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issue-291: Fix schema to match mixs.yaml #297

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Mar 17, 2021
Merged

issue-291: Fix schema to match mixs.yaml #297

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0c58d2c
Merge pull request #296 from microbiomedata/master
wdduncan Mar 5, 2021
60dab90
lint code using black
wdduncan Mar 5, 2021
bdfa168
test use of constant value for depth and update insturctions
wdduncan Mar 8, 2021
34cb864
add code for tranform constant values into json (e.g., depth is of th…
wdduncan Mar 8, 2021
576a43e
fix bugs
wdduncan Mar 9, 2021
4c8452a
udating spec
wdduncan Mar 10, 2021
72d305b
remove type information from property values; e.g. {has_raw_value: "f…
wdduncan Mar 10, 2021
fd4768d
reorder biosample slots
wdduncan Mar 11, 2021
f1a0583
configure class to use pickled data; allows for faster loading
wdduncan Mar 11, 2021
a6bccf9
delete remove_key_attributes and add_attriubtes
wdduncan Mar 11, 2021
ce0a832
fix "adn" typo ... was driving me crazy
wdduncan Mar 11, 2021
d0e28c2
add functionality to specify transform founctions in nmdc_data_source…
wdduncan Mar 11, 2021
a9edc7c
remove optional uriorcurie slot from attribute value
wdduncan Mar 12, 2021
7f3df00
add functionality to specify a pre-transform opertation
wdduncan Mar 13, 2021
3014642
add mapping for growth_temperature
wdduncan Mar 16, 2021
69788cd
add samp_vol_we_dna_ext mapping
wdduncan Mar 16, 2021
e1f1715
add sampling_strategy to mapping
wdduncan Mar 16, 2021
d72cd73
add salinity category field
wdduncan Mar 16, 2021
b6be262
remove slot usage definitions for mixs slots
wdduncan Mar 16, 2021
669f7ed
updating data source specs with new mapped fields
wdduncan Mar 16, 2021
9c5cc7a
upate schema yaml
wdduncan Mar 16, 2021
a87df93
upate schema yaml
wdduncan Mar 16, 2021
d134ca9
fix typo in omics processing
wdduncan Mar 16, 2021
25f92c0
add print statement for progress indicator
wdduncan Mar 16, 2021
b3bb575
upate schema yaml
wdduncan Mar 16, 2021
b3c1d5f
replace MIxS with mixs; the case mismatch was producing a lot of warn…
wdduncan Mar 16, 2021
457bae3
fix typo
wdduncan Mar 16, 2021
c827de3
change range of omics type to string
wdduncan Mar 16, 2021
a57cb07
fix typo
wdduncan Mar 17, 2021
a546c56
add new data source specificatons
wdduncan Mar 17, 2021
7b0cf9c
update execute script
wdduncan Mar 17, 2021
f775328
add new generated examples (passes make test)
wdduncan Mar 17, 2021
79bc978
add new data nmdc database based schema (passes validation)
wdduncan Mar 17, 2021
bf2f396
add new generated artifacts
wdduncan Mar 17, 2021
a4f0e2c
remove quotes from soil_annual_season_precpt
wdduncan Mar 17, 2021
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96 changes: 45 additions & 51 deletions examples/biosample_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,111 +4,105 @@
"id": "gold:Gb0101224",
"name": "Lithgow State Coal Mine Calcium nutrients (early)",
"description": "Bulk Aqueous phase filtered water",
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"type": "GeolocationValue",
"latitude": -33.460524,
"longitude": 150.168149
},
"geo_loc_name": "Lithgow",
"type": "nmdc:Biosample",
"env_broad_scale": {
"has_raw_value": "ENVO:00002030",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002030"
},
"env_local_scale": {
"has_raw_value": "ENVO:00002169",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002169"
},
"env_medium": {
"has_raw_value": "ENVO:00005792",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00005792"
},
"geo_loc_name": {
"has_raw_value": "Lithgow"
},
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"latitude": -33.460524,
"longitude": 150.168149
},
"ecosystem": "Environmental",
"ecosystem_category": "Aquatic",
"ecosystem_type": "Freshwater",
"ecosystem_subtype": "Groundwater",
"specific_ecosystem": "Coalbed water",
"type": "nmdc:Biosample",
"add_date": "28-JUL-14 12.00.00.000000000 AM",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"community": "microbial communities",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"habitat": "Coalbed water",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"sample_collection_site": "Lithgow State Coal Mine"
},
{
"id": "gold:Gb0101225",
"name": "Lithgow State Coal Mine Calcium nutrients Extra",
"description": "Bulk Aqueous phase filtered water",
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"type": "GeolocationValue",
"latitude": -33.460524,
"longitude": 150.168149
},
"geo_loc_name": "Lithgow",
"type": "nmdc:Biosample",
"env_broad_scale": {
"has_raw_value": "ENVO:00002030",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002030"
},
"env_local_scale": {
"has_raw_value": "ENVO:00002169",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002169"
},
"env_medium": {
"has_raw_value": "ENVO:00005792",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00005792"
},
"geo_loc_name": {
"has_raw_value": "Lithgow"
},
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"latitude": -33.460524,
"longitude": 150.168149
},
"ecosystem": "Environmental",
"ecosystem_category": "Aquatic",
"ecosystem_type": "Freshwater",
"ecosystem_subtype": "Groundwater",
"specific_ecosystem": "Coalbed water",
"type": "nmdc:Biosample",
"add_date": "28-JUL-14 12.00.00.000000000 AM",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"community": "microbial communities",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"habitat": "Coalbed water",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"sample_collection_site": "Lithgow State Coal Mine"
},
{
"id": "gold:Gb0101226",
"name": "Lithgow State Coal Mine Calcium nutrients",
"description": "Bulk Aqueous phase filtered water",
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"type": "GeolocationValue",
"latitude": -33.460524,
"longitude": 150.168149
},
"geo_loc_name": "Lithgow",
"type": "nmdc:Biosample",
"env_broad_scale": {
"has_raw_value": "ENVO:00002030",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002030"
},
"env_local_scale": {
"has_raw_value": "ENVO:00002169",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00002169"
},
"env_medium": {
"has_raw_value": "ENVO:00005792",
"type": "ControlledTermValue"
"has_raw_value": "ENVO:00005792"
},
"geo_loc_name": {
"has_raw_value": "Lithgow"
},
"lat_lon": {
"has_raw_value": "-33.460524 150.168149",
"latitude": -33.460524,
"longitude": 150.168149
},
"ecosystem": "Environmental",
"ecosystem_category": "Aquatic",
"ecosystem_type": "Freshwater",
"ecosystem_subtype": "Groundwater",
"specific_ecosystem": "Coalbed water",
"type": "nmdc:Biosample",
"add_date": "28-JUL-14 12.00.00.000000000 AM",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"community": "microbial communities",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"habitat": "Coalbed water",
"location": "from the Lithgow State Coal Mine, New South Wales, Australia",
"mod_date": "26-AUG-16 01.50.27.000000000 PM",
"ncbi_taxonomy_name": "coal metagenome",
"sample_collection_site": "Lithgow State Coal Mine"
}
]
Expand Down
24 changes: 15 additions & 9 deletions examples/emsl_project_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,15 @@
"has_output": [
"emsl:output_359123"
],
"omics_type": "Metabolomics",
"instrument_name": "Agilent_GC_MS_01",
"omics_type": {
"has_raw_value": "Metabolomics"
},
"part_of": [
"gold:Gs0110132"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Environmental Molecular Sciences Lab",
"instrument_name": "Agilent_GC_MS_01"
"type": "nmdc:OmicsProcessing"
},
{
"id": "emsl:359124",
Expand All @@ -22,13 +24,15 @@
"has_output": [
"emsl:output_359124"
],
"omics_type": "Metabolomics",
"instrument_name": "Agilent_GC_MS_01",
"omics_type": {
"has_raw_value": "Metabolomics"
},
"part_of": [
"gold:Gs0110132"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Environmental Molecular Sciences Lab",
"instrument_name": "Agilent_GC_MS_01"
"type": "nmdc:OmicsProcessing"
},
{
"id": "emsl:359129",
Expand All @@ -37,13 +41,15 @@
"has_output": [
"emsl:output_359129"
],
"omics_type": "Metabolomics",
"instrument_name": "Agilent_GC_MS_01",
"omics_type": {
"has_raw_value": "Metabolomics"
},
"part_of": [
"gold:Gs0110132"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Environmental Molecular Sciences Lab",
"instrument_name": "Agilent_GC_MS_01"
"type": "nmdc:OmicsProcessing"
}
]
}
36 changes: 21 additions & 15 deletions examples/gold_project_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -6,56 +6,62 @@
"has_input": [
"gold:Gb0108335"
],
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.13.12.927000000 PM",
"has_output": [
"jgi:551a20d30d878525404e90d5"
],
"omics_type": "Metagenome",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D",
"omics_type": {
"has_raw_value": "Metagenome"
},
"part_of": [
"gold:Gs0112340"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Joint Genome Institute",
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.13.12.927000000 PM",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D"
"type": "nmdc:OmicsProcessing"
},
{
"id": "gold:Gp0108340",
"name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M",
"has_input": [
"gold:Gb0108340"
],
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.10.59.590000000 PM",
"has_output": [
"jgi:551a20d50d878525404e90d7"
],
"omics_type": "Metagenome",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M",
"omics_type": {
"has_raw_value": "Metagenome"
},
"part_of": [
"gold:Gs0112340"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Joint Genome Institute",
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.10.59.590000000 PM",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M"
"type": "nmdc:OmicsProcessing"
},
{
"id": "gold:Gp0108341",
"name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S",
"has_input": [
"gold:Gb0108341"
],
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.09.46.171000000 PM",
"has_output": [
"jgi:551a20d90d878525404e90e1"
],
"omics_type": "Metagenome",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S",
"omics_type": {
"has_raw_value": "Metagenome"
},
"part_of": [
"gold:Gs0112340"
],
"type": "nmdc:OmicsProcessing",
"processing_institution": "Joint Genome Institute",
"add_date": "30-OCT-14 12.00.00.000000000 AM",
"mod_date": "22-MAY-20 06.09.46.171000000 PM",
"ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S"
"type": "nmdc:OmicsProcessing"
}
]
}
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