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Update GOLD NMDC ingest pipeline to ingest bioscales #113

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merged 28 commits into from
Mar 14, 2023
Merged

Update GOLD NMDC ingest pipeline to ingest bioscales #113

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955cc79
retrieve all fields from GOLD API
sujaypatil96 Dec 15, 2022
205403e
fix tests related to gold ingest pipeline
sujaypatil96 Dec 15, 2022
4771c40
Database output compatible with v7 of the schema
sujaypatil96 Dec 19, 2022
936a806
simplify compute_project_set() signature
sujaypatil96 Dec 20, 2022
0937ebb
collected_from slot populated with FieldResearchSite
sujaypatil96 Dec 27, 2022
084b35d
do not populate slots with empty strings
sujaypatil96 Jan 5, 2023
d033fd9
upgrade to v7 of NMDC Schema
sujaypatil96 Jan 5, 2023
5351936
biosample ids nmdc prefix and capture envo term labels
sujaypatil96 Jan 9, 2023
54eef6a
update EMP500 JSON output from current GOLD NMDC pipeline
sujaypatil96 Jan 10, 2023
797c01e
use nmdc prefix for identifiers
sujaypatil96 Jan 10, 2023
7efff85
nmdc id minting service to generate biosample ids
sujaypatil96 Jan 26, 2023
4657e2a
add .env example which needs to be in the project root
sujaypatil96 Jan 26, 2023
5cdcdcf
enable pulling of sequencing project information
sujaypatil96 Jan 26, 2023
0052df7
updated JSON output for EMP500 study
sujaypatil96 Jan 26, 2023
a695792
remove creds from .env file
sujaypatil96 Jan 26, 2023
605ebcc
capture samp_name and make ids for FieldResearchSite
sujaypatil96 Feb 2, 2023
f1f0678
pull in img_identifiers information from analysis project
sujaypatil96 Feb 6, 2023
1ff3256
update pipeline to use latest version of nmdc-schema package
sujaypatil96 Feb 7, 2023
223ee11
pull in host_taxid information from GOLD
sujaypatil96 Feb 7, 2023
f3363ed
EMP500 dataset output from transformation pipeline for test
sujaypatil96 Feb 7, 2023
c6d3700
use GOLD: prefix instead of gold: prefix
sujaypatil96 Feb 7, 2023
e6f8156
field research site ids processing and data portal enrichment
sujaypatil96 Feb 8, 2023
5274c7b
remove print statements
sujaypatil96 Feb 8, 2023
2d3227c
use correct GOLD API key to pull in host_taxid
sujaypatil96 Feb 9, 2023
a860805
update .env example to point to prod api rather than dev api
sujaypatil96 Feb 14, 2023
b13cf3d
update EMP500 export in test
sujaypatil96 Feb 14, 2023
e55db81
account for multiple IMG identifiers
sujaypatil96 Feb 28, 2023
0f34e06
Initial commit of submission portal code
Mar 10, 2023
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4 changes: 4 additions & 0 deletions .env.example
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
BASE_URL=https://api.microbiomedata.org
SITE_ID=
CLIENT_ID=
CLIENT_SECRET=
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