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

wdduncan · 2021-03-05T02:07:25Z

update branch issue-291

…e form <number> meter

…oo", type:AttributeValue}

….yaml; still some work to do on this, but looking good so far

…ings

wdduncan · 2021-03-17T00:14:40Z

@cmungall I've generated new data based on the updated schema. The database validates.

cmungall · 2021-03-17T00:27:43Z

schema/nmdc.yaml

@@ -1333,6 +1165,15 @@ slots:
  sample_collection_minute:
    range: integer

+  salinity_category:


add a see_also to a mixs ticket requesting this

cmungall · 2021-03-17T00:27:59Z

schema/nmdc.yaml

+      Examples: halophile, halotolerant, hypersaline, huryhaline
+    range: string
+
+  soluble_iron_micromol:


cmungall · 2021-03-17T00:29:54Z

schema/mappings/gold-to-mixs.sssom.tsv

@@ -40,8 +43,8 @@ gold.vocab:soil_store_condition	soil_store_condition	skos:exactMatch	mixs:store_
 gold.vocab:soil_link_climate_info	soil_link_climate_info	skos:exactMatch	mixs:link_climate_info	link_climate_info	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
 gold.vocab:soil_annual_season_temp	soil_annual_season_temp	skos:closeMatch	mixs:annual_temp	annual_temp	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
 gold.vocab:soil_annual_season_temp	soil_annual_season_temp	skos:closeMatch	mixs:season_temp	season_temp	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
-gold.vocab:soil_annual_season_precpt	soil_annual_season_precpt 	skos:closeMatch	mixs:season_precpt	season_precpt	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
-gold.vocab:soil_annual_season_precpt	soil_annual_season_precpt 	skos:closeMatch	mixs:annual_precpt	annual_precpt	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
+gold.vocab:soil_annual_season_precpt	"soil_annual_season_precpt "	skos:closeMatch	mixs:season_precpt	season_precpt	SSSOMC:HumanCurated	gold.vocab	mixs	1	.


this is a mistake. Don't introduce spaces, and even if trailing spaces are required, don't quote in a TSV

Not sure how the quotes got in there. Thanks for catching this!

cmungall · 2021-03-17T00:30:59Z

schema/mappings/gold-to-mixs.sssom.tsv

@@ -40,8 +43,8 @@ gold.vocab:soil_store_condition	soil_store_condition	skos:exactMatch	mixs:store_
 gold.vocab:soil_link_climate_info	soil_link_climate_info	skos:exactMatch	mixs:link_climate_info	link_climate_info	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
 gold.vocab:soil_annual_season_temp	soil_annual_season_temp	skos:closeMatch	mixs:annual_temp	annual_temp	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
 gold.vocab:soil_annual_season_temp	soil_annual_season_temp	skos:closeMatch	mixs:season_temp	season_temp	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
-gold.vocab:soil_annual_season_precpt	soil_annual_season_precpt 	skos:closeMatch	mixs:season_precpt	season_precpt	SSSOMC:HumanCurated	gold.vocab	mixs	1	.
-gold.vocab:soil_annual_season_precpt	soil_annual_season_precpt 	skos:closeMatch	mixs:annual_precpt	annual_precpt	SSSOMC:HumanCurated	gold.vocab	mixs	1	.


why did you drop this one? it's a closeMatch so ok if not 1:1

I don't remember dropping these, but I must have done it ... I will add the mappings back. Right now the algorithm only looks exact matches (i.e., the gold fields are only mapped to exact matches).

cmungall · 2021-03-17T02:06:59Z

as it should but let's keep closeMappings in when we don't have an exact

…

On Tue, Mar 16, 2021 at 5:54 PM Bill Duncan ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In schema/mappings/gold-to-mixs.sssom.tsv <#297 (comment)> : > @@ -40,8 +43,8 @@ gold.vocab:soil_store_condition soil_store_condition skos:exactMatch mixs:store_ gold.vocab:soil_link_climate_info soil_link_climate_info skos:exactMatch mixs:link_climate_info link_climate_info SSSOMC:HumanCurated gold.vocab mixs 1 . gold.vocab:soil_annual_season_temp soil_annual_season_temp skos:closeMatch mixs:annual_temp annual_temp SSSOMC:HumanCurated gold.vocab mixs 1 . gold.vocab:soil_annual_season_temp soil_annual_season_temp skos:closeMatch mixs:season_temp season_temp SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_precpt soil_annual_season_precpt skos:closeMatch mixs:season_precpt season_precpt SSSOMC:HumanCurated gold.vocab mixs 1 . -gold.vocab:soil_annual_season_precpt soil_annual_season_precpt skos:closeMatch mixs:annual_precpt annual_precpt SSSOMC:HumanCurated gold.vocab mixs 1 . I don't remember dropping these, but I must have done it ... I will add the mappings back. Right now the algorithm only looks exact matches (i.e., the gold fields are only mapped to exact matches). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#297 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMONXX45NO2E5XRHVSCTTD74WHANCNFSM4YULNC7Q> .

wdduncan and others added 30 commits March 4, 2021 21:03

Merge pull request #296 from microbiomedata/master

0c58d2c

update branch issue-291

lint code using black

60dab90

test use of constant value for depth and update insturctions

bdfa168

add code for tranform constant values into json (e.g., depth is of th…

34cb864

…e form <number> meter

fix bugs

576a43e

udating spec

4c8452a

remove type information from property values; e.g. {has_raw_value: "f…

72d305b

…oo", type:AttributeValue}

reorder biosample slots

fd4768d

configure class to use pickled data; allows for faster loading

f1a0583

delete remove_key_attributes and add_attriubtes

a6bccf9

fix "adn" typo ... was driving me crazy

ce0a832

add functionality to specify transform founctions in nmdc_data_source…

d0e28c2

….yaml; still some work to do on this, but looking good so far

remove optional uriorcurie slot from attribute value

a9edc7c

add functionality to specify a pre-transform opertation

7f3df00

add mapping for growth_temperature

3014642

add samp_vol_we_dna_ext mapping

69788cd

add sampling_strategy to mapping

e1f1715

add salinity category field

d72cd73

remove slot usage definitions for mixs slots

b6be262

updating data source specs with new mapped fields

669f7ed

upate schema yaml

9c5cc7a

upate schema yaml

a87df93

fix typo in omics processing

d134ca9

add print statement for progress indicator

25f92c0

upate schema yaml

b3bb575

replace MIxS with mixs; the case mismatch was producing a lot of warn…

b3c1d5f

…ings

fix typo

457bae3

change range of omics type to string

c827de3

fix typo

a57cb07

add new data source specificatons

a546c56

wdduncan added 4 commits March 16, 2021 20:09

update execute script

7b0cf9c

add new generated examples (passes make test)

f775328

add new data nmdc database based schema (passes validation)

79bc978

add new generated artifacts

bf2f396

wdduncan requested a review from cmungall March 17, 2021 00:13

wdduncan marked this pull request as ready for review March 17, 2021 00:15

cmungall reviewed Mar 17, 2021

View reviewed changes

schema/nmdc.yaml

Examples: halophile, halotolerant, hypersaline, huryhaline

range: string

soluble_iron_micromol:

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cmungall Mar 17, 2021

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ditto

cmungall suggested changes Mar 17, 2021

View reviewed changes

remove quotes from soil_annual_season_precpt

a4f0e2c

cmungall approved these changes Mar 17, 2021

View reviewed changes

cmungall merged commit 207758b into master Mar 17, 2021

wdduncan mentioned this pull request Mar 17, 2021

revert simplification of sample slot values #291

Closed

turbomam mentioned this pull request Aug 30, 2023

URLs/links to check microbiomedata/nmdc-schema#1093

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eecavanna mentioned this pull request Sep 8, 2023

GitHub Actions: check-links job is failing microbiomedata/NMDC_documentation#25

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eecavanna mentioned this pull request Dec 9, 2023

Identify all broken hyperlinks in NMDC Schema documentation microbiomedata/nmdc-schema#1465

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Markdown docs contain broken links microbiomedata/nmdc-schema#1825

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

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

wdduncan commented Mar 5, 2021

wdduncan commented Mar 17, 2021

cmungall Mar 17, 2021

wdduncan Mar 17, 2021

cmungall Mar 17, 2021

cmungall Mar 17, 2021

wdduncan Mar 17, 2021

cmungall Mar 17, 2021

wdduncan Mar 17, 2021

cmungall commented Mar 17, 2021 via email

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

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

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wdduncan commented Mar 5, 2021

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cmungall commented Mar 17, 2021 via email