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Standardize multiple examples #17

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merged 2 commits into from
Mar 14, 2023
Merged

Standardize multiple examples #17

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e7678b7
Ensure each example is a separate instance of `examples` slot; dedupl…
pkalita-lbl Mar 13, 2023
ec13911
Merge branch 'main' into issue-sheets-and-friends-42
pkalita-lbl Mar 14, 2023
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2 changes: 1 addition & 1 deletion schema_sheets/from_schema_sheets.lint_report.txt
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@@ -1,4 +1,4 @@
/Users/MAM/Documents/gitrepos/submission-schema/schema_sheets/yaml_out/from_schema_sheets.yaml
/Users/PAKalita/Work/submission-schema/schema_sheets/yaml_out/from_schema_sheets.yaml
warning Permissible value of Enum 'BioticRelationshipEnum' has name 'free living' (standard_naming)
warning Permissible value of Enum 'BioticRelationshipEnum' has name 'natural organic matter' (standard_naming)
warning Permissible value of Enum 'DnaSampleFormatEnum' has name '10 mM Tris-HCl' (standard_naming)
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10 changes: 5 additions & 5 deletions schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_slots.csv
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Expand Up @@ -24,9 +24,9 @@ dnase_rna placeholder Note DNAse treatment is required for all RNA samples. DNas
rna_cont_type Tube or plate (96-well) RNA container type 10 jgi_metatranscriptomics_section RnaContTypeEnum plate TRUE
rna_sample_format Solution in which the RNA sample has been suspended RNA sample format 12 jgi_metatranscriptomics_section RnaSampleFormatEnum Water TRUE
sample_type Type of sample being submitted This can vary from 'environmental package' if the sample is an extraction. sample type 2 emsl_section SampleTypeEnum water extracted soil TRUE
collection_date_inc Date the incubation was harvested/collected/ended. Only relevant for incubation samples. Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. incubation collection date 2 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only 2021-04-15, 2021-04 and 2021 are all acceptable. TRUE {date, arbitrary precision}
collection_time The time of sampling, either as an instance (single point) or interval. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter collection time, GMT 1 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33 or 13:33:55 TRUE {time, seconds optional}
collection_time_inc Time the incubation was harvested/collected/ended. Only relevant for incubation samples. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter incubation collection time, GMT 3 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33 or 13:33:55 TRUE {time, seconds optional}
collection_date_inc Date the incubation was harvested/collected/ended. Only relevant for incubation samples. Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. incubation collection date 2 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only 2021-04-15|2021-04|2021 TRUE {date, arbitrary precision}
collection_time The time of sampling, either as an instance (single point) or interval. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter collection time, GMT 1 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33|13:33:55 TRUE {time, seconds optional}
collection_time_inc Time the incubation was harvested/collected/ended. Only relevant for incubation samples. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter incubation collection time, GMT 3 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33|13:33:55 TRUE {time, seconds optional}
dh_section dh_section grouping slot
dna_absorb1 260/280 measurement of DNA sample purity Recommended value is between 1 and 3. DNA absorbance 260/280 7 jgi_metagenomics_section 2.02 TRUE {float}
dna_absorb2 260/230 measurement of DNA sample purity Recommended value is between 1 and 3. DNA absorbance 260/230 8 jgi_metagenomics_section 2.02 TRUE {float}
Expand Down Expand Up @@ -86,8 +86,8 @@ rna_volume placeholder Units must be in uL. Enter the numerical part only. Value
sample_id_section placeholder dh_section 1
sample_link A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample. This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) sample linkage 5 sample_id_section IGSN:DSJ0284 TRUE {text}:{text}
sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL sample shipped amount 3 emsl_section TRUE {float} {unit}
start_date_inc Date the incubation was started. Only relevant for incubation samples. Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. incubation start date 4 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only 2021-04-15, 2021-04 and 2021 are all acceptable. TRUE {date, arbitrary precision}
start_time_inc Time the incubation was started. Only relevant for incubation samples. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter incubation start time, GMT 5 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33 or 13:33:55 TRUE {time, seconds optional}
start_date_inc Date the incubation was started. Only relevant for incubation samples. Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. incubation start date 4 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only 2021-04-15|2021-04|2021 TRUE {date, arbitrary precision}
start_time_inc Time the incubation was started. Only relevant for incubation samples. Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter incubation start time, GMT 5 mixs_inspired_section MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only 13:33|13:33:55 TRUE {time, seconds optional}
technical_reps If sending multiple technical replicates of the same sample, indicate how many replicates are being sent number technical replicate 5 emsl_section TRUE {integer}
type required by AttributeValue
dna_cont_well placeholder Required when 'plate' is selected for container type. Corner wells must be blank. For partial plates, fill by columns. Leave blank if the sample will be shipped in a tube. DNA well number 11 jgi_metagenomics_section B2 TRUE {96 well plate pos}
17 changes: 12 additions & 5 deletions schema_sheets/yaml_out/from_schema_sheets.yaml
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Expand Up @@ -1204,7 +1204,9 @@ slots:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://example.com/nmdc_submission_schema
rank: 2
string_serialization: '{date, arbitrary precision}'
Expand All @@ -1220,7 +1222,8 @@ slots:
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
rank: 1
string_serialization: '{time, seconds optional}'
Expand All @@ -1237,7 +1240,8 @@ slots:
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
rank: 3
string_serialization: '{time, seconds optional}'
Expand Down Expand Up @@ -2108,7 +2112,9 @@ slots:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://example.com/nmdc_submission_schema
rank: 4
string_serialization: '{date, arbitrary precision}'
Expand All @@ -2124,7 +2130,8 @@ slots:
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
rank: 5
string_serialization: '{time, seconds optional}'
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17 changes: 12 additions & 5 deletions schema_sheets/yaml_out/from_schema_sheets.yaml.raw
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Original file line number Diff line number Diff line change
Expand Up @@ -946,7 +946,9 @@ slots:
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://example.com/nmdc_submission_schema
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
Expand All @@ -960,7 +962,8 @@ slots:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
description: The time of sampling, either as an instance (single point) or interval.
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
Expand All @@ -976,7 +979,8 @@ slots:
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
Expand Down Expand Up @@ -1770,7 +1774,9 @@ slots:
are all acceptable.
description: Date the incubation was started. Only relevant for incubation samples.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://example.com/nmdc_submission_schema
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
Expand All @@ -1784,7 +1790,8 @@ slots:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
description: Time the incubation was started. Only relevant for incubation samples.
examples:
- value: 13:33 or 13:33:55
- value: '13:33'
- value: '13:33:55'
from_schema: https://example.com/nmdc_submission_schema
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
Expand Down
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