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antgonzaantgonza
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fix tests
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‎CHANGELOG.md

+2-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,8 @@ Version 2023.06
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* Admin Sample Validation now uses tube_id; mainly contributed by @CatFish47.
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* Registered users cannot start sample deletion jobs within public studies.
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* The qp-knight-lab-processing now links the SPP job to the preparation it creates and links the created files to that preparation. Note that no files are being moved to the upload folder.
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* Fixed the following issues [#3227](https://github.com/qiita-spots/qiita/issues/3227), [#3279](https://github.com/qiita-spots/qiita/issues/3279).
11+
* Fixed the following issues [#3227](https://github.com/qiita-spots/qiita/issues/3227), [#3279](https://github.com/qiita-spots/qiita/issues/3280), [#3227](https://github.com/qiita-spots/qiita/issues/3280).
12+
* Added ProcessingJob.external_id to status-report messages generated, and added sending an email to our system-admin when a (wet-lab) admin job errors.
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Version 2023.05

‎qiita_db/processing_job.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -759,7 +759,7 @@ def _generate_notification_message(self, value, error_msg):
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study_id = study_ids.pop()
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761761
# there should be at least one prep_id and probably more.
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prep_ids = set(prep_ids)
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prep_ids = list(set(prep_ids))
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if len(prep_ids) == 0:
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raise qdb.exceptions.QiitaError("No Prep IDs were "
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"found")
@@ -782,7 +782,7 @@ def _generate_notification_message(self, value, error_msg):
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f"{data_types}")
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data_type = data_types.pop()
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785-
message = f'Processing Job: {self.command.name}\n'
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message = f'{self.command.name}\n'
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message += f'Prep IDs: {prep_ids}\n'
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message += f'{study_url}\n'
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message += f'Data Type: {data_type}\n'

‎qiita_db/test/test_processing_job.py

+23-26
Original file line numberDiff line numberDiff line change
@@ -870,50 +870,47 @@ def test_notification_mail_generation(self):
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# messages of type 'error'.
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obs = self.tester1._generate_notification_message('error', None)
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873-
exp = {'subject': ('Split libraries FASTQ: error '
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'(063e553b-327c-4818-ab4a-adfe58e49860)'),
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'message': ('Processing Job: Split libraries FASTQ\n'
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f'{qiita_config.base_url}/study/description/1'
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'\nPrep IDs: 1\nData Type: 18S\nNew '
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'status: error')}
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exp = {'subject': ('Split libraries FASTQ: error, 063e553b-327c-4818-'
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'ab4a-adfe58e49860 [Not Available]'),
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'message': ('Split libraries FASTQ\nPrep IDs: 1'
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f'\n{qiita_config.base_url}/study/description/1?'
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'prep_id=1\nData Type: 18S\nNew status: error')}
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self.assertDictEqual(obs, exp)
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obs = self.tester1._generate_notification_message('error',
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'An Error Message')
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exp = {'subject': ('Split libraries FASTQ: error '
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'(063e553b-327c-4818-ab4a-adfe58e49860)'),
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'message': ('Processing Job: Split libraries FASTQ\n'
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f'{qiita_config.base_url}/study/description/1\n'
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'Prep IDs: 1\nData Type: 18S\nNew status'
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': error\n\nError:\nAn Error Message')}
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exp = {'subject': ('Split libraries FASTQ: error, 063e553b-327c-4818-'
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'ab4a-adfe58e49860 [Not Available]'),
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'message': ('Split libraries FASTQ\nPrep IDs: 1'
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f'\n{qiita_config.base_url}/study/description/1?'
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'prep_id=1\nData Type: 18S\nNew status: error'
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'\n\nError:\nAn Error Message')}
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self.assertDictEqual(obs, exp)
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# The inclusion of an error message has no effect on other valid
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# status types e.g. 'running'.
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obs = self.tester1._generate_notification_message('running', None)
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exp = {'subject': ('Split libraries FASTQ: running '
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'(063e553b-327c-4818-ab4a-adfe58e49860)'),
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'message': ('Processing Job: Split libraries FASTQ\n'
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f'{qiita_config.base_url}/study/description/1\n'
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'Prep IDs: 1\nData Type: 18S\nNew status'
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': running')}
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exp = {'subject': ('Split libraries FASTQ: running, 063e553b-327c-'
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'4818-ab4a-adfe58e49860 [Not Available]'),
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'message': ('Split libraries FASTQ\nPrep IDs: 1'
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f'\n{qiita_config.base_url}/study/description/1?'
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'prep_id=1\nData Type: 18S\nNew status: running')}
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self.assertDictEqual(obs, exp)
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902900
obs = self.tester1._generate_notification_message('running', 'Yahoo!')
903-
exp = {'subject': ('Split libraries FASTQ: running '
904-
'(063e553b-327c-4818-ab4a-adfe58e49860)'),
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'message': ('Processing Job: Split libraries FASTQ\n'
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f'{qiita_config.base_url}/study/description/1\n'
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'Prep IDs: 1\nData Type: 18S\nNew status'
908-
': running')}
901+
exp = {'subject': ('Split libraries FASTQ: running, 063e553b-327c-'
902+
'4818-ab4a-adfe58e49860 [Not Available]'),
903+
'message': ('Split libraries FASTQ\nPrep IDs: 1'
904+
f'\n{qiita_config.base_url}/study/description/1?'
905+
'prep_id=1\nData Type: 18S\nNew status: running')}
909906
self.assertDictEqual(obs, exp)
910907

911908
# checking analysis emails
912909
jid = '8a7a8461-e8a1-4b4e-a428-1bc2f4d3ebd0'
913910
pj = qdb.processing_job.ProcessingJob(jid)
914911
obs = pj._generate_notification_message('running', 'Yahoo!')
915-
exp = {'subject': 'Single Rarefaction: running '
916-
'(8a7a8461-e8a1-4b4e-a428-1bc2f4d3ebd0)',
912+
exp = {'subject': ('Single Rarefaction: running, 8a7a8461-e8a1-'
913+
'4b4e-a428-1bc2f4d3ebd0 [Not Available]'),
917914
'message': 'Analysis Job Single Rarefaction\n'
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f'{qiita_config.base_url}/analysis/description/1/\n'
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'New status: running'}

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