Merge pull request #339 from EBI-Metagenomics/develop

Develop

emgapi/migrations/0012_alter_publication_pub_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.18 on 2023-11-08 09:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emgapi', '0011_analysisjob_analysis_summary_json'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='publication',
+            name='pub_type',
+            field=models.CharField(blank=True, db_column='PUB_TYPE', max_length=300, null=True),
+        ),
+    ]

emgapi/models.py

@@ -502,14 +502,25 @@ class Publication(models.Model):
         db_column='PUBLISHED_YEAR', blank=True, null=True,
         help_text='Published year')
     pub_type = models.CharField(
-        db_column='PUB_TYPE', max_length=150, blank=True, null=True)
+        db_column='PUB_TYPE', max_length=300, blank=True, null=True)
 
     objects = PublicationManager()
 
     class Meta:
         db_table = 'PUBLICATION'
         ordering = ('pubmed_id',)
 
+    def save(self, *args, **kwargs):
+        for field in self._meta.fields:
+            if isinstance(field, models.TextField) or isinstance(field, models.CharField):
+                field_name = field.name
+                max_length = field.max_length
+                field_value = getattr(self, field_name)
+                if field_value and len(field_value) > max_length:
+                    logger.error(f"Publication field {field_name} content was truncated at {max_length}")
+                    setattr(self, field_name, field_value[:max_length])
+        super(Publication, self).save(*args, **kwargs)
+
     def __str__(self):
         return str(self.pubmed_id)
 

emgapianns/management/commands/import_publication.py

@@ -16,7 +16,9 @@
 import logging
 from django.core.management import BaseCommand
 from emgapi import models as emg_models
-from emgapianns.management.lib.europe_pmc_api.europe_pmc_api_handler import EuropePMCApiHandler
+from emgapianns.management.lib.europe_pmc_api.europe_pmc_api_handler import (
+    EuropePMCApiHandler,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -29,15 +31,17 @@ def lookup_publication_by_pubmed_id(pubmed_id):
 def update_or_create_publication(publication):
     return emg_models.Publication.objects.update_or_create(
         pubmed_id=publication.pmid,
-        defaults={'authors': publication.author_string,
-                  'doi': publication.doi,
-                  'isbn': publication.journal_issn,
-                  'iso_journal': publication.journal_title,
-                  'pub_title': publication.title,
-                  'raw_pages': publication.page_info,
-                  'volume': publication.journal_volume,
-                  'published_year': publication.pub_year,
-                  'pub_type': publication.pub_type},
+        defaults={
+            "authors": publication.author_string,
+            "doi": publication.doi,
+            "isbn": publication.journal_issn,
+            "iso_journal": publication.journal_title,
+            "pub_title": publication.title,
+            "raw_pages": publication.page_info,
+            "volume": publication.journal_volume,
+            "published_year": publication.pub_year,
+            "pub_type": publication.pub_type,
+        },
     )
 
 
@@ -47,19 +51,18 @@ def lookup_publication_by_project_id(project_id):
 
 
 class Command(BaseCommand):
-    help = 'Creates or updates a publication in EMG.'
+    help = "Creates or updates a publication in EMG."
 
     def add_arguments(self, parser):
         # TODO: Consider lookup by project id
-        parser.add_argument('pubmed-id',
-                            help='PubMed identifier (PMID)',
-                            type=int,
-                            action='store')
+        parser.add_argument(
+            "pubmed-id", help="PubMed identifier (PMID)", type=int, action="store"
+        )
 
     def handle(self, *args, **options):
         logger.info("CLI %r" % options)
 
-        pubmed_id = options['pubmed-id']
+        pubmed_id = options["pubmed-id"]
         publications = lookup_publication_by_pubmed_id(pubmed_id)
         for publication in publications:
             update_or_create_publication(publication)

emgapianns/management/lib/europe_pmc_api/europe_pmc_api_handler.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2019-2022 EMBL - European Bioinformatics Institute
+# Copyright 2019-2023 EMBL - European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -34,7 +34,7 @@ def get_default_connection_headers():
     }
 
 
-class Publication(object):
+class Publication:
     def __init__(
         self,
         pub_year,

emgcli/__init__.py

@@ -1 +1 @@
-__version__: str = "2.4.34"
+__version__: str = "2.4.35"

emgena/serializers.py

@@ -81,18 +81,13 @@ def is_valid(self):
         return super().is_valid()
 
     def create(self, validated_data):
-        """Create an RT ticket.
-        If this is a consent approval then the procedure is:
-        - create ticket in ENA-MG queue
-        otherwise:
-        - create ticket in EMG queue
+        """Create an RT ticket in EMG queue
         Note: remember to setup valid credentials (i.e. url, user and token token) in the config.rt
         """
         import requests
         n = ena_models.Notify(**validated_data)
 
         emg_queue = settings.RT["emg_queue"]
-        ena_queue = settings.RT["ena_queue"]
 
         ticket = {
             "Requestor": n.from_email,
@@ -104,7 +99,7 @@ def create(self, validated_data):
             ticket["Cc"] = n.cc
 
         if n.is_consent:
-            ticket["Queue"] = ena_queue
+            return 404
         else:
             ticket["Queue"] = emg_queue
 

pyproject.toml

@@ -78,6 +78,7 @@ tests = [
     "pytest-cov==2.12.1",
     "pandas==1.3.2",
     "responses==0.23.1",
+    "Faker==19.6.2",
 ]
 
 dev = [
@@ -116,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.34"
+current_version = "2.4.35"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"

tests/webuploader/test_import_publication.py

@@ -16,28 +16,39 @@
 
 import pytest
 
-from emgapianns.management.commands.import_publication import lookup_publication_by_pubmed_id
-
-
-@pytest.mark.parametrize("pubmed_id, expected_pub_title, expected_year_of_pub, expected_authors, expected_doi", [
-    (4838818,
-     "Proceedings: The morphological variation of nervous structures in the atrial endocardium of the dog.",
-     1974,
-     "Floyd K, Linden RJ, Saunders DA.",
-     "n/a"),
-    (31138692,
-     "Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse "
-     "model of infant undernutrition.",
-     2019,
-     "Cowardin CA, Ahern PP, Kung VL, Hibberd MC, Cheng J, Guruge JL, Sundaresan V, Head RD, Barile D,"
-     " Mills DA, Barratt MJ, Huq S, Ahmed T, Gordon JI.",
-     "10.1073/pnas.1821770116")
-])
-def test_lookup_publication_by_pubmed_id_should_return(pubmed_id,
-                                                       expected_pub_title,
-                                                       expected_year_of_pub,
-                                                       expected_authors,
-                                                       expected_doi):
+from emgapi.models import Publication
+from model_bakery import baker
+
+
+from emgapianns.management.commands.import_publication import (
+    lookup_publication_by_pubmed_id,
+)
+
+
+@pytest.mark.parametrize(
+    "pubmed_id, expected_pub_title, expected_year_of_pub, expected_authors, expected_doi",
+    [
+        (
+            4838818,
+            "Proceedings: The morphological variation of nervous structures in the atrial endocardium of the dog.",
+            1974,
+            "Floyd K, Linden RJ, Saunders DA.",
+            "n/a",
+        ),
+        (
+            31138692,
+            "Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse "
+            "model of infant undernutrition.",
+            2019,
+            "Cowardin CA, Ahern PP, Kung VL, Hibberd MC, Cheng J, Guruge JL, Sundaresan V, Head RD, Barile D,"
+            " Mills DA, Barratt MJ, Huq S, Ahmed T, Gordon JI.",
+            "10.1073/pnas.1821770116",
+        ),
+    ],
+)
+def test_lookup_publication_by_pubmed_id_should_return(
+    pubmed_id, expected_pub_title, expected_year_of_pub, expected_authors, expected_doi
+):
     publications = lookup_publication_by_pubmed_id(pubmed_id)
     assert len(publications) == 1
 
@@ -49,18 +60,38 @@ def test_lookup_publication_by_pubmed_id_should_return(pubmed_id,
     assert publication.doi == expected_doi
 
 
-@pytest.mark.parametrize("pubmed_id", [
-    (0),
-    (000)
-])
+@pytest.mark.parametrize("pubmed_id", [(0), (000)])
 def test_lookup_publication_by_pubmed_id_(pubmed_id):
     with pytest.raises(ValueError):
         lookup_publication_by_pubmed_id(pubmed_id)
 
 
-@pytest.mark.parametrize("pubmed_id", [
-    ("test")
-])
+@pytest.mark.parametrize("pubmed_id", [("test")])
 def test_lookup_publication_by_pubmed_id_raises_exception_on_string(pubmed_id):
     with pytest.raises(TypeError):
         lookup_publication_by_pubmed_id(pubmed_id)
+
+
+@pytest.mark.django_db
+def test_text_fields_longer_than_expected(faker):
+    PUB_TITLE_MAX = 740
+    PUB_TYPE_MAX = 300
+    VOLUME_MAX = 55
+
+    # I've picked 3 fields as representatives
+    publications = baker.prepare(
+        Publication,
+        pub_title=faker.text(max_nb_chars=PUB_TITLE_MAX + 1000),
+        pub_type=faker.text(max_nb_chars=PUB_TYPE_MAX + 1000),
+        volume=faker.text(max_nb_chars=VOLUME_MAX + 1000),
+        _quantity=5,
+    )
+
+    for publication in publications:
+        assert len(publication.pub_title) > PUB_TITLE_MAX
+        assert len(publication.pub_type) > PUB_TYPE_MAX
+        assert len(publication.volume) > VOLUME_MAX
+        publication.save()
+        assert len(publication.pub_title) <= PUB_TITLE_MAX
+        assert len(publication.pub_type) <= PUB_TYPE_MAX
+        assert len(publication.volume) <= VOLUME_MAX

tests/webuploader/test_notify.py

@@ -70,42 +70,6 @@ def test_notify_not_consent(self):
             HTTP_AUTHORIZATION='Bearer {}'.format(self.get_token())
         )
 
-        assert len(responses.calls) == 1
-        call = responses.calls[0]
-        assert call.request.url == settings.RT["url"]
-        assert call.request.body == json.dumps(expected_body)
-
-    @responses.activate
-    @pytest.mark.skipif(sys.version_info < (3, 6), reason="requires python3.6 or higher")
-    def test_notify_consent(self):
-        """Test notify endpoint for consent requests
-        """
-        expected_body = {
-            "Requestor": "[email protected]",
-            "Priority": "4",
-            "Subject": "Test email subject",
-            "Content": "Hi this is just an example",
-            "Queue": settings.RT["ena_queue"],
-        }
-
-        responses.add(
-            responses.POST,
-            settings.RT["url"],
-            status=200)
-
-        post_data = {
-            "from_email": "[email protected]",
-            "subject": "Test email subject",
-            "message": "Hi this is just an example",
-            "is_consent": True
-        }
-
-        self.client.post(
-            reverse('emgapi_v1:csrf-notify'),
-            data=post_data, format='json',
-            HTTP_AUTHORIZATION='Bearer {}'.format(self.get_token())
-        )
-
         assert len(responses.calls) == 1
         call = responses.calls[0]
         assert call.request.url == settings.RT["url"]