…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

…mode

…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

* 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

…oidc

…/qiita into auth_oidc

…hub.com/antgonza/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