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Submission portal metadata ingest#118

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Commits

Commits on Dec 15, 2022

• retrieve all fields from GOLD API

  sujaypatil96

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  955cc79

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• fix tests related to gold ingest pipeline

  sujaypatil96

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Commits on Dec 19, 2022

• Database output compatible with v7 of the schema

  sujaypatil96

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Commits on Dec 20, 2022

• simplify compute_project_set() signature

  sujaypatil96

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Commits on Dec 27, 2022

• collected_from slot populated with FieldResearchSite

  sujaypatil96

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Commits on Jan 5, 2023

• do not populate slots with empty strings

  sujaypatil96

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  084b35d

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• upgrade to v7 of NMDC Schema

  sujaypatil96

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Commits on Jan 9, 2023

• biosample ids nmdc prefix and capture envo term labels

  sujaypatil96

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Commits on Jan 10, 2023

• update EMP500 JSON output from current GOLD NMDC pipeline

  sujaypatil96

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• use nmdc prefix for identifiers

  sujaypatil96

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Commits on Jan 26, 2023

• nmdc id minting service to generate biosample ids

  sujaypatil96

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• add .env example which needs to be in the project root

  sujaypatil96

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  4657e2a

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• enable pulling of sequencing project information

  sujaypatil96

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• updated JSON output for EMP500 study

  sujaypatil96

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• remove creds from .env file

  sujaypatil96

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Commits on Feb 2, 2023

• capture samp_name and make ids for FieldResearchSite

  sujaypatil96

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Commits on Feb 6, 2023

• pull in img_identifiers information from analysis project

  sujaypatil96

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Commits on Feb 7, 2023

• update pipeline to use latest version of nmdc-schema package

  sujaypatil96

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• pull in host_taxid information from GOLD

  sujaypatil96

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• EMP500 dataset output from transformation pipeline for test

  sujaypatil96

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• use GOLD: prefix instead of gold: prefix

  sujaypatil96

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Commits on Feb 8, 2023

• field research site ids processing and data portal enrichment

  sujaypatil96

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• remove print statements

  sujaypatil96

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Commits on Feb 9, 2023

• use correct GOLD API key to pull in host_taxid

  sujaypatil96

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Commits on Feb 14, 2023

• update .env example to point to prod api rather than dev api

  sujaypatil96

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• update EMP500 export in test

  sujaypatil96

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Commits on Feb 28, 2023

• account for multiple IMG identifiers

  sujaypatil96

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Commits on Mar 10, 2023

• Initial commit of submission portal code

  

  James Tessmer

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Commits on Mar 13, 2023

• Some changes to include API calls

  

  James Tessmer

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• Changing file structure a little bit to match current structure better

  

  James Tessmer

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Commits on Mar 24, 2023

• Removing some files and relocating others to where they should be.

  

  James Tessmer

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• added API interaction and refactored for new formatting

  

  James Tessmer

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Commits on Mar 30, 2023

• Addressing PR comments: date format, ENVO format, parsing quantities

  

  James Tessmer

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• Pushing for error checking. Water content issue.

  

  James Tessmer

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Commits on Mar 31, 2023

• Removing main.py, modified to be unit tests.

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  James Tessmer

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