Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[For TEST and PROD] Welling/soft assay types start #398

Merged
merged 56 commits into from
Dec 18, 2023
Merged

[For TEST and PROD] Welling/soft assay types start #398

merged 56 commits into from
Dec 18, 2023

Commits on Sep 13, 2023

  1. Add the blueprint and API endpoints

    @jswelling
    jswelling committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    ddf851b View commit details
    Browse the repository at this point in the history

Commits on Sep 14, 2023

  1. WIP

    @jswelling
    jswelling committed Sep 14, 2023
    Configuration menu
    Copy the full SHA
    4496a22 View commit details
    Browse the repository at this point in the history

  2. Add rule-engine to requirements

    @jswelling
    jswelling committed Sep 14, 2023
    Configuration menu
    Copy the full SHA
    6237ba6 View commit details
    Browse the repository at this point in the history

  3. Working rule chain implementation

    @jswelling
    jswelling committed Sep 14, 2023
    Configuration menu
    Copy the full SHA
    6097a1c View commit details
    Browse the repository at this point in the history

Commits on Sep 16, 2023

  1. Connect rule chain logic to api.

    @jswelling
    jswelling committed Sep 16, 2023
    Configuration menu
    Copy the full SHA
    69bfd8c View commit details
    Browse the repository at this point in the history

Commits on Sep 17, 2023

  1. Get rule chain from URI in config

    @jswelling
    jswelling committed Sep 17, 2023
    Configuration menu
    Copy the full SHA
    7218ad8 View commit details
    Browse the repository at this point in the history

  2. Add 'reload' endpoint

    @jswelling
    jswelling committed Sep 17, 2023
    Configuration menu
    Copy the full SHA
    4e9c080 View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2023

  1. Interim rule tester

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    ca8136a View commit details
    Browse the repository at this point in the history

  2. rule chain mods so things default to null

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    23d0a62 View commit details
    Browse the repository at this point in the history

  3. Better exceptions, return {} on no match

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    27c4e73 View commit details
    Browse the repository at this point in the history

  4. Test a broader range of examples

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    d00f69d View commit details
    Browse the repository at this point in the history

  5. First draft rule generator

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    7cc272f View commit details
    Browse the repository at this point in the history

  6. Add some examples

    @jswelling
    jswelling committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    5e34a46 View commit details
    Browse the repository at this point in the history

Commits on Sep 26, 2023

  1. Pulled in copy of prototype rule chain

    @jswelling
    jswelling committed Sep 26, 2023
    Configuration menu
    Copy the full SHA
    1b017dc View commit details
    Browse the repository at this point in the history

Commits on Oct 13, 2023

  1. Some real examples, some DCWG metadata

    @jswelling
    jswelling committed Oct 13, 2023
    Configuration menu
    Copy the full SHA
    5d07619 View commit details
    Browse the repository at this point in the history

Commits on Oct 16, 2023

  1. Sync with the latest main branch

    @yuanzhou
    yuanzhou committed Oct 16, 2023
    Configuration menu
    Copy the full SHA
    87f0175 View commit details
    Browse the repository at this point in the history

Commits on Oct 20, 2023

  1. Add dir schema logic and rules

    @jswelling
    jswelling committed Oct 20, 2023
    Configuration menu
    Copy the full SHA
    ad4876d View commit details
    Browse the repository at this point in the history

  2. reload method becomes reload-assaytypes

    @jswelling
    jswelling committed Oct 20, 2023
    Configuration menu
    Copy the full SHA
    1f6bba5 View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2023

  1. Add rules for many DCWG assays

    @jswelling
    jswelling committed Nov 1, 2023
    Configuration menu
    Copy the full SHA
    a0f8f3f View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2023

  1. Add tbl_schema field to non-DCWG primary data

    @jswelling
    jswelling committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    a222ec3 View commit details
    Browse the repository at this point in the history

Commits on Nov 30, 2023

  1. Added visium examples

    @jswelling
    jswelling committed Nov 30, 2023
    Configuration menu
    Copy the full SHA
    9a82ab4 View commit details
    Browse the repository at this point in the history

  2. case insensitive metadata checking, string digits (e.g. version numbe… 

    …rs) converted to ints
    @gesinaphillips
    gesinaphillips committed Nov 30, 2023
    Configuration menu
    Copy the full SHA
    d3c5dbc View commit details
    Browse the repository at this point in the history

Commits on Dec 1, 2023

  1. Git fix and sync with main

    @yuanzhou
    yuanzhou committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    22b47ab View commit details
    Browse the repository at this point in the history

Commits on Dec 5, 2023

  1. Merge branch 'main' of https://github.com/hubmapconsortium/ingest-api … 

    …into welling/soft_assay_types_start
    @yuanzhou
    yuanzhou committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    f98d5fc View commit details
    Browse the repository at this point in the history

  2. updates to rules

    @gesinaphillips
    gesinaphillips committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    e14a873 View commit details
    Browse the repository at this point in the history

  3. Clean up simple DCWG and DCWG Histology

    @jswelling
    jswelling committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    34ee345 View commit details
    Browse the repository at this point in the history

  4. Overwrite some case-insensitive-matching code

    @jswelling
    jswelling committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    6a0b218 View commit details
    Browse the repository at this point in the history

  5. pprint no longer needed in __init__.py

    @jswelling
    jswelling committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    039660b View commit details
    Browse the repository at this point in the history

  6. Rebuild testing_rule_chain

    @jswelling
    jswelling committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    1c35f3f View commit details
    Browse the repository at this point in the history

  7. Working Visium no probes.

    @jswelling
    jswelling committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    d0068b6 View commit details
    Browse the repository at this point in the history

  8. fix to rnaseq (with probes), cleanup rule_description

    @gesinaphillips
    gesinaphillips committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    e4cdb98 View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2023

  1. added bulk ATACseq and RNAseq, updated field name rna_probe_panel to … 

    …oligo_probe_panel
    @gesinaphillips
    gesinaphillips committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    5001023 View commit details
    Browse the repository at this point in the history

  2. Added ATACseq rules. Restructured Bulk.

    @jswelling
    jswelling committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    8a0b979 View commit details
    Browse the repository at this point in the history

Commits on Dec 9, 2023

  1. Add multiome; other bugfixes

    @jswelling
    jswelling committed Dec 9, 2023
    Configuration menu
    Copy the full SHA
    9ccbf7b View commit details
    Browse the repository at this point in the history

  2. Fix some rule descriptions

    @jswelling
    jswelling committed Dec 9, 2023
    Configuration menu
    Copy the full SHA
    7d49198 View commit details
    Browse the repository at this point in the history

Commits on Dec 11, 2023

  1. General: Update to point to latest IVT commit

    Juan Puerto committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    2fa3b06 View commit details
    Browse the repository at this point in the history

Commits on Dec 12, 2023

  1. General: Update to include contains-pii and primary in value sets.

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    aa4c971 View commit details
    Browse the repository at this point in the history

  2. General: Update to include contains-pii and primary in value sets.

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    97cf9b3 View commit details
    Browse the repository at this point in the history

  3. General: Update to include contains-pii and primary in value sets.

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    ccb0bd4 View commit details
    Browse the repository at this point in the history

  4. General: Update must_contain to must-contain

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    ab66e13 View commit details
    Browse the repository at this point in the history

  5. General: Point IVT to the latest commit

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    6a81885 View commit details
    Browse the repository at this point in the history

  6. General: Set contains-pii to true for Visium

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    8658c8f View commit details
    Browse the repository at this point in the history

  7. General: Fix broken dir-schemas

    Juan Puerto committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    15c70ba View commit details
    Browse the repository at this point in the history

Commits on Dec 13, 2023

  1. General: Point to latest main

    Juan Puerto committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    c0b51f6 View commit details
    Browse the repository at this point in the history

Commits on Dec 14, 2023

  1. Patch around data_type array

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    0aa31e8 View commit details
    Browse the repository at this point in the history

  2. Further patch data_types array

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    4b24ac0 View commit details
    Browse the repository at this point in the history

  3. Further patch data_types array

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    3247f31 View commit details
    Browse the repository at this point in the history

  4. Add 'is_support' to vis-lifted dataset vitessce_hints

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    0aebb8a View commit details
    Browse the repository at this point in the history

  5. seqFISH_pyramid is not a primary dataset

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    cc5e41e View commit details
    Browse the repository at this point in the history

  6. regenerated with recent changes

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    9320f82 View commit details
    Browse the repository at this point in the history

  7. Add uuid for an unpublished dataset to tests

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    a7a6c6e View commit details
    Browse the repository at this point in the history

  8. Try to access entity-api with no token if token fails

    @jswelling
    jswelling committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    a7c89b8 View commit details
    Browse the repository at this point in the history

Commits on Dec 15, 2023

  1. changes to 10x multiome and snareseq to remove barcode and umi values… 

    …, change to 2 of 3 atacseq single nucleus rules to make umi values not applicable
    @gesinaphillips
    gesinaphillips committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    094d524 View commit details
    Browse the repository at this point in the history

Commits on Dec 18, 2023

  1. General: Check for auth header and set groups_toekn to blank if no au… 

    …th header
    Juan Puerto committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    a488f43 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'main' of github.com:hubmapconsortium/ingest-api into we… 

    …lling/soft_assay_types_start
    @gesinaphillips
    gesinaphillips committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    deae5c6 View commit details
    Browse the repository at this point in the history

  3. change empty string to None

    @gesinaphillips
    gesinaphillips committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    edc4916 View commit details
    Browse the repository at this point in the history