Merge pull request #3206 from antgonza/2022.07

2022.07

Author: charles-cowart

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Qiita changelog
 
+Version 2022.07
+---------------
+
+* Users can opt-in to get emails when their jobs change status in their User Information preferences.
+* Added BIOM artifact archiving to the system; this unlinks artifacts from the main processing but leaves them in the system in case they are needed in the future.
+* Added [qiime2.2022.02](https://github.com/qiita-spots/qp-qiime2/pull/68) to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization
+* Users can now select multiple artifacts for analysis [qp-qiime2](https://github.com/qiita-spots/qp-qiime2/pull/69), which gives access to new commands like PCoA biplots.
+* [qtp-sequencing](https://github.com/qiita-spots/qtp-sequencing/pull/41/files) now uses fqtools to count the number of sequences in fastq/fastq.gz files as part as the artifact summary.
+* Artifact summaries can now be updated [qiita-spots #3205](https://github.com/qiita-spots/qiita/pull/3205).
+* Added to the internal (Sequence Processing Pipeline)[https://github.com/qiita-spots/qp-knight-lab-processing] the CHM13 genome so human studies are now filtered by GRCh38 genome + PhiX and CHM13 genome.
+
 Version 2022.05
 -----------------
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2022.04"
+__version__ = "2022.07"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2022.04"
+__version__ = "2022.07"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

qiita_db/processing_job.py

@@ -753,14 +753,17 @@ def status(self):
             qdb.sql_connection.TRN.add(sql, [self.id])
             return qdb.sql_connection.TRN.execute_fetchlast()
 
-    def _set_status(self, value):
+    def _set_status(self, value, error_msg=None):
         """Sets the status of the job
 
         Parameters
         ----------
         value : str, {'queued', 'running', 'success', 'error',
                       'in_construction', 'waiting'}
             The new status of the job
+        error_msg : str, optional
+            If not None this is the message that is going to be sent to the
+            user when the value is 'error'
 
         Raises
         ------
@@ -781,14 +784,22 @@ def _set_status(self, value):
             new_status = qdb.util.convert_to_id(
                 value, "processing_job_status")
 
-            if self.user.info['receive_processing_job_emails']:
-                # skip if software is internal
-                ignore_software = ('Qiita')
-                if self.command.software.name not in ignore_software:
-                    subject = ('Job status change: %s (%s)' % (
-                        self.command.name, self.id))
-                    message = ('New status: %s' % (new_status))
-                    qdb.util.send_email(self.user.email, subject, message)
+            if value not in {'waiting'}:
+                if self.user.info['receive_processing_job_emails']:
+                    # skip if software is artifact definition
+                    ignore_software = ('artifact definition', )
+                    if self.command.software.name not in ignore_software:
+                        ignore_commands = ('Validate', 'complete_job',
+                                           'release_validators')
+                        if self.command.name not in ignore_commands:
+                            subject = 'Job status change: %s (%s)' % (
+                                self.command.name, self.id)
+                            message = 'New status: %s' % (value)
+
+                            if value == 'error' and error_msg is not None:
+                                message += f'\n\nError:\n{error_msg}'
+                            qdb.util.send_email(
+                                self.user.email, subject, message)
 
             sql = """UPDATE qiita.processing_job
                      SET processing_job_status_id = %s
@@ -1463,7 +1474,6 @@ def _set_error(self, error):
                 raise qdb.exceptions.QiitaDBOperationNotPermittedError(
                     "Can only set up the log for jobs whose status is 'error'")
 
-            self._set_status('error')
             log = qdb.logger.LogEntry.create('Runtime', error)
 
             sql = """UPDATE qiita.processing_job
@@ -1476,6 +1486,9 @@ def _set_error(self, error):
             for c in self.children:
                 c.complete(False, error="Parent job '%s' failed." % self.id)
 
+            # set as error after everything is in place
+            self._set_status('error', error_msg=error)
+
     @property
     def heartbeat(self):
         """The timestamp of the last heartbeat received from the job

qiita_db/software.py

@@ -51,9 +51,9 @@ class Command(qdb.base.QiitaObject):
     -------------
     create
     exists
-    get_commands_by_input_type(cls, artifact_types, active_only=True,
-    get_html_generator(cls, artifact_type):
-    get_validator(cls, artifact_type):
+    get_commands_by_input_type
+    get_html_generator
+    get_validator
 
     See Also
     --------

qiita_db/sql_connection.py

@@ -198,7 +198,7 @@ def _raise_execution_error(self, sql, sql_args, error):
             ec_lu = errorcodes.lookup(error.pgcode)
             raise ValueError(
                 "Error running SQL: %s. MSG: %s\n" % (ec_lu, str(error)))
-        except (KeyError, AttributeError):
+        except (KeyError, AttributeError, TypeError):
             raise ValueError("Error running SQL query: %s" % str(error))
 
     @_checker

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2022.04"
+__version__ = "2022.07"

qiita_pet/handlers/analysis_handlers/listing_handlers.py

@@ -118,13 +118,15 @@ def get(self):
 
         # finding common metadata fields
         metadata = analysis.metadata_categories
-        common = []
+        common = {'sample': set(), 'prep': set()}
         for i, (_, m) in enumerate(metadata.items()):
-            if i == 0:
-                common = {'sample': set(m['sample']), 'prep': set(m['prep'])}
-            else:
-                common['sample'] = common['sample'] & set(m['sample'])
-                common['prep'] = common['prep'] & set(m['prep'])
+            svals = set(m['sample'])
+            pvals = set(m['prep'])
+            if i != 0:
+                svals = common['sample'] & svals
+                pvals = common['prep'] & pvals
+            common['sample'] = svals
+            common['prep'] = pvals
 
         self.render("analysis_selected.html", sel_data=sel_data,
                     proc_info=proc_data_info, metadata=metadata, common=common)

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__ = "2022.04"
+__version__ = "2022.07"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst

@@ -87,6 +87,10 @@ Note that the command produces up to 6 output artifacts based on the aligner and
 - Per genome Predictions: contains the per genome level taxonomic predictions BIOM table
 - Per gene Predictions: Only WoLr1, contains the per gene level taxonomic predictions BIOM table
 
+.. note::
+   Woltka provides easy transformations for the "per gene Prediction table" to generate functional
+   profiles, `more information <https://github.com/qiyunzhu/woltka/blob/master/doc/wol.md#comparison>`
+
 Aligners
 ^^^^^^^^
 

qiita_pet/templates/study_ajax/prep_summary.html

@@ -407,6 +407,9 @@
       $('#new-prep-name').focus();
       $('#new-prep-name').select();
     });
+
+    qiita_websocket.init(window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', error, error);
+    qiita_websocket.add_callback('sel', show_alert);
   });
 
   function toggleCheckboxes(element){

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2022.04"
+__version__ = "2022.07"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2022.04"
+__version__ = "2022.07"
 
 
 classes = """