cnr-ibba /
IMAGE-InjectTool
| @@ 23-102 (lines=80) @@ | ||
| 20 | logger = get_task_logger(__name__) |
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| 21 | ||
| 22 | ||
| 23 | class BatchDeleteAnimals(MyTask): |
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| 24 | name = "Batch delete animals" |
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| 25 | description = """Batch remove animals and associated samples""" |
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| 26 | ||
| 27 | # Ovverride default on failure method |
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| 28 | # This is not a failed validation for a wrong value, this is an |
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| 29 | # error in task that mean an error in coding |
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| 30 | def on_failure(self, exc, task_id, args, kwargs, einfo): |
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| 31 | logger.error('{0!r} failed: {1!r}'.format(task_id, exc)) |
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| 32 | ||
| 33 | # get submission object |
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| 34 | submission_obj = Submission.objects.get(pk=args[0]) |
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| 35 | ||
| 36 | # mark submission with ERROR |
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| 37 | submission_obj.status = ERROR |
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| 38 | submission_obj.message = ("Error in batch delete for animals: %s" |
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| 39 | % (str(exc))) |
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| 40 | submission_obj.save() |
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| 41 | ||
| 42 | send_message(submission_obj) |
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| 43 | ||
| 44 | # send a mail to the user with the stacktrace (einfo) |
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| 45 | submission_obj.owner.email_user( |
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| 46 | "Error in batch delete for animals: %s" % (args[0]), |
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| 47 | ("Something goes wrong in batch delete for animals. Please report " |
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| 48 | "this to InjectTool team\n\n %s" % str(einfo)), |
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| 49 | ) |
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| 50 | ||
| 51 | # TODO: submit mail to admin |
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| 52 | ||
| 53 | def run(self, submission_id, animal_ids): |
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| 54 | """Function for batch update attribute in animals |
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| 55 | Args: |
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| 56 | submission_id (int): id of submission |
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| 57 | animal_ids (list): set with ids to delete |
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| 58 | """ |
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| 59 | ||
| 60 | logger.info("Start batch delete for animals") |
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| 61 | success_ids = list() |
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| 62 | failed_ids = list() |
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| 63 | for animal_id in animal_ids: |
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| 64 | try: |
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| 65 | name = Name.objects.get(name=animal_id) |
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| 66 | animal_object = Animal.objects.get(name=name) |
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| 67 | samples = animal_object.sample_set.all() |
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| 68 | with transaction.atomic(): |
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| 69 | for sample in samples: |
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| 70 | sample_name = sample.name |
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| 71 | sample.delete() |
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| 72 | sample_name.delete() |
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| 73 | name.mother_of.clear() |
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| 74 | name.father_of.clear() |
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| 75 | animal_object.delete() |
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| 76 | name.delete() |
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| 77 | success_ids.append(animal_id) |
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| 78 | except Name.DoesNotExist: |
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| 79 | failed_ids.append(animal_id) |
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| 80 | except Animal.DoesNotExist: |
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| 81 | failed_ids.append(animal_id) |
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| 82 | # Update submission |
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| 83 | submission_obj = Submission.objects.get(pk=submission_id) |
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| 84 | submission_obj.status = NEED_REVISION |
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| 85 | if len(failed_ids) != 0: |
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| 86 | submission_obj.message = f"You've removed {len(success_ids)} " \ |
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| 87 | f"animals. It wasn't possible to find records with these ids: " \ |
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| 88 | f"{', '.join(failed_ids)}. Rerun validation please!" |
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| 89 | else: |
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| 90 | submission_obj.message = f"You've removed {len(success_ids)} " \ |
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| 91 | f"animals. Rerun validation please!" |
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| 92 | submission_obj.save() |
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| 93 | ||
| 94 | summary_obj, created = ValidationSummary.objects.get_or_create( |
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| 95 | submission=submission_obj, type='animal') |
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| 96 | summary_obj.reset_all_count() |
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| 97 | ||
| 98 | send_message( |
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| 99 | submission_obj, construct_validation_message(submission_obj) |
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| 100 | ) |
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| 101 | ||
| 102 | return 'success' |
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| 103 | ||
| 104 | ||
| 105 | # register explicitly tasks |
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| @@ 23-95 (lines=73) @@ | ||
| 20 | logger = get_task_logger(__name__) |
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| 21 | ||
| 22 | ||
| 23 | class BatchDeleteSamples(MyTask): |
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| 24 | name = "Batch delete samples" |
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| 25 | description = """Batch remove samples""" |
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| 26 | ||
| 27 | # Ovverride default on failure method |
|
| 28 | # This is not a failed validation for a wrong value, this is an |
|
| 29 | # error in task that mean an error in coding |
|
| 30 | def on_failure(self, exc, task_id, args, kwargs, einfo): |
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| 31 | logger.error('{0!r} failed: {1!r}'.format(task_id, exc)) |
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| 32 | ||
| 33 | # get submission object |
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| 34 | submission_obj = Submission.objects.get(pk=args[0]) |
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| 35 | ||
| 36 | # mark submission with ERROR |
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| 37 | submission_obj.status = ERROR |
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| 38 | submission_obj.message = ("Error in batch delete for samples: %s" |
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| 39 | % (str(exc))) |
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| 40 | submission_obj.save() |
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| 41 | ||
| 42 | send_message(submission_obj) |
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| 43 | ||
| 44 | # send a mail to the user with the stacktrace (einfo) |
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| 45 | submission_obj.owner.email_user( |
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| 46 | "Error in batch delete for samples: %s" % (args[0]), |
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| 47 | ("Something goes wrong in batch delete for samples. Please report " |
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| 48 | "this to InjectTool team\n\n %s" % str(einfo)), |
|
| 49 | ) |
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| 50 | ||
| 51 | # TODO: submit mail to admin |
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| 52 | ||
| 53 | def run(self, submission_id, sample_ids): |
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| 54 | """Function for batch update attribute in animals |
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| 55 | Args: |
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| 56 | submission_id (int): id of submission |
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| 57 | sample_ids (list): set with ids to delete |
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| 58 | """ |
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| 59 | ||
| 60 | logger.info("Start batch delete for samples") |
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| 61 | success_ids = list() |
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| 62 | failed_ids = list() |
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| 63 | for sample_id in sample_ids: |
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| 64 | try: |
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| 65 | name = Name.objects.get(name=sample_id) |
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| 66 | object = Sample.objects.get(name=name) |
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| 67 | with transaction.atomic(): |
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| 68 | object.delete() |
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| 69 | name.delete() |
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| 70 | success_ids.append(sample_id) |
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| 71 | except Name.DoesNotExist: |
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| 72 | failed_ids.append(sample_id) |
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| 73 | except Sample.DoesNotExist: |
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| 74 | failed_ids.append(sample_id) |
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| 75 | # Update submission |
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| 76 | submission_obj = Submission.objects.get(pk=submission_id) |
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| 77 | submission_obj.status = NEED_REVISION |
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| 78 | if len(failed_ids) != 0: |
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| 79 | submission_obj.message = f"You've removed {len(success_ids)} " \ |
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| 80 | f"samples. It wasn't possible to find records with these ids:" \ |
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| 81 | f" {', '.join(failed_ids)}. Rerun validation please!" |
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| 82 | else: |
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| 83 | submission_obj.message = f"You've removed {len(success_ids)} " \ |
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| 84 | f"samples. Rerun validation please!" |
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| 85 | submission_obj.save() |
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| 86 | ||
| 87 | summary_obj, created = ValidationSummary.objects.get_or_create( |
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| 88 | submission=submission_obj, type='sample') |
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| 89 | summary_obj.reset_all_count() |
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| 90 | ||
| 91 | send_message( |
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| 92 | submission_obj, construct_validation_message(submission_obj) |
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| 93 | ) |
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| 94 | ||
| 95 | return 'success' |
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| 96 | ||
| 97 | ||
| 98 | # register explicitly tasks |
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