Merge branch 'dev' of github.com:biocore/qiita

Author: antgonza

Diff for: CHANGELOG.md

@@ -1,5 +1,17 @@
 # Qiita changelog
 
+Version 2025.01
+---------------
+
+Deployed on January 15th, 2025
+
+* The Analysis owner is now displayed in the analysis list and the individual analysis page.
+* Admins can now use the per-preparation "Download Data Release" button to get a "BIOM" release; this version is focus on NPH data releases.
+* Improved complete_job creation time, which should result in Qiita jobs ([multiple steps](https://qiita.ucsd.edu/static/doc/html/dev/resource_allocation.html) finishing faster; for bencharks visit [patch 93.sql](https://github.com/qiita-spots/qiita/blob/master/qiita_db/support_files/patches/93.sql).
+* SPP improvements: TellSeq support added; plugin refactored to allow for easier additions like TellSeq in the future. Job restart greatly improved. Much improved handling of sample-names and ids that contain substrings like ‘I1’ and ‘R2’. New SequenceCount job can count sequences and base-pairs in parallel for any list of fastq files.
+* Other general fixes [#3440](https://github.com/qiita-spots/qiita/pull/3440), [#3445](https://github.com/qiita-spots/qiita/pull/3445), [#3446](https://github.com/qiita-spots/qiita/pull/3446),
+
+
 Version 2024.10
 ---------------
 
@@ -206,7 +218,7 @@ Version 2021.11
 * Allow chucked download of metadata files in analyses; this allows to process large meta-analysis (like those for The Microsetta Initiative) without worker blockage.
 * Added to the qp-qiime2 plugin the possibility of filtering tables based on system available "FeatureData[Sequence]"; to start we added 90/100/150 bps bloom tables.
 * Now we can instantiate a study via their title (Study.from_title); this will facilitate orchestration with qebil.
-* Speed up Study listing for admins and general users; the admin study display came down from 20 to 2 seconds.  
+* Speed up Study listing for admins and general users; the admin study display came down from 20 to 2 seconds.
 * Fixed the following issues: [3142](https://github.com/qiita-spots/qiita/issues/3142), [3149](https://github.com/qiita-spots/qiita/issues/3149), [3150](https://github.com/qiita-spots/qiita/issues/3150), [3119](https://github.com/qiita-spots/qiita/issues/3119), and [3160](https://github.com/qiita-spots/qiita/issues/3160).
 
 

Diff for: qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2024.10"
+__version__ = "2025.01"

Diff for: qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2024.10"
+__version__ = "2025.01"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

Diff for: qiita_db/analysis.py

@@ -215,6 +215,22 @@ def create(cls, owner, name, description, from_default=False,
         job.submit()
         return instance
 
+    @classmethod
+    def delete_analysis_artifacts(cls, _id):
+        """Deletes the artifacts linked to an artifact and then the analysis
+
+        Parameters
+        ----------
+        _id : int
+            The analysis id
+        """
+        analysis = cls(_id)
+        aids = [a.id for a in analysis.artifacts if not a.parents]
+        aids.sort(reverse=True)
+        for aid in aids:
+            qdb.artifact.Artifact.delete(aid)
+        cls.delete(analysis.id)
+
     @classmethod
     def delete(cls, _id):
         """Deletes an analysis

Diff for: qiita_db/archive.py

@@ -116,6 +116,7 @@ def get_merging_scheme_from_job(cls, job):
             acmd = job.command
             parent = job.input_artifacts[0]
             parent_pparameters = parent.processing_parameters
+            phms = None
             if parent_pparameters is None:
                 parent_cmd_name = None
                 parent_parameters = None
@@ -125,12 +126,26 @@ def get_merging_scheme_from_job(cls, job):
                 parent_cmd_name = pcmd.name
                 parent_parameters = parent_pparameters.values
                 parent_merging_scheme = pcmd.merging_scheme
-
-            return qdb.util.human_merging_scheme(
+                if not parent_merging_scheme['ignore_parent_command']:
+                    gp = parent.parents[0]
+                    gp_params = gp.processing_parameters
+                    if gp_params is not None:
+                        gp_cmd = gp_params.command
+                        phms = qdb.util.human_merging_scheme(
+                            parent_cmd_name, parent_merging_scheme,
+                            gp_cmd.name, gp_cmd.merging_scheme,
+                            parent_parameters, [], gp_params.values)
+
+            hms = qdb.util.human_merging_scheme(
                 acmd.name, acmd.merging_scheme,
                 parent_cmd_name, parent_merging_scheme,
                 job.parameters.values, [], parent_parameters)
 
+            if phms is not None:
+                hms = qdb.util.merge_overlapping_strings(hms, phms)
+
+            return hms
+
     @classmethod
     def retrieve_feature_values(cls, archive_merging_scheme=None,
                                 features=None):

Diff for: qiita_db/handlers/processing_job.py

@@ -146,7 +146,9 @@ def post(self, job_id):
                 cmd, values_dict={'job_id': job_id,
                                   'payload': self.request.body.decode(
                                       'ascii')})
-            job = qdb.processing_job.ProcessingJob.create(job.user, params)
+            # complete_job are unique so it is fine to force them to be created
+            job = qdb.processing_job.ProcessingJob.create(
+                job.user, params, force=True)
             job.submit()
 
         self.finish()

Diff for: qiita_db/handlers/tests/test_processing_job.py

@@ -233,9 +233,9 @@ def test_post_job_success(self):
         self.assertIsNotNone(cj)
         # additionally we can test that job.print_trace is correct
         self.assertEqual(job.trace, [
-            f'{job.id} [Not Available]: Validate | '
+            f'{job.id} [Not Available] (success): Validate | '
             '-p qiita -N 1 -n 1 --mem 90gb --time 150:00:00 --nice=10000',
-            f'  {cj.id} [{cj.external_id}] | '
+            f'  {cj.id} [{cj.external_id}] (success)| '
             '-p qiita -N 1 -n 1 --mem 16gb --time 10:00:00 --nice=10000'])
 
     def test_post_job_success_with_archive(self):

Diff for: qiita_db/metadata_template/prep_template.py

@@ -135,7 +135,7 @@ def create(cls, md_template, study, data_type, investigation_type=None,
             # data_type being created - if possible
             if investigation_type is None:
                 if data_type_str in TARGET_GENE_DATA_TYPES:
-                    investigation_type = 'Amplicon'
+                    investigation_type = 'AMPLICON'
                 elif data_type_str == 'Metagenomic':
                     investigation_type = 'WGS'
                 elif data_type_str == 'Metatranscriptomic':
@@ -280,8 +280,22 @@ def delete(cls, id_):
             qdb.sql_connection.TRN.add(sql, args)
             archived_artifacts = set(
                 qdb.sql_connection.TRN.execute_fetchflatten())
+            ANALYSIS = qdb.analysis.Analysis
             if archived_artifacts:
                 for aid in archived_artifacts:
+                    # before we can delete the archived artifact, we need
+                    # to delete the analyses where they were used.
+                    sql = """SELECT analysis_id
+                             FROM qiita.analysis
+                             WHERE analysis_id IN (
+                                SELECT DISTINCT analysis_id
+                                FROM qiita.analysis_sample
+                                WHERE artifact_id IN %s)"""
+                    qdb.sql_connection.TRN.add(sql, [tuple([aid])])
+                    analyses = set(
+                        qdb.sql_connection.TRN.execute_fetchflatten())
+                    for _id in analyses:
+                        ANALYSIS.delete_analysis_artifacts(_id)
                     qdb.artifact.Artifact.delete(aid)
 
             # Delete the prep template filepaths
@@ -794,14 +808,24 @@ def _get_node_info(workflow, node):
 
             parent_cmd_name = None
             parent_merging_scheme = None
+            phms = None
             if pcmd is not None:
                 parent_cmd_name = pcmd.name
                 parent_merging_scheme = pcmd.merging_scheme
+                if not parent_merging_scheme['ignore_parent_command']:
+                    phms = _get_node_info(workflow, parent)
 
-            return qdb.util.human_merging_scheme(
+            hms = qdb.util.human_merging_scheme(
                 ccmd.name, ccmd.merging_scheme, parent_cmd_name,
                 parent_merging_scheme, cparams, [], pparams)
 
+            # if the parent should not ignore its parent command, then we need
+            # to merge the previous result with the new one
+            if phms is not None:
+                hms = qdb.util.merge_overlapping_strings(hms, phms)
+
+            return hms
+
         def _get_predecessors(workflow, node):
             # recursive method to get predecessors of a given node
             pred = []
@@ -857,7 +881,7 @@ def _get_predecessors(workflow, node):
                          'artifact transformation']
         merging_schemes = {
             qdb.archive.Archive.get_merging_scheme_from_job(j): {
-                x: y.id for x, y in j.outputs.items()}
+                x: str(y.id) for x, y in j.outputs.items()}
             # we are going to select only the jobs that were a 'success', that
             # are not 'hidden' and that have an output - jobs that are not
             # hidden and a successs but that do not have outputs are jobs which
@@ -975,7 +999,7 @@ def _get_predecessors(workflow, node):
                     init_artifacts = {
                         wkartifact_type: f'{starting_job.id}:'}
                 else:
-                    init_artifacts = {wkartifact_type: self.artifact.id}
+                    init_artifacts = {wkartifact_type: str(self.artifact.id)}
 
             cmds_to_create.reverse()
             current_job = None

Diff for: qiita_db/metadata_template/test/test_prep_template.py

@@ -911,7 +911,7 @@ def _common_creation_checks(self, pt, fp_count, name):
         self.assertEqual(pt.data_type(), self.data_type)
         self.assertEqual(pt.data_type(ret_id=True), self.data_type_id)
         self.assertEqual(pt.artifact, None)
-        self.assertEqual(pt.investigation_type, 'Amplicon')
+        self.assertEqual(pt.investigation_type, 'AMPLICON')
         self.assertEqual(pt.study_id, self.test_study.id)
         self.assertEqual(pt.status, "sandbox")
         exp_sample_ids = {'%s.SKB8.640193' % self.test_study.id,
@@ -1076,7 +1076,7 @@ def test_create_warning(self):
         self.assertEqual(pt.data_type(), self.data_type)
         self.assertEqual(pt.data_type(ret_id=True), self.data_type_id)
         self.assertEqual(pt.artifact, None)
-        self.assertEqual(pt.investigation_type, 'Amplicon')
+        self.assertEqual(pt.investigation_type, 'AMPLICON')
         self.assertEqual(pt.study_id, self.test_study.id)
         self.assertEqual(pt.status, 'sandbox')
         exp_sample_ids = {'%s.SKB8.640193' % self.test_study.id,
@@ -1247,7 +1247,7 @@ def test_investigation_type_setter(self):
         """Able to update the investigation type"""
         pt = qdb.metadata_template.prep_template.PrepTemplate.create(
             self.metadata, self.test_study, self.data_type_id)
-        self.assertEqual(pt.investigation_type, 'Amplicon')
+        self.assertEqual(pt.investigation_type, 'AMPLICON')
         pt.investigation_type = "Other"
         self.assertEqual(pt.investigation_type, 'Other')
         with self.assertRaises(qdb.exceptions.QiitaDBColumnError):

Diff for: qiita_db/processing_job.py

@@ -582,10 +582,10 @@ def create(cls, user, parameters, force=False):
         TTRN = qdb.sql_connection.TRN
         with TTRN:
             command = parameters.command
-
-            # check if a job with the same parameters already exists
-            sql = """SELECT processing_job_id, email, processing_job_status,
-                        COUNT(aopj.artifact_id)
+            if not force:
+                # check if a job with the same parameters already exists
+                sql = """SELECT processing_job_id, email,
+                        processing_job_status, COUNT(aopj.artifact_id)
                      FROM qiita.processing_job
                      LEFT JOIN qiita.processing_job_status
                         USING (processing_job_status_id)
@@ -596,41 +596,42 @@ def create(cls, user, parameters, force=False):
                      GROUP BY processing_job_id, email,
                         processing_job_status"""
 
-            # we need to use ILIKE because of booleans as they can be
-            # false or False
-            params = []
-            for k, v in parameters.values.items():
-                # this is necessary in case we have an Iterable as a value
-                # but that is string
-                if isinstance(v, Iterable) and not isinstance(v, str):
-                    for vv in v:
-                        params.extend([k, str(vv)])
+                # we need to use ILIKE because of booleans as they can be
+                # false or False
+                params = []
+                for k, v in parameters.values.items():
+                    # this is necessary in case we have an Iterable as a value
+                    # but that is string
+                    if isinstance(v, Iterable) and not isinstance(v, str):
+                        for vv in v:
+                            params.extend([k, str(vv)])
+                    else:
+                        params.extend([k, str(v)])
+
+                if params:
+                    # divided by 2 as we have key-value pairs
+                    len_params = int(len(params)/2)
+                    sql = sql.format(' AND ' + ' AND '.join(
+                        ["command_parameters->>%s ILIKE %s"] * len_params))
+                    params = [command.id] + params
+                    TTRN.add(sql, params)
                 else:
-                    params.extend([k, str(v)])
-
-            if params:
-                # divided by 2 as we have key-value pairs
-                len_params = int(len(params)/2)
-                sql = sql.format(' AND ' + ' AND '.join(
-                    ["command_parameters->>%s ILIKE %s"] * len_params))
-                params = [command.id] + params
-                TTRN.add(sql, params)
-            else:
-                # the sql variable expects the list of parameters but if there
-                # is no param we need to replace the {0} with an empty string
-                TTRN.add(sql.format(""), [command.id])
-
-            # checking that if the job status is success, it has children
-            # [2] status, [3] children count
-            existing_jobs = [r for r in TTRN.execute_fetchindex()
-                             if r[2] != 'success' or r[3] > 0]
-            if existing_jobs and not force:
-                raise ValueError(
-                    'Cannot create job because the parameters are the same as '
-                    'jobs that are queued, running or already have '
-                    'succeeded:\n%s' % '\n'.join(
-                        ["%s: %s" % (jid, status)
-                         for jid, _, status, _ in existing_jobs]))
+                    # the sql variable expects the list of parameters but if
+                    # there is no param we need to replace the {0} with an
+                    # empty string
+                    TTRN.add(sql.format(""), [command.id])
+
+                # checking that if the job status is success, it has children
+                # [2] status, [3] children count
+                existing_jobs = [r for r in TTRN.execute_fetchindex()
+                                 if r[2] != 'success' or r[3] > 0]
+                if existing_jobs:
+                    raise ValueError(
+                        'Cannot create job because the parameters are the '
+                        'same as jobs that are queued, running or already '
+                        'have succeeded:\n%s' % '\n'.join(
+                            ["%s: %s" % (jid, status)
+                             for jid, _, status, _ in existing_jobs]))
 
             sql = """INSERT INTO qiita.processing_job
                         (email, command_id, command_parameters,
@@ -2052,23 +2053,25 @@ def complete_processing_job(self):
     def trace(self):
         """ Returns as a text array the full trace of the job, from itself
             to validators and complete jobs"""
-        lines = [f'{self.id} [{self.external_id}]: '
+        lines = [f'{self.id} [{self.external_id}] ({self.status}): '
                  f'{self.command.name} | {self.resource_allocation_info}']
         cjob = self.complete_processing_job
         if cjob is not None:
-            lines.append(f'  {cjob.id} [{cjob.external_id}] | '
+            lines.append(f'  {cjob.id} [{cjob.external_id}] ({cjob.status})| '
                          f'{cjob.resource_allocation_info}')
             vjob = self.release_validator_job
             if vjob is not None:
                 lines.append(f'    {vjob.id} [{vjob.external_id}] '
-                             f'| {vjob.resource_allocation_info}')
+                             f' ({vjob.status}) | '
+                             f'{vjob.resource_allocation_info}')
         for v in self.validator_jobs:
-            lines.append(f'     {v.id} [{v.external_id}]: '
+            lines.append(f'     {v.id} [{v.external_id}] ({v.status}): '
                          f'{v.command.name} | {v.resource_allocation_info}')
             cjob = v.complete_processing_job
             if cjob is not None:
                 lines.append(f'         {cjob.id} [{cjob.external_id}] '
-                             f'| {cjob.resource_allocation_info}')
+                             f'({cjob.status}) | '
+                             f'{cjob.resource_allocation_info}')
         return lines