052020

CHANGELOG.md

@@ -1,5 +1,23 @@
 # Qiita changelog
 
+Version 052020
+--------------
+
+* Added Metatrascriptomics as a data type, added a Ribosomal read filtering step and documentation on how to use it in the processing recommendations
+* Fixed issue that prevented creating new artifacts when it was the children of a public parent
+* Qiita now keeps track of artifact deletion jobs, prevents submitting duplicated deletions, and the GUI is updated when an artifact is being deleted
+* We now display the `redbiom` DB release date in the redbiom Qiita page
+* Fixed EBA-ENA duplicated sample submission in multiple preparations - this could happen when a sample existed in more than one preparation
+* Add the ability to deprecate a preparation; this is useful when there is an unsuccessful run or preparation
+* The study page now has a markdown `Notes` section so users add problematic samples, explaining certain metadata columns, etc
+* Added user documentation to better explain how to split your samples in preparations
+* Fix a bug where repeated sample names were incorrectly handled during meta-analysis (#2978). Removed unused-legacy code to deal with duplicated sample names while building analyses
+* Improved headings in the stats page to avoid confusions
+* Fixed issue that only deleted selected samples within the page's viewing frame
+* Qiita now uses `gnu=True` in the `humanize.naturalsize` so the size display matches what a user sees when they `ls` the file
+* Updated code so it works with `pandas v1.0.3`
+* Added qiime2.2020.02 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization
+
 Version 012020
 --------------
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "092019"
+__version__ = "052020"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "092019"
+__version__ = "052020"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

qiita_db/util.py

@@ -1405,7 +1405,8 @@ def generate_study_list(user, visibility):
       visibility
             (SELECT array_agg(row_to_json((prep_template_id, data_type,
                  artifact_id, artifact_type, deprecated,
-                 qiita.bioms_from_preparation_artifacts(artifact_id)), true))
+                 qiita.bioms_from_preparation_artifacts(prep_template_id)),
+                 true))
                 FROM qiita.study_prep_template
                 LEFT JOIN qiita.prep_template USING (prep_template_id)
                 LEFT JOIN qiita.data_type USING (data_type_id)
@@ -1458,7 +1459,8 @@ def generate_study_list(user, visibility):
                 AS number_samples_collected,
             (SELECT array_agg(row_to_json((prep_template_id, data_type,
                  artifact_id, artifact_type, deprecated,
-                 qiita.bioms_from_preparation_artifacts(artifact_id)), true))
+                 qiita.bioms_from_preparation_artifacts(prep_template_id)),
+                 true))
                 FROM qiita.study_prep_template
                 LEFT JOIN qiita.prep_template USING (prep_template_id)
                 LEFT JOIN qiita.data_type USING (data_type_id)

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "092019"
+__version__ = "052020"

qiita_pet/handlers/analysis_handlers/base_handlers.py

@@ -145,6 +145,7 @@ def analyisis_graph_handler_get_request(analysis_id, user):
 
     nodes = []
     edges = []
+    artifacts_being_deleted = []
     wf_id = None
     # Loop through all the initial artifacts of the analysis
     for a in analysis.artifacts:
@@ -153,13 +154,22 @@ def analyisis_graph_handler_get_request(analysis_id, user):
             nodes, edges, a_wf_id = get_network_nodes_edges(
                 g, full_access, nodes=nodes, edges=edges)
 
+            # nodes returns [node_type, node_name, element_id]; here we
+            # are looking for the node_type == artifact, and check by
+            # the element/artifact_id if it's being deleted
+            for a in nodes:
+                if (a[0] == 'artifact' and
+                        Artifact(a[2]).being_deleted_by is not None):
+                    artifacts_being_deleted(a[2])
+
             if wf_id is None:
                 wf_id = a_wf_id
             elif a_wf_id is not None and wf_id != a_wf_id:
                 # This should never happen, but worth having a useful message
                 raise ValueError('More than one workflow in a single analysis')
 
-    return {'edges': edges, 'nodes': nodes, 'workflow': wf_id}
+    return {'edges': edges, 'nodes': nodes, 'workflow': wf_id,
+            'artifacts_being_deleted': artifacts_being_deleted}
 
 
 class AnalysisGraphHandler(BaseHandler):

qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py

@@ -123,6 +123,7 @@ def test_analyisis_graph_handler_get_request(self):
         # it here. There is only 1 job in the first artifact of the analysis
         job_id = Analysis(1).artifacts[0].jobs()[0].id
         exp = {'edges': [(8, job_id), (job_id, 9)],
+               'artifacts_being_deleted': [],
                'nodes': [
                     ('job', 'job', job_id, 'Single Rarefaction', 'success'),
                     ('artifact', 'BIOM', 9, 'noname\n(BIOM)', 'outdated'),
@@ -210,6 +211,7 @@ def test_get_analysis_graph_handler(self):
         job_id = Analysis(1).artifacts[0].jobs()[0].id
         obs = loads(response.body)
         exp = {'edges': [[8, job_id], [job_id, 9]],
+               'artifacts_being_deleted': [],
                'nodes': [
                     ['job', 'job', job_id, 'Single Rarefaction', 'success'],
                     ['artifact', 'BIOM', 9, 'noname\n(BIOM)', 'artifact'],
@@ -256,6 +258,7 @@ def test_get_analysis_graph_handler(self):
         obs = loads(response.body)
         exp = {'edges': [[artifacts[0].id, job_id],
                          [job_id, '%s:taxa_summary' % job_id]],
+               'artifacts_being_deleted': [],
                'nodes': [
                     ['job', 'job', job_id, 'Summarize Taxa',
                      'in_construction'],
@@ -289,6 +292,7 @@ def test_get_analysis_graph_handler(self):
                          [job_id, '%s:taxa_summary' % job_id],
                          [artifacts[1].id, job_id_2],
                          [job_id_2, '%s:rarefied_table' % job_id_2]],
+               'artifacts_being_deleted': [],
                'nodes': [
                     ['job', 'job', job_id, 'Summarize Taxa',
                      'in_construction'],

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__ = "092019"
+__version__ = "052020"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "092019"
+__version__ = "052020"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "092019"
+__version__ = "052020"
 
 
 classes = """