Code

Feature/metagenomics exchange#325

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mberacochea merged 36 commits intodevelopEBI-Metagenomics/emgapi:developfrom feature/metagenomics_exchangeEBI-Metagenomics/emgapi:feature/metagenomics_exchangeCopy head branch name to clipboardFeb 8, 2024

+859-29

Commits

Commits on Jan 29, 2024

• adds incremental ebi search dumping for analysisjobs

  mberacochea

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  0a8a761

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• integrates indexable sample data into analyses ebi search dump

  mberacochea

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• adds ebi search dump for studies/projects (plus some tweaks to analyses)

  mberacochea

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• resolve migration merge conflicts

  

  SandyRogers

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  mberacochea

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• adds support for chunking of analysis-runs ebi search dump

  mberacochea

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• bugfixes on analysis-run dumper

  mberacochea

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• Add metagenomics exchange support

  

  KateSakharova

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  mberacochea

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• Added 2 tests for ME, population script WIP

  mberacochea

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• Move metagenomic exchange commands to separate Class. Tests fail in POST request

  

  KateSakharova

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  mberacochea

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• My revised version:

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  mberacochea

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• Modified ME dj function to add new ME records, fixed tests for ME and api

  

  KateSakharova

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  mberacochea

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• Move test for mock API to test_mgx_api.py

  

  KateSakharova

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  mberacochea

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• Add settings

  

  KateSakharova

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  mberacochea

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• change models and add patch and delete to ME

  mberacochea

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• Add delete and patch commands with tests to ME API

  

  KateSakharova

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  mberacochea

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• add population scripts and tests for dry-run

  mberacochea

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• add population scripts and tests for dry-run

  

  KateSakharova

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  mberacochea

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• change api adress

  

  KateSakharova

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  mberacochea

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• change api adress

  

  KateSakharova

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  mberacochea

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• WIP

  

  KateSakharova

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  mberacochea

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• Minor refactor of the MGX indexation process WIP

  mberacochea

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• This is still a WIP - MGX

  mberacochea

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• Fixed the migrations for EBI Search and MGX.

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  mberacochea

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• Fix some ME tests

  KateSakharova

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• WIP - migration tidy up

  mberacochea

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• Merge branch 'feature/metagenomics_exchange' of github.com:EBI-Metagenomics/emgapi into feature/metagenomics_exchange

  mberacochea

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• Adjust field names to new convention (last_ebi_search_indexed)

  mberacochea

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Commits on Jan 30, 2024

• WIP testing

  KateSakharova

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Commits on Jan 31, 2024

• Tests for populate ME

  KateSakharova

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• rm dev from tests and leave only DEV API

  KateSakharova

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• fix pipeline mock

  KateSakharova

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Commits on Feb 1, 2024

• fixes

  KateSakharova

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• add mock to patch test

  KateSakharova

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Commits on Feb 6, 2024

• some fixes after review

  KateSakharova

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Commits on Feb 7, 2024

• Rename EBI Seach last_indexed fields

  mberacochea

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• Add an extra migrate step to rename last_indexed -> last_ebi_search_indexed

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  mberacochea

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