From 398d15ff4501d0f0e25e0783ecdb5ac1245e7f98 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Fri, 11 Jul 2025 07:12:16 -0600 Subject: [PATCH 1/2] changes for 2025.07 --- CHANGELOG.md | 16 ++++++++++++++++ qiita_core/__init__.py | 2 +- qiita_db/__init__.py | 2 +- qiita_pet/__init__.py | 2 +- qiita_pet/handlers/api_proxy/__init__.py | 2 +- qiita_pet/templates/study_ajax/prep_summary.html | 9 +++++---- qiita_ware/__init__.py | 2 +- setup.py | 2 +- 8 files changed, 27 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 57675f86a..d5017bae7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,20 @@ # Qiita changelog +Version 2025.07 +--------------- + +Deployed on July 14th, 2025 + +* During EBI-ENA submissions now we automatically renmae `country` to `geographic location (country and/or sea)` and `collection_date` to `collection date`; as the ENA requirements changed. +* Added platform `DNBSEQ1` and instruments: `DNBSEQ-G400`, `DNBSEQ-T7`, `DNBSEQ-G800` for EBI-ENA submissions. +* Other general fixes [#3474](https://github.com/qiita-spots/qiita/pull/3474), [#3475](https://github.com/qiita-spots/qiita/pull/3475). +* SPP: merged and deprecated [mg-scripts](https://github.com/qiita-spots/mg-scripts) to [qp-knight-lab-processing](https://github.com/qiita-spots/qp-knight-lab-processing). +* SPP: Added integration tests via a couple of PRs: [#129](https://github.com/qiita-spots/qp-knight-lab-processing/pull/129) & [#131](https://github.com/qiita-spots/qp-knight-lab-processing/pull/131). +* SPP: Added new command `Human Filter & QC existing Prep` to facilitate human-filtering existing preparations. +* SPP: Cleaned and centralized sequencers information to [kl-metapool](https://github.com/biocore/kl-metapool), thank you @AmandaBirmingham. + + + Version 2025.04 --------------- @@ -10,6 +25,7 @@ Deployed on April 11th, 2025 * SPP: General updates and clean up: [#169](https://github.com/biocore/mg-scripts/pull/169), [#101](https://github.com/qiita-spots/qp-knight-lab-processing/pull/101). * `Remove SynDNA plasmid, insert, & CP026085 reads` superseded `Remove SynDNA inserts & plasmid reads`; which now removes SynDNA plasmids, inserts, and CP026085 reads, in this order. + Version 2025.02 --------------- diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py index 02965cb48..09b55f2b0 100644 --- a/qiita_core/__init__.py +++ b/qiita_core/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2025.04" +__version__ = "2025.07" diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py index a4794ceca..43e9b34c6 100644 --- a/qiita_db/__init__.py +++ b/qiita_db/__init__.py @@ -27,7 +27,7 @@ from . import user from . import processing_job -__version__ = "2025.04" +__version__ = "2025.07" __all__ = ["analysis", "artifact", "archive", "base", "commands", "environment_manager", "exceptions", "investigation", "logger", diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py index 02965cb48..09b55f2b0 100644 --- a/qiita_pet/__init__.py +++ b/qiita_pet/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2025.04" +__version__ = "2025.07" diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py index ed0583693..ce95603ab 100644 --- a/qiita_pet/handlers/api_proxy/__init__.py +++ b/qiita_pet/handlers/api_proxy/__init__.py @@ -38,7 +38,7 @@ from .user import (user_jobs_get_req) from .util import check_access, check_fp -__version__ = "2025.04" +__version__ = "2025.07" __all__ = ['prep_template_summary_get_req', 'data_types_get_req', 'study_get_req', 'sample_template_filepaths_get_req', diff --git a/qiita_pet/templates/study_ajax/prep_summary.html b/qiita_pet/templates/study_ajax/prep_summary.html index a36dcbd1c..8c46de071 100644 --- a/qiita_pet/templates/study_ajax/prep_summary.html +++ b/qiita_pet/templates/study_ajax/prep_summary.html @@ -433,11 +433,12 @@

{% end %} {{name}} - ID {{prep_id}} ({{data_type}}) - {% if user_level in ('admin', 'wet-lab admin') and creation_job is not None %} - SampleSheet - {% if creation_job_artifact_summary is not None %} - Creation Job Output + + {% if editable and creation_job is not None and creation_job_artifact_summary is not None %} + {% if creation_job_filename != 'None' %} + SampleSheet {% end %} + Creation Job Output {% end %} Edit name Prep info diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py index 02965cb48..09b55f2b0 100644 --- a/qiita_ware/__init__.py +++ b/qiita_ware/__init__.py @@ -6,4 +6,4 @@ # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- -__version__ = "2025.04" +__version__ = "2025.07" diff --git a/setup.py b/setup.py index fd933970e..e764c7326 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ from setuptools import setup from glob import glob -__version__ = "2025.04" +__version__ = "2025.07" classes = """ From 2ce6ca35b120df22452ea542bc86e20696344ee6 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Fri, 11 Jul 2025 07:33:06 -0600 Subject: [PATCH 2/2] self.assertEqual -> self.assertCountEqual --- CHANGELOG.md | 2 +- qiita_db/test/test_user.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d5017bae7..44c87f752 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ Deployed on July 14th, 2025 * SPP: merged and deprecated [mg-scripts](https://github.com/qiita-spots/mg-scripts) to [qp-knight-lab-processing](https://github.com/qiita-spots/qp-knight-lab-processing). * SPP: Added integration tests via a couple of PRs: [#129](https://github.com/qiita-spots/qp-knight-lab-processing/pull/129) & [#131](https://github.com/qiita-spots/qp-knight-lab-processing/pull/131). * SPP: Added new command `Human Filter & QC existing Prep` to facilitate human-filtering existing preparations. -* SPP: Cleaned and centralized sequencers information to [kl-metapool](https://github.com/biocore/kl-metapool), thank you @AmandaBirmingham. +* SPP: Cleaned and centralized sequencers information to [kl-metapool](https://github.com/biocore/kl-metapool) & added `MiSeq i100`, thank you @AmandaBirmingham. diff --git a/qiita_db/test/test_user.py b/qiita_db/test/test_user.py index 0d14d2c8a..17110c7db 100644 --- a/qiita_db/test/test_user.py +++ b/qiita_db/test/test_user.py @@ -482,12 +482,12 @@ def test_mark_messages(self): user.mark_messages([1, 2]) obs = user.messages() exp = [True, True, False] - self.assertEqual([x[3] for x in obs], exp) + self.assertCountEqual([x[3] for x in obs], exp) user.mark_messages([1], read=False) obs = user.messages() exp = [False, True, False] - self.assertEqual([x[3] for x in obs], exp) + self.assertCountEqual([x[3] for x in obs], exp) def test_delete_messages(self): user = qdb.user.User.create('deletemsg@test.bar', 'password')