From cf3ba056136fde0ebc560b964c0ec33e07d9a6ed Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Fri, 24 Mar 2023 07:54:56 -0600 Subject: [PATCH 1/2] 2023.03 --- CHANGELOG.md | 14 ++++++++++++++ qiita_core/__init__.py | 2 +- qiita_db/__init__.py | 2 +- qiita_pet/__init__.py | 2 +- qiita_pet/handlers/api_proxy/__init__.py | 2 +- qiita_ware/__init__.py | 2 +- setup.py | 2 +- 7 files changed, 20 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa3087bcb..4e1dac536 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,19 @@ # Qiita changelog +Version 2023.03 +--------------- + +* Added "Sample Validation" for all Admin levels. +* Tools and Plugins can add preparation information via the endpoint: `/qiita_db/prep_template/`. +* Users can now access specific preparations via the URL by adding it as a parameter: `/study/description/?prep_id=`. +* The internal [Sequence Processing Pipeline](https://github.com/qiita-spots/qp-knight-lab-processing) now automatically inserts new BLANKs to the sample information file, adds the preparation information file to Qiita, and keeps a record of which preparations were inserted to which studies. +* Added the possibility of processing BIOM artifacts in the processing pipeline. +* Added qiime2.2023.2 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization. +* Added q2-greengeenes2 to the system, specifically actions: `filter_features` and `non_v4_16s`. This is the first processing (vs. analysis) plugin added to the system. +* Fixed the [diversity pcoa_biplot](https://github.com/qiita-spots/qiita/issues/3266) functionality and added the [emperor biplot](https://github.com/qiita-spots/qiita/issues/3255) action. +* The system can now validate QIIME 2 `FeatureData[Sequences]` via `qtp-diversity`. +* Fixed the following issues [#3249](https://github.com/qiita-spots/qiita/issues/3249), [#3264](https://github.com/qiita-spots/qiita/issues/3264), [#3245](https://github.com/qiita-spots/qiita/issues/3245), [#3243](https://github.com/qiita-spots/qiita/issues/3243). + Version 2023.02 --------------- diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py index e736319f6..0ab412bfc 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__ = "2023.02" +__version__ = "2023.03" diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py index f4c9f6bc9..bbbc9f9e3 100644 --- a/qiita_db/__init__.py +++ b/qiita_db/__init__.py @@ -27,7 +27,7 @@ from . import user from . import processing_job -__version__ = "2023.02" +__version__ = "2023.03" __all__ = ["analysis", "artifact", "archive", "base", "commands", "environment_manager", "exceptions", "investigation", "logger", diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py index e736319f6..0ab412bfc 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__ = "2023.02" +__version__ = "2023.03" diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py index f686e0382..765847ffc 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__ = "2023.02" +__version__ = "2023.03" __all__ = ['prep_template_summary_get_req', 'data_types_get_req', 'study_get_req', 'sample_template_filepaths_get_req', diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py index e736319f6..0ab412bfc 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__ = "2023.02" +__version__ = "2023.03" diff --git a/setup.py b/setup.py index a148445f5..1ac6cc04b 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ from setuptools import setup from glob import glob -__version__ = "2023.02" +__version__ = "2023.03" classes = """ From c6349a3f0e9e5886d4c1ec88dd34b6df213a29f3 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Fri, 24 Mar 2023 12:17:30 -0600 Subject: [PATCH 2/2] cover redbiom error during search --- qiita_pet/handlers/qiita_redbiom.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/qiita_pet/handlers/qiita_redbiom.py b/qiita_pet/handlers/qiita_redbiom.py index f18d5593e..62157b89b 100644 --- a/qiita_pet/handlers/qiita_redbiom.py +++ b/qiita_pet/handlers/qiita_redbiom.py @@ -61,7 +61,13 @@ def _redbiom_metadata_search(self, query, contexts): for ctx in contexts: # redbiom.fetch.data_from_samples returns a biom, which we # will ignore, and a dict: {sample_id_in_table: original_id} - _, data = redbiom.fetch.data_from_samples(ctx, redbiom_samples) + try: + # if redbiom can't find a valid sample in the context it + # will raise a ValueError: max() arg is an empty sequence + _, data = redbiom.fetch.data_from_samples( + ctx, redbiom_samples) + except ValueError: + continue for idx in data.keys(): sample_id, aid = idx.rsplit('.', 1) sid = sample_id.split('.', 1)[0]