Change db names

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20240418.1
+
+Removed dbname option from classes where it was not used. Renamed StatusDB database variables to attempt to standardize them.
+
 ## 20240410.1
 
 Expand test coverage by starting and checking demultiplexing for a NovaSeqXPlus run.

taca/analysis/analysis.py

@@ -110,7 +110,7 @@ def _upload_to_statusdb(run):
     """
     couch_conf = CONFIG["statusdb"]
     couch_connection = statusdb.StatusdbSession(couch_conf).connection
-    db = couch_connection[couch_conf["xten_db"]]
+    x_flowcells_db = couch_connection[couch_conf["xten_db"]]
     parser = run.runParserObj
     # Check if I have NoIndex lanes
     for element in parser.obj["samplesheet_csv"]:
@@ -155,7 +155,7 @@ def _upload_to_statusdb(run):
         parser.obj["DemultiplexConfig"] = {
             "Setup": {"Software": run.CONFIG.get("bcl2fastq", {})}
         }
-    statusdb.update_doc(db, parser.obj, over_write_db_entry=True)
+    statusdb.update_doc(x_flowcells_db, parser.obj, over_write_db_entry=True)
 
 
 def transfer_run(run_dir, software):

taca/backup/backup.py

@@ -265,12 +265,14 @@ def _log_pdc_statusdb(self, run):
                 run_date = run_vals[0]
             run_fc = f"{run_date}_{run_vals[-1]}"
             couch_connection = statusdb.StatusdbSession(self.couch_info).connection
-            db = couch_connection[self.couch_info["db"]]
-            fc_names = {e.key: e.id for e in db.view("names/name", reduce=False)}
+            x_flowcells_db = couch_connection[self.couch_info["db"]]
+            fc_names = {
+                e.key: e.id for e in x_flowcells_db.view("names/name", reduce=False)
+            }
             d_id = fc_names[run_fc]
-            doc = db.get(d_id)
+            doc = x_flowcells_db.get(d_id)
             doc["pdc_archived"] = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
-            db.save(doc)
+            x_flowcells_db.save(doc)
             logger.info(
                 f'Logged "pdc_archived" timestamp for fc {run} in statusdb doc "{d_id}"'
             )

taca/utils/bioinfo_tab.py

@@ -55,8 +55,8 @@ def update_statusdb(run_dir):
     statusdb_conf = CONFIG.get("statusdb")
     couch_connection = statusdb.StatusdbSession(statusdb_conf).connection
     valueskey = datetime.datetime.now().isoformat()
-    db = couch_connection["bioinfo_analysis"]
-    view = db.view("latest_data/sample_id")
+    bioinfo_db = couch_connection["bioinfo_analysis"]
+    view = bioinfo_db.view("latest_data/sample_id")
     # Construction and sending of individual records, if samplesheet is incorrectly formatted the loop is skipped
     if project_info:
         for flowcell in project_info:
@@ -87,8 +87,8 @@ def update_statusdb(run_dir):
                         if len(view[[project, run_id, lane, sample]].rows) >= 1:
                             remote_id = view[[project, run_id, lane, sample]].rows[0].id
                             lane = str(lane)
-                            remote_doc = db[remote_id]["values"]
-                            remote_status = db[remote_id]["status"]
+                            remote_doc = bioinfo_db[remote_id]["values"]
+                            remote_status = bioinfo_db[remote_id]["status"]
                             # Only updates the listed statuses
                             if (
                                 remote_status
@@ -110,16 +110,16 @@ def update_statusdb(run_dir):
                                     )
                                 )
                                 # Update record cluster
-                                obj["_rev"] = db[remote_id].rev
+                                obj["_rev"] = bioinfo_db[remote_id].rev
                                 obj["_id"] = remote_id
-                                db.save(obj)
+                                bioinfo_db.save(obj)
                         # Creates new entry
                         else:
                             logger.info(
                                 f"Creating {run_id} {project} {flowcell} {lane} {sample} as {sample_status}"
                             )
                             # Creates record
-                            db.save(obj)
+                            bioinfo_db.save(obj)
                         # Sets FC error flag
                         if project_info[flowcell].value is not None:
                             if (

taca/utils/misc.py

@@ -214,11 +214,11 @@ def run_is_demuxed(run, couch_info=None, seq_run_type=None):
         run_name = f"{run_date}_{run_fc}"
         try:
             couch_connection = statusdb.StatusdbSession(couch_info).connection
-            fc_db = couch_connection[couch_info["xten_db"]]
-            for fc in fc_db.view("names/name", reduce=False, descending=True):
+            x_flowcells_db = couch_connection[couch_info["xten_db"]]
+            for fc in x_flowcells_db.view("names/name", reduce=False, descending=True):
                 if fc.key != run_name:
                     continue
-                fc_doc = fc_db.get(fc.id)
+                fc_doc = x_flowcells_db.get(fc.id)
                 if not fc_doc or not fc_doc.get("illumina", {}).get(
                     "Demultiplex_Stats", {}
                 ):

taca/utils/statusdb.py

@@ -83,57 +83,61 @@ def get_project_flowcell(
 
 
 class ProjectSummaryConnection(StatusdbSession):
-    def __init__(self, config, dbname="projects"):
+    def __init__(self, config):
         super().__init__(config)
-        self.db = self.connection[dbname]
+        self.projects_db = self.connection["projects"]
         self.name_view = {
-            k.key: k.id for k in self.db.view("project/project_name", reduce=False)
+            k.key: k.id
+            for k in self.projects_db.view("project/project_name", reduce=False)
         }
         self.id_view = {
-            k.key: k.id for k in self.db.view("project/project_id", reduce=False)
+            k.key: k.id
+            for k in self.projects_db.view("project/project_id", reduce=False)
         }
 
 
 class FlowcellRunMetricsConnection(StatusdbSession):
-    def __init__(self, config, dbname="flowcells"):
+    def __init__(self, config):
         super().__init__(config)
-        self.db = self.connection[dbname]
+        self.flowcells_db = self.connection["flowcells"]
         self.name_view = {k.key: k.id for k in self.db.view("names/name", reduce=False)}
         self.proj_list = {
             k.key: k.value
-            for k in self.db.view("names/project_ids_list", reduce=False)
+            for k in self.flowcells_db.view("names/project_ids_list", reduce=False)
             if k.key
         }
 
 
 class X_FlowcellRunMetricsConnection(StatusdbSession):
     def __init__(self, config, dbname="x_flowcells"):
         super().__init__(config)
-        self.db = self.connection[dbname]
-        self.name_view = {k.key: k.id for k in self.db.view("names/name", reduce=False)}
+        self.x_flowcells_db = self.connection["x_flowcells"]
+        self.name_view = {
+            k.key: k.id for k in self.x_flowcells_db.view("names/name", reduce=False)
+        }
         self.proj_list = {
             k.key: k.value
-            for k in self.db.view("names/project_ids_list", reduce=False)
+            for k in self.x_flowcells_db.view("names/project_ids_list", reduce=False)
             if k.key
         }
 
 
 class NanoporeRunsConnection(StatusdbSession):
-    def __init__(self, config, dbname="nanopore_runs"):
+    def __init__(self, config):
         super().__init__(config)
-        self.db = self.connection[dbname]
+        self.nanopore_runs_db = self.connection["nanopore_runs"]
 
     def check_run_exists(self, ont_run) -> bool:
-        view_names = self.db.view("names/name")
+        view_names = self.nanopore_runs_db.view("names/name")
         if len(view_names[ont_run.run_name].rows) > 0:
             return True
         else:
             return False
 
     def check_run_status(self, ont_run) -> str:
-        view_all_stats = self.db.view("names/name")
+        view_all_stats = self.nanopore_runs_db.view("names/name")
         doc_id = view_all_stats[ont_run.run_name].rows[0].id
-        return self.db[doc_id]["run_status"]
+        return self.nanopore_runs_db[doc_id]["run_status"]
 
     def create_ongoing_run(
         self, ont_run, run_path_file: str, pore_count_history_file: str
@@ -151,19 +155,19 @@ def create_ongoing_run(
             "pore_count_history": pore_counts,
         }
 
-        new_doc_id, new_doc_rev = self.db.save(new_doc)
+        new_doc_id, new_doc_rev = self.nanopore_runs_db.save(new_doc)
         logger.info(
             f"New database entry created: {ont_run.run_name}, id {new_doc_id}, rev {new_doc_rev}"
         )
 
     def finish_ongoing_run(self, ont_run, dict_json: dict):
-        view_names = self.db.view("names/name")
+        view_names = self.nanopore_runs_db.view("names/name")
         doc_id = view_names[ont_run.run_name].rows[0].id
-        doc = self.db[doc_id]
+        doc = self.nanopore_runs_db[doc_id]
 
         doc.update(dict_json)
         doc["run_status"] = "finished"
-        self.db[doc.id] = doc
+        self.nanopore_runs_db[doc.id] = doc
 
 
 def update_doc(db, obj, over_write_db_entry=False):