Replace couchdb calls with cloudant; remove statusdb package dependency

LIMS2DB/classes.py

@@ -1,5 +1,4 @@
 import copy
-import http.client as http_client
 import re
 from datetime import datetime
 
@@ -14,6 +13,7 @@
     ReagentType,
     Researcher,
 )
+from ibm_cloud_sdk_core.api_exception import ApiException
 from requests import get as rget
 from sqlalchemy import text
 from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
@@ -452,14 +452,19 @@ def save(self, update_modification_time=True):
         doc = None
         # When running for a single project, sometimes the connection is lost so retry
         try:
-            self.couch["projects"]
-        except http_client.BadStatusLine:
+            self.couch.get_server_information().get_result()
+        except ApiException:
             self.log.warning(f"Access to couch failed before trying to save new doc for project {self.pid}")
             pass
-        db = self.couch["projects"]
-        view = db.view("project/project_id")
-        for row in view[self.pid]:
-            doc = db.get(row.id)
+        result = self.couch.post_view(
+            db="projects",
+            ddoc="project",
+            view="project_id",
+            key=self.pid,
+            include_docs=True,
+        ).get_result()["rows"]
+        if result:
+            doc = result[0]["doc"]
         if doc:
             fields_saved = [
                 "_id",
@@ -502,7 +507,11 @@ def save(self, update_modification_time=True):
                     self.obj["order_details"] = doc["order_details"]
 
                 self.log.info(f"Trying to save new doc for project {self.pid}")
-                db.save(self.obj)
+                self.couch.put_document(
+                    db="projects",
+                    doc_id=self.obj["_id"],
+                    document=self.obj,
+                ).get_result()
                 if self.obj.get("details", {}).get("type", "") == "Application":
                     lib_method_text = f"Library method: {self.obj['details'].get('library_construction_method', 'N/A')}"
                     application = self.obj.get("details", {}).get("application", "")
@@ -537,7 +546,10 @@ def save(self, update_modification_time=True):
             self.obj["creation_time"] = datetime.now().isoformat()
             self.obj["modification_time"] = self.obj["creation_time"]
             self.log.info(f"Trying to save new doc for project {self.pid}")
-            db.save(self.obj)
+            self.couch.post_document(
+                db="projects",
+                document=self.obj,
+            ).get_result()
             if self.obj.get("details", {}).get("type", "") == "Application":
                 genstat_url = f"{self.genstat_proj_url}{self.obj['project_id']}"
                 lib_method_text = f"Library method: {self.obj['details'].get('library_construction_method', 'N/A')}"

LIMS2DB/diff.py

@@ -1,37 +1,38 @@
-import http.client as http_client
-
 from genologics_sql.utils import get_configuration, get_session
+from ibm_cloud_sdk_core.api_exception import ApiException
 
 from LIMS2DB.utils import setupLog
 
 
-def diff_project_objects(pj_id, couch, proj_db, logfile, oconf):
+def diff_project_objects(pj_id, couch, logfile, oconf):
     # Import is put here to defer circular imports
     from LIMS2DB.classes import ProjectSQL
 
     log = setupLog(f"diff - {pj_id}", logfile)
 
-    view = proj_db.view("projects/lims_followed")
-
     def fetch_project(pj_id):
-        try:
-            old_project_couchid = view[pj_id].rows[0].value
-        except (KeyError, IndexError):
-            log.error(f"No such project {pj_id}")
+        result = couch.post_view(
+            db="projects",
+            ddoc="projects",
+            view="lims_followed",
+            key=pj_id,
+            include_docs=True,
+        ).get_result()["rows"]
+        if not result:
+            log.error(f"No project found in couch for {pj_id}")
             return None
-        return old_project_couchid
+        return result[0]["doc"]
 
     try:
-        old_project_couchid = fetch_project(pj_id)
-    except http_client.BadStatusLine:
-        log.error("BadStatusLine received after large project")
+        old_project = fetch_project(pj_id)
+    except ApiException:
+        log.error("Connection issues after large project")
         # Retry
-        old_project_couchid = fetch_project(pj_id)
+        old_project = fetch_project(pj_id)
 
-    if old_project_couchid is None:
+    if old_project is None:
         return None
 
-    old_project = proj_db.get(old_project_couchid)
     old_project.pop("_id", None)
     old_project.pop("_rev", None)
     old_project.pop("modification_time", None)

LIMS2DB/flowcell_sql.py

@@ -76,11 +76,10 @@ def upload_to_couch(couch, runid, lims_data, pro):
     elif pc_cg.SEQUENCING.get(str(pro.typeid), "") in ["AVITI Run v1.0"]:
         dbname = "element_runs"
 
-    db = couch[dbname]
-    view = db.view("info/id")
     doc = None
-    for row in view[runid]:
-        doc = db.get(row.value)
+    result = couch.post_view(db=dbname, ddoc="info", view="id", key=runid, include_docs=True).get_result()["rows"]
+    if result:
+        doc = result[0]["doc"]
 
     if doc:
         running_notes = {}
@@ -89,4 +88,7 @@ def upload_to_couch(couch, runid, lims_data, pro):
         doc["lims_data"] = lims_data
         if running_notes:
             doc["lims_data"]["container_running_notes"] = running_notes
-        db.save(doc)
+        couch.post_document(
+            db=dbname,
+            document=doc,
+        ).get_result()