refactor SampleSheetTableBuilder init (#1509)

irodsadmin/management/commands/irodsorphans.py

@@ -21,6 +21,7 @@
 
 
 logger = ManagementCommandLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 
 
 def get_assay_collections(assays, irods_backend):
@@ -30,12 +31,10 @@ def get_assay_collections(assays, irods_backend):
 
 def get_assay_subcollections(studies, irods_backend):
     """Return a list of all assay row colletion names."""
-    tb = SampleSheetTableBuilder()
     collections = []
-
     for study in studies:
         try:
-            study_tables = tb.get_study_tables(study)
+            study_tables = table_builder.get_study_tables(study)
         except Exception as ex:
             logger.error(
                 'Study table building exception for "{}" '
@@ -60,7 +59,6 @@ def get_assay_subcollections(studies, irods_backend):
                     )
                     if row_path not in collections:
                         collections.append(row_path)
-
                 shortcuts = assay_plugin.get_shortcuts(assay)
                 if shortcuts:
                     for shortcut in shortcuts:
@@ -70,7 +68,6 @@ def get_assay_subcollections(studies, irods_backend):
                 collections.append(assay_path + '/' + TRACK_HUBS_COLL)
                 collections.append(assay_path + '/' + RESULTS_COLL)
                 collections.append(assay_path + '/' + MISC_FILES_COLL)
-
     return collections
 
 
@@ -154,7 +151,6 @@ def get_orphans(irods, irods_backend, expected, assays):
         ):
             if collection.path not in expected:
                 orphans.append(collection.path)
-
     return orphans
 
 
@@ -163,7 +159,6 @@ def get_output(orphans, irods_backend, irods):
     for orphan in orphans:
         stats = irods_backend.get_object_stats(irods, orphan)
         m = re.search(r'/projects/([^/]{2})/(\1[^/]+)', orphan)
-
         if m:
             uuid = m.group(2)
             try:
@@ -174,7 +169,6 @@ def get_output(orphans, irods_backend, irods):
         else:
             uuid = '<ERROR>'
             title = '<ERROR>'
-
         lines.append(
             ';'.join(
                 [

samplesheets/plugins.py

@@ -50,6 +50,7 @@
 
 app_settings = AppSettingAPI()
 logger = logging.getLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 
 
 # SODAR constants
@@ -898,7 +899,6 @@ def _update_cache_rows(self, app_name, name=None, project=None, user=None):
         if not cache_backend or not irods_backend:
             return
 
-        tb = SampleSheetTableBuilder()
         projects = (
             [project]
             if project
@@ -924,7 +924,7 @@ def _update_cache_rows(self, app_name, name=None, project=None, user=None):
 
         # Get assay paths
         for study in studies:
-            study_tables = tb.get_study_tables(study)
+            study_tables = table_builder.get_study_tables(study)
             for assay in [a for a in study.assays.all() if a in config_assays]:
                 assay_table = study_tables['assays'][str(assay.sodar_uuid)]
                 assay_path = irods_backend.get_path(assay)

samplesheets/sheet_config.py

@@ -15,6 +15,7 @@
 
 app_settings = AppSettingAPI()
 logger = logging.getLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 
 
 # Local constants
@@ -106,8 +107,7 @@ def get_sheet_config(self, investigation, inv_tables=None):
         if not sheet_ok:
             logger.info(msg)
             if not inv_tables:
-                tb = SampleSheetTableBuilder()
-                inv_tables = tb.build_inv_tables(
+                inv_tables = table_builder.build_inv_tables(
                     investigation, use_config=False
                 )
             sheet_config = self.build_sheet_config(investigation, inv_tables)

samplesheets/studyapps/cancer/plugins.py

@@ -23,12 +23,12 @@
 
 
 logger = logging.getLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 User = auth.get_user_model()
 
 
 # SODAR constants
 PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
-
 # Local constants
 APP_NAME = 'samplesheets.studyapps.cancer'
 
@@ -268,7 +268,6 @@ def update_cache(self, name=None, project=None, user=None):
         if not cache_backend:
             return
 
-        tb = SampleSheetTableBuilder()
         projects = (
             [project]
             if project
@@ -301,7 +300,7 @@ def update_cache(self, name=None, project=None, user=None):
                 vcf_paths = {}
 
                 # Get/build render tables
-                study_tables = tb.get_study_tables(study)
+                study_tables = table_builder.get_study_tables(study)
                 for library in get_study_libraries(study, study_tables):
                     if not library.assay:
                         continue

samplesheets/studyapps/cancer/views.py

@@ -25,6 +25,9 @@
 from samplesheets.studyapps.cancer.utils import get_library_file_path
 
 
+table_builder = SampleSheetTableBuilder()
+
+
 class BaseCancerConfigView(
     LoginRequiredMixin,
     LoggedInPermissionMixin,
@@ -85,8 +88,7 @@ def get(self, request, *args, **kwargs):
             return redirect(self.redirect_url)
 
         # Get/build render tables
-        tb = SampleSheetTableBuilder()
-        study_tables = tb.get_study_tables(self.material.study)
+        study_tables = table_builder.get_study_tables(self.material.study)
         # Get libraries
         libraries = get_sample_libraries(samples, study_tables)
         bam_urls = {}

samplesheets/studyapps/germline/plugins.py

@@ -23,6 +23,7 @@
 )
 
 logger = logging.getLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 User = auth.get_user_model()
 
 
@@ -294,8 +295,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
         bam_paths = {}
         vcf_paths = {}
         # Get/build render tables
-        tb = SampleSheetTableBuilder()
-        study_tables = tb.get_study_tables(study)
+        study_tables = table_builder.get_study_tables(study)
 
         # Pre-fetch study objects to eliminate redundant queries
         obj_len = 0

samplesheets/studyapps/germline/views.py

@@ -26,6 +26,9 @@
 from sodar.users.auth import fallback_to_auth_basic
 
 
+table_builder = SampleSheetTableBuilder()
+
+
 class BaseGermlineConfigView(
     LoginRequiredMixin,
     LoggedInPermissionMixin,
@@ -64,10 +67,8 @@ def get(self, request, *args, **kwargs):
         if not settings.IRODS_WEBDAV_ENABLED or not settings.IRODS_WEBDAV_URL:
             messages.error(self.request, 'iRODS WebDAV not available')
             return redirect(self.redirect_url)
-
         # Get/build render tables
-        tb = SampleSheetTableBuilder()
-        self.study_tables = tb.get_study_tables(self.source.study)
+        self.study_tables = table_builder.get_study_tables(self.source.study)
 
 
 @fallback_to_auth_basic

samplesheets/views_api.py

@@ -46,6 +46,7 @@
 
 app_settings = AppSettingAPI()
 logger = logging.getLogger(__name__)
+table_builder = SampleSheetTableBuilder()
 
 
 MD5_RE = re.compile(r'([a-fA-F\d]{32})')
@@ -399,11 +400,10 @@ def get(self, request, **kwargs):
         # Rendered tables
         if not isa or int(isa) != 1:
             ret = {'studies': {}}
-            tb = SampleSheetTableBuilder()
             # Get/build study tables
             for study in investigation.studies.all():
                 try:
-                    tables = tb.get_study_tables(study)
+                    tables = table_builder.get_study_tables(study)
                 except Exception as ex:
                     return Response(str(ex), status=500)
                 ret['studies'][str(study.sodar_uuid)] = tables