Merge pull request #3265 from antgonza/minor-fixes-2023.03

fix #3264 + processing_job email subject

Author: charles-cowart

qiita_db/processing_job.py

@@ -729,7 +729,7 @@ def _generate_notification_message(self, value, error_msg):
             return None
 
         # generate subject line
-        subject = 'Job status change: %s (%s)' % (self.command.name, self.id)
+        subject = '%s: %s (%s)' % (self.command.name, value, self.id)
 
         # generate message line
         message = ''
@@ -1386,6 +1386,8 @@ def _complete_artifact_transformation(self, artifacts_data):
 
             # Submit m validator jobs as n lists of jobs
             n = qiita_config.job_scheduler_dependency_q_cnt
+            if n is None:
+                n = 2
 
             # taken from:
             # https://www.geeksforgeeks.org/break-list-chunks-size-n-python/

qiita_db/test/test_processing_job.py

@@ -870,7 +870,7 @@ def test_notification_mail_generation(self):
         # messages of type 'error'.
         obs = self.tester1._generate_notification_message('error', None)
 
-        exp = {'subject': ('Job status change: Split libraries FASTQ '
+        exp = {'subject': ('Split libraries FASTQ: error '
                            '(063e553b-327c-4818-ab4a-adfe58e49860)'),
                'message': ('Processing Job: Split libraries FASTQ\n'
                            f'{qiita_config.base_url}/study/description/1'
@@ -880,7 +880,7 @@ def test_notification_mail_generation(self):
 
         obs = self.tester1._generate_notification_message('error',
                                                           'An Error Message')
-        exp = {'subject': ('Job status change: Split libraries FASTQ '
+        exp = {'subject': ('Split libraries FASTQ: error '
                            '(063e553b-327c-4818-ab4a-adfe58e49860)'),
                'message': ('Processing Job: Split libraries FASTQ\n'
                            f'{qiita_config.base_url}/study/description/1\n'
@@ -891,7 +891,7 @@ def test_notification_mail_generation(self):
         # The inclusion of an error message has no effect on other valid
         # status types e.g. 'running'.
         obs = self.tester1._generate_notification_message('running', None)
-        exp = {'subject': ('Job status change: Split libraries FASTQ '
+        exp = {'subject': ('Split libraries FASTQ: running '
                            '(063e553b-327c-4818-ab4a-adfe58e49860)'),
                'message': ('Processing Job: Split libraries FASTQ\n'
                            f'{qiita_config.base_url}/study/description/1\n'
@@ -900,7 +900,7 @@ def test_notification_mail_generation(self):
         self.assertDictEqual(obs, exp)
 
         obs = self.tester1._generate_notification_message('running', 'Yahoo!')
-        exp = {'subject': ('Job status change: Split libraries FASTQ '
+        exp = {'subject': ('Split libraries FASTQ: running '
                            '(063e553b-327c-4818-ab4a-adfe58e49860)'),
                'message': ('Processing Job: Split libraries FASTQ\n'
                            f'{qiita_config.base_url}/study/description/1\n'
@@ -912,7 +912,7 @@ def test_notification_mail_generation(self):
         jid = '8a7a8461-e8a1-4b4e-a428-1bc2f4d3ebd0'
         pj = qdb.processing_job.ProcessingJob(jid)
         obs = pj._generate_notification_message('running', 'Yahoo!')
-        exp = {'subject': 'Job status change: Single Rarefaction '
+        exp = {'subject': 'Single Rarefaction: running '
                           '(8a7a8461-e8a1-4b4e-a428-1bc2f4d3ebd0)',
                'message': 'Analysis Job Single Rarefaction\n'
                           f'{qiita_config.base_url}/analysis/description/1/\n'

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

@@ -71,7 +71,6 @@ wetlab processing and we provide the following host references for your convenie
 - auto-detect adapters and `cow <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/205/GCA_000003205.6_Btau_5.0.1/GCA_000003205.6_Btau_5.0.1_genomic.fna.gz>`_ + phix filtering
 - auto-detect adapters and `hamster <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/639/785/GCF_017639785.1_BCM_Maur_2.0/GCF_017639785.1_BCM_Maur_2.0_genomic.fna.gz>`_ + phix filtering
 - auto-detect adapters and `horse <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/305/GCA_000002305.1_EquCab2.0/GCA_000002305.1_EquCab2.0_genomic.fna.gz>`_ + phix filtering
-- auto-detect adapters and merge_genomes + phix filtering : is the combined genomes of a cheetah, cow, hamster, horse, human, mouse, pig, rabbit, and rat
 - auto-detect adapters and `mouse <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.fna.gz>`_ + phix filtering
 - auto-detect adapters and `pig <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz>`_ + phix filtering
 - auto-detect adapters and `rabbit <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/625/GCF_000003625.3_OryCun2.0/GCF_000003625.3_OryCun2.0_genomic.fna.gz>`_ + phix filtering