K8s config with stefans changes#17
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Anna-Rehm merged 56 commits intok8s_config_changefrom Mar 4, 2026
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…bs, but the later must also made known by the DB
…o file delivery method respectively
… to avoid lazy client from downloading whole BASE_DATA_DIR
…alsoDirs Tornado fetch file from central handler also dirs
…alsoDirs_debug Tornado fetch file from central handler also dirs debug
…delete add ability to delete files/dirs through API, but only in qiita test …
* general fixes 11-2025 * fix TestWorkflowHandler
* allow multiple standalone steps in workflows * flake8 * adding a test * 2 commands from start & extra commands * more tests * artifact.parents
* download public prep data * addressing @lucaspatel comments
* TST: study associations endpoint test * MAINT: be defensive on artifact prep assocation expectations * API: add /api/v1/study/<id>/associations to retrieve comprehensive id, path, processing information for a study * DOC: note schema, add some additiona doc strings and comments * LINT: pass w/ ruff check * LINT: now with flake8 * Rollback: allow an artifact to be unlinked * DOC: note internal rest endpoint * LINT: flake8 * Remove extraneous sort * An incomplete prep will not have an artifact
* add parents ArtifactHandler * fixing test * add job_id to ArtifactAPItestHandler * flake8
* flake8 to ruff * . import * check_analysis_access
* add analysis id to validate parameters * adding artifacts to job creation * add analysis to release * mv up pvals * artifacs -> artifacts * rm counts * rewrite scenarios * fix analysis error * no prep_template, parents or analysis provided * data_type * rm parents * params=None * overwrite_lock
* TST: study associations endpoint test * API: add /api/v1/study/<id>/associations to retrieve comprehensive id, path, processing information for a study * SQL: draft schema changes to support additional identifiers * API: unique_ids stub on base metadata object * TST: check unique_ids * TST: check unique_ids * API: passing SampleTemplate.unique_ids * API: passing PrepTemplate.unique_ids * API: passing Artifact.unique_ids * Constrain returned values * Based relative to Qiita schema * lint * Quality to schema
* 2026.01 * Apply suggestions from code review Co-authored-by: Amanda Birmingham <AmandaBirmingham@users.noreply.github.com> * rm å [skip ci] --------- Co-authored-by: Amanda Birmingham <AmandaBirmingham@users.noreply.github.com>
Corrected the spelling of 'January' and updated the description of new commands in 'qp-pacbio'.
…do_FetchFileFromCentralHandler
…/qiita into auth_oidc
* autoremove files created during testing * artifact.id <= 9
… also from identity provider
* discriminate nginx and direct requests and either use nginx or tornado file delivery method respectively * codestyle * don't complain about overwriting files IF in test mode * don't read config from file, but from DB * allow to push whole directories to qiita main * extended FetchFileFromCentralHandler to directories, but very limited to avoid lazy client from downloading whole BASE_DATA_DIR * assert presence/absence of directory transfer flag * codestyle * adding debug information * move debug to individual files * more debug when composing zip * debug * modify nginx file list for ZIP * use correct function * fix path computation * clean up * clean download.py * add ability to delete files/dirs through API, but only in qiita test mode * also delete non managed dirs * avoid deleting BIOM sub-dir :-/ * also allow downloading of html summary directories
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