Merge pull request #370 from EBI-Metagenomics/develop

Develop

emgapi/models.py

@@ -1702,7 +1702,6 @@ def available(self, request=None):
         """
         query_filters = {
             "all": [
-                Q(study__is_suppressed=False),
                 Q(study__is_private=False),
                 Q(run__is_private=False) | Q(assembly__is_private=False),
                 Q(is_suppressed=False),

emgapianns/management/commands/import_extra_run_annotations.py

@@ -7,7 +7,7 @@
 from django.core.management import BaseCommand
 
 logger = logging.getLogger(__name__)
-
+import re
 
 class Command(BaseCommand):
     help = "Imports a directory of GFFs that as 'extra run annotations', " \
@@ -61,15 +61,15 @@ def handle(self, *args, **options):
             logger.info('Looking for RO Crates (.zips')
             for file in Path(self.gffs_dir).glob('**/*.zip'):
                 logger.info(f'Handling RO Crate Zip file {file}')
-                # erz = 'ERZ' + file.name.split('ERZ')[1].strip('.zip')
                 logger.info('this is the FILE NAME ' +  file.name)
-                srr = 'SRR' + file.name.split('SRR')[1].strip('.zip')
+                accession_prefix = re.search(r'[A-Z]{3}\d+', file.name)
+                accession_prefix = accession_prefix.group().strip()
                 try:
-                    run = emg_models.Run.objects.get(accession=srr)
+                    run = emg_models.Run.objects.get(accession=accession_prefix)
                 except emg_models.Run.DoesNotExist:
-                    logger.warning(f'No Run found for RO Crate apparent ERZ {srr}')
+                    logger.warning(f'No Run found for RO Crate  {accession_prefix}')
                     continue
-                logger.info(f'Will upload RO Crate for {srr}')
+                logger.info(f'Will upload RO Crate for {accession_prefix}')
                 self.upload_rocrate(run, gffs_directory, file.name)
 
     def upload_rocrate(

emgcli/__init__.py

@@ -1 +1 @@
-__version__: str = "2.4.49"
+__version__: str = "2.4.50"

pyproject.toml

@@ -117,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.49"
+current_version = "2.4.50"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"