Merge pull request #3273 from antgonza/2023.03

2023.03

Author: charles-cowart

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/<study_id>?prep_id=<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
 ---------------
 

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"

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",

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"

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',

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]

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"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2023.02"
+__version__ = "2023.03"
 
 
 classes = """