_default/hugo.yaml +++ b/hugo/config.yaml @@ -12,11 +12,9 @@ markup: endLevel: 4 ordered: false -permalinks: - section: - species: /:sections[1:] - page: - species: /:sections[1:]/:slug +module: + imports: + - path: genome-portal-kit menus: main: diff --git a/hugo/config/production/hugo.yaml b/hugo/config/production/hugo.yaml deleted file mode 100644 index 94144a66..00000000 --- a/hugo/config/production/hugo.yaml +++ /dev/null @@ -1 +0,0 @@ -panicOnWarning: true diff --git a/hugo/themes/genome-portal-kit/README.md b/hugo/themes/genome-portal-kit/README.md new file mode 100644 index 00000000..252a4636 --- /dev/null +++ b/hugo/themes/genome-portal-kit/README.md @@ -0,0 +1,8 @@ +# Genome portal +A Hugo theme for a genome portal embedding the JBrowse2 genome browser. + +## Features + +## Installation + +## Configuration diff --git a/hugo/archetypes/species/_index.md b/hugo/themes/genome-portal-kit/archetypes/species/_index.md similarity index 100% rename from hugo/archetypes/species/_index.md rename to hugo/themes/genome-portal-kit/archetypes/species/_index.md diff --git a/hugo/archetypes/species/assembly/assembly.yaml b/hugo/themes/genome-portal-kit/archetypes/species/assembly/assembly.yaml similarity index 100% rename from hugo/archetypes/species/assembly/assembly.yaml rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/assembly.yaml diff --git a/hugo/archetypes/species/assembly/contrib.md b/hugo/themes/genome-portal-kit/archetypes/species/assembly/contrib.md similarity index 100% rename from hugo/archetypes/species/assembly/contrib.md rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/contrib.md diff --git a/hugo/archetypes/species/assembly/index.md b/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md similarity index 100% rename from hugo/archetypes/species/assembly/index.md rename to hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md diff --git a/hugo/archetypes/species/download/data_tracks.json b/hugo/themes/genome-portal-kit/archetypes/species/download/data_tracks.json similarity index 100% rename from hugo/archetypes/species/download/data_tracks.json rename to hugo/themes/genome-portal-kit/archetypes/species/download/data_tracks.json diff --git a/hugo/archetypes/species/download/index.md b/hugo/themes/genome-portal-kit/archetypes/species/download/index.md similarity index 100% rename from hugo/archetypes/species/download/index.md rename to hugo/themes/genome-portal-kit/archetypes/species/download/index.md diff --git a/hugo/archetypes/species/lineage.default.yaml b/hugo/themes/genome-portal-kit/archetypes/species/lineage.default.yaml similarity index 100% rename from hugo/archetypes/species/lineage.default.yaml rename to hugo/themes/genome-portal-kit/archetypes/species/lineage.default.yaml diff --git a/hugo/archetypes/species/placeholder.png b/hugo/themes/genome-portal-kit/archetypes/species/placeholder.png similarity index 100% rename from hugo/archetypes/species/placeholder.png rename to hugo/themes/genome-portal-kit/archetypes/species/placeholder.png diff --git a/hugo/themes/genome-portal-kit/config/_default/hugo.yaml b/hugo/themes/genome-portal-kit/config/_default/hugo.yaml new file mode 100644 index 00000000..231d7231 --- /dev/null +++ b/hugo/themes/genome-portal-kit/config/_default/hugo.yaml @@ -0,0 +1,3 @@ +permalinks: + page: + species_bundle: /:sections[1:]/:slug diff --git a/hugo/config/_default/params.yaml b/hugo/themes/genome-portal-kit/config/_default/params.yaml similarity index 100% rename from hugo/config/_default/params.yaml rename to hugo/themes/genome-portal-kit/config/_default/params.yaml diff --git a/hugo/layouts/partials/species_bundle/GetGbifKey.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetGbifKey.html similarity index 100% rename from hugo/layouts/partials/species_bundle/GetGbifKey.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetGbifKey.html diff --git a/hugo/layouts/partials/species_bundle/GetTaxId.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetTaxId.html similarity index 100% rename from hugo/layouts/partials/species_bundle/GetTaxId.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/GetTaxId.html diff --git a/hugo/layouts/partials/species_bundle/LineageConfig.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/LineageConfig.html similarity index 100% rename from hugo/layouts/partials/species_bundle/LineageConfig.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/LineageConfig.html diff --git a/hugo/layouts/partials/species_bundle/TaxonomyRanks.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/TaxonomyRanks.html similarity index 100% rename from hugo/layouts/partials/species_bundle/TaxonomyRanks.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/TaxonomyRanks.html diff --git a/hugo/layouts/partials/species_bundle/assembly_description.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_description.html similarity index 100% rename from hugo/layouts/partials/species_bundle/assembly_description.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_description.html diff --git a/hugo/layouts/partials/species_bundle/assembly_stats.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_stats.html similarity index 100% rename from hugo/layouts/partials/species_bundle/assembly_stats.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/assembly_stats.html diff --git a/hugo/layouts/partials/species_bundle/download_table.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/download_table.html similarity index 100% rename from hugo/layouts/partials/species_bundle/download_table.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/download_table.html diff --git a/hugo/layouts/partials/species_bundle/get-remote-data.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/get-remote-data.html similarity index 100% rename from hugo/layouts/partials/species_bundle/get-remote-data.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/get-remote-data.html diff --git a/hugo/layouts/partials/species_bundle/lineage.html b/hugo/themes/genome-portal-kit/layouts/partials/species_bundle/lineage.html similarity index 100% rename from hugo/layouts/partials/species_bundle/lineage.html rename to hugo/themes/genome-portal-kit/layouts/partials/species_bundle/lineage.html diff --git a/hugo/layouts/species_bundle/assembly.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/assembly.html similarity index 100% rename from hugo/layouts/species_bundle/assembly.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/assembly.html diff --git a/hugo/layouts/species_bundle/download.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/download.html similarity index 100% rename from hugo/layouts/species_bundle/download.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/download.html diff --git a/hugo/layouts/species_bundle/intro.html b/hugo/themes/genome-portal-kit/layouts/species_bundle/intro.html similarity index 100% rename from hugo/layouts/species_bundle/intro.html rename to hugo/themes/genome-portal-kit/layouts/species_bundle/intro.html From 0c0c454bb60d998460c83a214dcf9621afd18113 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Fri, 29 Nov 2024 11:08:56 +0100 Subject: [PATCH 58/59] Restore assembly page weight Co-authored-by: Rory Crean <49672044+RMCrean@users.noreply.github.com> --- .../genome-portal-kit/archetypes/species/assembly/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md b/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md index 1531b6b6..7fd94418 100644 --- a/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md +++ b/hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md @@ -2,6 +2,7 @@ title: "Genome assembly" type: species_bundle layout: assembly +weight: 2 lastmod: {{ .Date }} --- From eccba118926da70f3f761fe6f8c445ae95a6ba95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Quentin=20=C3=85gren?= Date: Fri, 29 Nov 2024 11:40:42 +0100 Subject: [PATCH 59/59] Restore alias_file_url parameter --- .../genome-portal-kit/archetypes/species/download/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/hugo/themes/genome-portal-kit/archetypes/species/download/index.md b/hugo/themes/genome-portal-kit/archetypes/species/download/index.md index d7df21ce..ed79c888 100644 --- a/hugo/themes/genome-portal-kit/archetypes/species/download/index.md +++ b/hugo/themes/genome-portal-kit/archetypes/species/download/index.md @@ -4,4 +4,6 @@ type: species_bundle layout: download weight: 3 lastmod: {{ .Date }} +params: + alias_file_url: ---