[pull] master from PGScatalog:master

curation/imports/curation.py

@@ -150,7 +150,11 @@ def run_curation_import(self):
                         self.failed_studies[study_import.study_name] = 'curation tracker error'
 
                 if curation_pub != None:
-                    curation_pub.curation_status = 'Imported - Awaiting Release'
+                    curation_pub.pgp_id = study_import.study_publication.id
+                    if study_import.study_publication.curation_status == 'E':
+                        curation_pub.curation_status = 'Embargo Imported - Awaiting Publication'
+                    else:
+                        curation_pub.curation_status = 'Imported - Awaiting Release'
                     curation_pub.save()
                     print("  > Curation status updated in the Curation Tracker")
 

curation_tracker/admin.py

@@ -448,7 +448,7 @@ def save_model(self, request, obj, form, change):
 
             # Desembargo the study
             if obj.embargoed == False and (not db_obj or db_obj.embargoed == True):
-                if obj.curation_status == 'Embargo Imported - Awaiting Release':
+                if obj.curation_status == 'Embargo Imported - Awaiting Publication':
                     if obj.doi or obj.PMID:
                         obj.curation_status = 'Imported - Awaiting Release'
                 elif obj.curation_status == 'Embargo Curated - Awaiting Import':
@@ -465,7 +465,7 @@ def save_model(self, request, obj, form, change):
                 if obj.curation_status == 'Curated - Awaiting Import':
                     obj.curation_status = 'Embargo Curated - Awaiting Import'
                 elif obj.curation_status == 'Imported - Awaiting Release':
-                    obj.curation_status == 'Embargo Imported - Awaiting Release'
+                    obj.curation_status = 'Embargo Imported - Awaiting Publication'
 
             # Eligibility - part 2
             if obj.curation_status == 'Abandoned/Ineligible':

curation_tracker/litsuggest.py

@@ -10,6 +10,7 @@
 pgs_db = 'default'
 curation_tracker_db = 'curation_tracker'
 
+
 class CurationPublicationAnnotationImport():
     """Wrapper class for CurationPublicationAnnotation for providing additional transient attributes"""
     error: str
@@ -18,7 +19,7 @@ class CurationPublicationAnnotationImport():
     triage_info: dict
 
     def __init__(self, model: CurationPublicationAnnotation = CurationPublicationAnnotation()):
-        self.annotation = model# if model else CurationPublicationAnnotation()
+        self.annotation = model  # if model else CurationPublicationAnnotation()
         self.error = None
         self.skip_reason = None
         self.triage_info = {}
@@ -32,34 +33,37 @@ def to_dict(self) -> dict:
     def is_valid(self) -> bool:
         """Should be used before saving"""
         return self.error == None
-    
+
     def is_importable(self) -> bool:
         return self.skip_reason == None
-    
+
     def __next_id_number(self) -> int:
         assigned = 1
         if len(CurationPublicationAnnotation.objects.using(curation_tracker_db).all()) != 0:
             assigned = CurationPublicationAnnotation.objects.using(curation_tracker_db).latest().pk + 1
         return assigned
-    
+
     def save(self, *args, **kwargs) -> None:
         """Set the identifiers and save the contained CurationPublicationAnnotation object"""
         annotation = self.annotation
         if annotation.num == None:
             annotation.set_annotation_ids(self.__next_id_number())
         return annotation.save(*args, **kwargs)
 
+
 class ImportException(Exception):
     pass
 
+
 def get_pgs_publication(pmid):
     publication = None
     try:
-           publication = Publication.objects.get(PMID=pmid)
+        publication = Publication.objects.get(PMID=pmid)
     except Publication.DoesNotExist:
-           publication = None
+        publication = None
     return publication
 
+
 def assert_study_doesnt_exist(pmid):
     """
     Checks if the study is already present as a Publication or CurationPublicationAnnotation. If yes, throws an ImportException.
@@ -68,7 +72,7 @@ def assert_study_doesnt_exist(pmid):
         raise ImportException(f'Study {pmid} already exists in the PGS Catalog database')
     if CurationPublicationAnnotation.objects.using(curation_tracker_db).filter(PMID=pmid).exists():
         raise ImportException(f'Study annotation {pmid} already exists in the Curation Tracker database')
-    
+
 
 def get_publication_info_from_epmc(pmid) -> dict:
     payload = {'format': 'json'}
@@ -90,6 +94,7 @@ def get_publication_info_from_epmc(pmid) -> dict:
         raise ImportException("This pubmed ID returned no result")
     return info
 
+
 def get_publication_info_from_epmc_doi(doi) -> dict:
     payload = {'format': 'json'}
     query = f'doi:{doi}'
@@ -110,9 +115,11 @@ def get_publication_info_from_epmc_doi(doi) -> dict:
         raise ImportException("This DOI returned no result")
     return info
 
+
 def get_next_unique_study_name(study_name):
     unique_name = study_name
-    for existing_study_name in CurationPublicationAnnotation.objects.using(curation_tracker_db).filter(study_name__startswith=study_name):
+    for existing_study_name in CurationPublicationAnnotation.objects.using(curation_tracker_db).filter(
+            study_name__startswith=study_name):
         name_elements = existing_study_name.split('_')
         name_stub = name_elements[0]
         name_index = 0
@@ -121,40 +128,45 @@ def get_next_unique_study_name(study_name):
             if last_element.isnumeric():
                 name_index = int(last_element)
         name_index += 1
-        unique_name = name_stub+'_'+name_index
+        unique_name = name_stub + '_' + name_index
 
     return unique_name
 
+
 def create_new_annotation(publication_info) -> CurationPublicationAnnotation:
     model = CurationPublicationAnnotation()
-    for attr in ['PMID','journal','doi','title','year','publication_date']:
-        value = publication_info.get(attr, None) 
+    for attr in ['PMID', 'journal', 'doi', 'title', 'year', 'publication_date']:
+        value = publication_info.get(attr, None)
         setattr(model, attr, value)
 
-    authors = publication_info.get('authors',None)
+    authors = publication_info.get('authors', None)
     if authors is None:
-        authors = 'NoAuthor N' # last char so the string has the same format as a regular authors string
+        authors = 'NoAuthor N'  # last char so the string has the same format as a regular authors string
+
+    model.study_name = '-'.join(authors.split(',')[0].split(' ')[:-1]) \
+                       + publication_info.get('year', 'NoDate')
 
-    model.study_name = '-'.join(authors.split(',')[0].split(' ')[:-1])\
-          + publication_info.get('year','NoDate')
-
     return model
 
+
 def annotation_import_to_dict(annotation_import: CurationPublicationAnnotationImport) -> dict:
     d = dict()
-    for attr in ['error','skip_reason']:
-        d[attr] = getattr(annotation_import,attr)
+    for attr in ['error', 'skip_reason']:
+        d[attr] = getattr(annotation_import, attr)
     d['model'] = annotation_to_dict(annotation_import.annotation)
     return d
 
+
 def annotation_to_dict(model: CurationPublicationAnnotation) -> dict:
     model_dict = dict()
-    for attr in ['PMID','study_name','doi','journal','title','year','eligibility','comment',
-                 'eligibility_dev_score','eligibility_eval_score','eligibility_description','first_level_curation_status','curation_status',
+    for attr in ['PMID', 'study_name', 'doi', 'journal', 'title', 'year', 'eligibility', 'comment',
+                 'eligibility_dev_score', 'eligibility_eval_score', 'eligibility_description',
+                 'first_level_curation_status', 'curation_status',
                  'publication_date']:
-        model_dict[attr] = getattr(model,attr)
+        model_dict[attr] = getattr(model, attr)
     return model_dict
 
+
 def dict_to_annotation_import(d: dict) -> CurationPublicationAnnotationImport:
     model = CurationPublicationAnnotation()
     model_import = CurationPublicationAnnotationImport()
@@ -166,15 +178,17 @@ def dict_to_annotation_import(d: dict) -> CurationPublicationAnnotationImport:
         del d['skip_reason']
     model_dict = d['model']
     for k in model_dict.keys():
-        setattr(model,k,model_dict[k])
+        setattr(model, k, model_dict[k])
     model_import.annotation = model
     return model_import
 
-def check_study_name(study_name: str) -> str:
-    ''' Check that the study_name is unique. Otherwise it will add incremental number as suffix '''
+
+def check_study_name(study_name: str, imported_study_names: list[str]) -> str:
+    """ Check that the study_name is unique. Otherwise, it will add incremental number as suffix """
     queryset = CurationPublicationAnnotation.objects.using(curation_tracker_db).filter(study_name=study_name).count()
     if queryset:
-        sn_list = CurationPublicationAnnotation.objects.using(curation_tracker_db).values_list('study_name',flat=True)
+        sn_list = imported_study_names + list(
+            CurationPublicationAnnotation.objects.using(curation_tracker_db).values_list('study_name', flat=True))
         num = 2
         new_study_name = f'{study_name}_{num}'
         while new_study_name in sn_list:
@@ -183,12 +197,14 @@ def check_study_name(study_name: str) -> str:
         study_name = new_study_name
     return study_name
 
+
 def _litsuggest_IO_to_annotation_imports(litsuggest_file) -> List[CurationPublicationAnnotationImport]:
     models = []
     reader = csv.DictReader(litsuggest_file, delimiter='\t')
+    imported_study_names = []
     for row in reader:
         if not row['pmid']:
-            break # litsuggest files might contain a lot of empty rows after the relevant ones
+            break  # litsuggest files might contain a lot of empty rows after the relevant ones
         pmid = str(int(row['pmid']))
         try:
             triage_decision = row['triage.decision']
@@ -198,7 +214,9 @@ def _litsuggest_IO_to_annotation_imports(litsuggest_file) -> List[CurationPublic
             assert_study_doesnt_exist(pmid)
             study_epmc_info = get_publication_info_from_epmc(pmid)
             annotationModel = create_new_annotation(study_epmc_info)
-            annotationModel.study_name = check_study_name(annotationModel.study_name)
+            study_name = check_study_name(annotationModel.study_name, imported_study_names)
+            annotationModel.study_name = study_name
+            imported_study_names.append(study_name)
 
             triage_note = row['triage.note']
             annotationModel.eligibility_description = triage_note
@@ -219,7 +237,7 @@ def _litsuggest_IO_to_annotation_imports(litsuggest_file) -> List[CurationPublic
                         annotationModel.first_level_curation_status = 'Contact author'
                     annotationModel.curation_status = 'Awaiting L1'
                 case 'TBD':
-                    #annotationModel.eligibility = True
+                    # annotationModel.eligibility = True
                     annotationModel.first_level_curation_status = 'Awaiting access'
                 case 'PGS Relevant':
                     annotationModel.eligibility = False
@@ -236,7 +254,7 @@ def _litsuggest_IO_to_annotation_imports(litsuggest_file) -> List[CurationPublic
                     annotationModel.eligibility_eval_score = 'y'
                 case _:
                     raise ImportException(f'Unexpected triage decision: {triage_decision}')
-                
+
             models.append(annotation_import)
         except ImportException as e:
             annotation_import = CurationPublicationAnnotationImport(CurationPublicationAnnotation())
@@ -246,10 +264,12 @@ def _litsuggest_IO_to_annotation_imports(litsuggest_file) -> List[CurationPublic
 
     return models
 
+
 def litsuggest_filename_to_annotation_imports(litsuggest_file_name: str) -> List[CurationPublicationAnnotationImport]:
     with open(litsuggest_file_name, 'r') as litsuggest_file:
         return _litsuggest_IO_to_annotation_imports(litsuggest_file)
-
+
+
 def litsuggest_fileupload_to_annotation_imports(litsuggest_file_upload: InMemoryUploadedFile) -> List[CurationPublicationAnnotationImport]:
     file_wrapper = TextIOWrapper(litsuggest_file_upload.file)
-    return _litsuggest_IO_to_annotation_imports(file_wrapper)
+    return _litsuggest_IO_to_annotation_imports(file_wrapper)

curation_tracker/migrations/0005_alter_curationpublicationannotation_curation_status.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.10 on 2024-04-19 14:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('curation_tracker', '0004_emailtemplate'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='curationpublicationannotation',
+            name='curation_status',
+            field=models.CharField(blank=True, choices=[('Abandoned/Ineligible', 'Abandoned/Ineligible'), ('Pending author response', 'Pending author response'), ('Awaiting L1', 'Awaiting L1'), ('Awaiting L2', 'Awaiting L2'), ('Curated - Awaiting Import', 'Curated - Awaiting Import'), ('Imported - Awaiting Release', 'Imported - Awaiting Release'), ('Released', 'Released'), ('Embargo Curated - Awaiting Import', 'Embargo Curated - Awaiting Import'), ('Embargo Imported - Awaiting Publication', 'Embargo Imported - Awaiting Publication'), ('Embargo Lifted - Awaiting Release', 'Embargo Lifted - Awaiting Release'), ('Retired', 'Retired')], default='Awaiting L1', max_length=50, null=True, verbose_name='Curation Status'),
+        ),
+    ]

curation_tracker/models.py

@@ -83,7 +83,7 @@ class CurationPublicationAnnotation(models.Model):
         ('Imported - Awaiting Release','Imported - Awaiting Release'),
         ('Released','Released'),
         ('Embargo Curated - Awaiting Import','Embargo Curated - Awaiting Import'),
-        ('Embargo Imported - Awaiting Release','Embargo Imported - Awaiting Release'),
+        ('Embargo Imported - Awaiting Publication','Embargo Imported - Awaiting Publication'),
         ('Embargo Lifted - Awaiting Release','Embargo Lifted - Awaiting Release'),
         ('Retired','Retired')
     ]

curation_tracker/scripts/import_litsuggest.py

@@ -3,6 +3,7 @@
 
 litsuggest_dir = '/home/florent/PGS_Catalog/Curation/Litsuggest/'
 
+
 def run():
 
     files = [f for f in os.listdir(litsuggest_dir) if os.path.isfile(f'{litsuggest_dir}/{f}')]

curation_tracker/views.py

@@ -37,10 +37,10 @@ def browse_release_ready(request):
         import_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Curated - Awaiting Import')
         context['table_to_import'] = Browse_CurationPublicationAnnotationReleaseReady(import_ready)
 
-    release_ready_count = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Imported - Awaiting Release').count()
+    release_ready_count = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status__in=('Imported - Awaiting Release', 'Embargo Lifted - Awaiting Release')).count()
     context['studies_to_release_count'] = release_ready_count
     if release_ready_count:
-        release_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Imported - Awaiting Release')
+        release_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status__in=('Imported - Awaiting Release', 'Embargo Lifted - Awaiting Release'))
         context['table_to_release'] = Browse_CurationPublicationAnnotationReleaseReady(release_ready)
 
     if context:

release/scripts/run_release_script.py

@@ -205,7 +205,7 @@ def update_curation_tracker():
                 curation_pub.pgp_id = pgp_id
                 print('  - Updating curation_status on the Curation Tracker')
                 if publication.curation_status == 'E':
-                    curation_pub.curation_status = 'Embargo Imported - Awaiting Release'
+                    curation_pub.curation_status = 'Embargo Imported - Awaiting Publication'
                 else:
                     curation_pub.curation_status = 'Released'
                     curation_pub.release_date = new_release_date