Merge pull request #883 from kedhammar/ci-fixes

CI pt. 2: Fixes
NationalGenomicsInfrastructure · Oct 24, 2024 · f87693d · f87693d
2 parents 21e4014 + 0ed5291
commit f87693d
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diff --git a/setup.py b/setup.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 """Setup file and install script SciLife python scripts.
 """
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 try:
-    with open("requirements.txt", "r") as f:
+    with open("requirements.txt") as f:
         install_requires = [x.strip() for x in f.readlines()]
-except IOError:
+except OSError:
     install_requires = []
 
 setup(

diff --git a/status/applications.py b/status/applications.py
@@ -2,6 +2,7 @@
 """
 import json
 from collections import Counter
+
 from status.util import SafeHandler
 
 

diff --git a/status/authorization.py b/status/authorization.py
@@ -1,8 +1,9 @@
-import tornado.web
-import tornado.auth
 import json
 
-from status.util import UnsafeHandler, GoogleUser
+import tornado.auth
+import tornado.web
+
+from status.util import GoogleUser, UnsafeHandler
 
 
 class LoginHandler(tornado.web.RequestHandler, tornado.auth.GoogleOAuth2Mixin):
@@ -34,9 +35,7 @@ def get(self):
                 if url is None:
                     url = "/"
             else:
-                url = "/unauthorized?email={0}&contact={1}".format(
-                    user.emails[0], self.application.settings["contact_person"]
-                )
+                url = f"/unauthorized?email={user.emails[0]}&contact={self.application.settings['contact_person']}"
             self.redirect(url)
 
         else:

diff --git a/status/barcode.py b/status/barcode.py
@@ -1,9 +1,10 @@
 """Handlers related to test for barcode printing
 """
 
+import re
 import subprocess
+
 from status.util import SafeHandler
-import re
 
 
 class BarcodeHandler(SafeHandler):
@@ -156,7 +157,7 @@ def make_barcode(label, print_bc):
             xpositionText = "440"  # moves the text position because the bc is longer
             textHeight = "38"
         formattedLabel.append(
-            "^FO{0},27^AFN,{1},{2}^FN1^FS".format(xpositionText, textHeight, ch_size)
+            f"^FO{xpositionText},27^AFN,{textHeight},{ch_size}^FN1^FS"
         )  # AF = assign font F, field number 1 (FN1), print text at position field origin (FO) rel. to home
         formattedLabel.append(
             "^FO80,17^BCN,70,N,N^FN2^FS"
@@ -172,14 +173,14 @@ def make_barcode(label, print_bc):
             yposition = "30"
         # Scalable font ^A0N,32,32 should fit roughly 42 chars on our current labels
         formattedLabel.append(
-            "^FO20,{0}^A0N,{1},{1}^FB640,1,0,C,0^FN1^FS".format(yposition, ch_size)
+            f"^FO20,{yposition}^A0N,{ch_size},{ch_size}^FB640,1,0,C,0^FN1^FS"
         )  # FO = x,y relative field origin; A0N = scalable font height,width; FB = make into one line field block and center
     formattedLabel.append("^XZ")  # end format
     formattedLabel.append("^XA")  # start of label format
     formattedLabel.append("^XFFORMAT^FS")  # label home posision
-    formattedLabel.append("^FN1^FD{}^FS".format(label))  # this is readable
+    formattedLabel.append(f"^FN1^FD{label}^FS")  # this is readable
     if print_bc:
-        formattedLabel.append("^FN2^FD{}^FS".format(label))  # this is the barcode
+        formattedLabel.append(f"^FN2^FD{label}^FS")  # this is the barcode
     formattedLabel.append("^XZ")
     return formattedLabel
 
@@ -204,5 +205,5 @@ def print_barcode(barcodeFile):
     sp.stdin.write(barcodeFile.encode("utf-8"))
     print("lp command is called for printing.")
     stdout, stderr = sp.communicate()  # Will wait for sp to finish
-    print("lp stdout: {0}".format(stdout))
+    print(f"lp stdout: {stdout}")
     sp.stdin.close()
diff --git a/status/bioinfo_analysis.py b/status/bioinfo_analysis.py
@@ -1,8 +1,9 @@
-import json
 import datetime
-import dateutil
+import json
 import traceback
 
+import dateutil
+
 from status.util import SafeHandler
 
 
@@ -77,12 +78,10 @@ def post(self, project_id):
         # couchdb bulk update
         try:
             save_result = self.application.bioinfo_db.update(to_save)
-        except Exception as err:
+        except Exception:
             self.set_status(400)
             self.finish(
-                "<html><body><p>Could not save bioinfo data. Please try again later.</p><pre>{}</pre></body></html>".format(
-                    traceback.format_exc()
-                )
+                f"<html><body><p>Could not save bioinfo data. Please try again later.</p><pre>{traceback.format_exc()}</pre></body></html>"
             )
             return None
         neg_save_res = []

diff --git a/status/clone_project.py b/status/clone_project.py
@@ -1,11 +1,11 @@
 
 
 import requests
-from status.util import SafeHandler
-
 from genologics import lims
+from genologics.config import BASEURI, PASSWORD, USERNAME
 from genologics.entities import Project
-from genologics.config import BASEURI, USERNAME, PASSWORD
+
+from status.util import SafeHandler
 
 
 class CloneProjectHandler(SafeHandler):

diff --git a/status/controls.py b/status/controls.py
@@ -1,9 +1,10 @@
 """
     Handler related to Controls page
 """
+from genologics.config import BASEURI
+
 from status.util import SafeHandler
-from genologics import lims
-from genologics.config import BASEURI, USERNAME, PASSWORD
+
 
 class ControlsHandler(SafeHandler):
 

diff --git a/status/data_deliveries_plot.py b/status/data_deliveries_plot.py
@@ -1,5 +1,6 @@
-import json
 import datetime
+import json
+
 from status.util import SafeHandler
 
 

diff --git a/status/deliveries.py b/status/deliveries.py
@@ -1,11 +1,12 @@
 from collections import OrderedDict
 
-from status.util import SafeHandler
-from status.running_notes import LatestRunningNoteHandler
-
-from genologics.config import BASEURI, USERNAME, PASSWORD
 from genologics import lims
-from genologics.entities import Udfconfig, Project as LIMSProject
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.entities import Project as LIMSProject
+from genologics.entities import Udfconfig
+
+from status.running_notes import LatestRunningNoteHandler
+from status.util import SafeHandler
 
 lims = lims.Lims(BASEURI, USERNAME, PASSWORD)
 
@@ -21,13 +22,13 @@ def post(self):
         lims_project = LIMSProject(lims, id=project_id)
         if not lims_project:
             self.set_status(400)
-            self.write("lims project not found: {}".format(project_id))
+            self.write(f"lims project not found: {project_id}")
             return
         project_name = lims_project.name
         stepname = ["Project Summary 1.3"]
         processes = lims.get_processes(type=stepname, projectname=project_name)
         if processes == []:
-            error = "{} for {} is not available in LIMS.".format(stepname, project_name)
+            error = f"{stepname} for {project_name} is not available in LIMS."
             self.set_status(400)
             self.write(error)
             return
@@ -51,7 +52,7 @@ def post(self):
         for row in view[project_id]:
             doc_id = row.value
             break
-        if doc_id == None:
+        if doc_id is None:
             self.set_status(400)
             self.write("Status DB has not been updated: project not found")
             return
@@ -290,17 +291,15 @@ def get(self):
 
             else:
                 project_data = {
-                    "error": "could not find project information for {}".format(
-                        project_id
-                    )
+                    "error": f"could not find project information for {project_id}"
                 }
 
             ongoing_deliveries[project_id].update(project_data)
         try:
             lims_responsibles = ["unassigned"] + sorted(
                 Udfconfig(lims, id="1128").presets
             )
-        except Exception as e:
+        except Exception:
             lims_responsibles = ["unassigned"] + sorted(responsible_list)
         template = self.application.loader.load("deliveries.html")
         self.write(

diff --git a/status/flowcell.py b/status/flowcell.py
@@ -1,10 +1,11 @@
-from status.util import SafeHandler
+import os
+import re
 from datetime import datetime
 from typing import Optional
+
 import pandas as pd
-import re
-import os
 
+from status.util import SafeHandler
 
 thresholds = {
     "HiSeq X": 320,
@@ -453,7 +454,7 @@ def get(self, name):
         reports_dir = self.application.minknow_path
         report_path = os.path.join(reports_dir, f"report_{name}.html")
 
-        self.write(open(report_path, "r").read())
+        self.write(open(report_path).read())
 
 class ElementFlowcellHandler(SafeHandler):
     def get(self, name):

diff --git a/status/flowcells.py b/status/flowcells.py
@@ -1,21 +1,20 @@
 """Set of handlers related with Flowcells
 """
 
-import json
 import datetime
-import re
+import json
 import logging
-
-from dateutil.relativedelta import relativedelta
+import re
 from collections import OrderedDict
 
-from genologics import lims
-from genologics.config import BASEURI, USERNAME, PASSWORD
 import pandas as pd
+from dateutil.relativedelta import relativedelta
+from genologics import lims
+from genologics.config import BASEURI, PASSWORD, USERNAME
 
-from status.util import SafeHandler
 from status.flowcell import fetch_ont_run_stats, thresholds
 from status.running_notes import LatestRunningNoteHandler
+from status.util import SafeHandler
 
 application_log = logging.getLogger("tornado.application")
 
@@ -142,7 +141,7 @@ def list_ont_flowcells(self):
                     view_mux_scans=view_mux_scans,
                     view_pore_count_history=view_pore_count_history,
                 )
-            except Exception as e:
+            except Exception:
                 unfetched_runs.append(row.key)
                 application_log.exception(f"Failed to fetch run {row.key}")
 
@@ -156,8 +155,8 @@ def list_ont_flowcells(self):
 
                 # Convert back to dictionary and return
                 ont_flowcells = df.to_dict(orient="index")
-            except Exception as e:
-                application_log.exception(f"Failed to compile ONT flowcell dataframe")
+            except Exception:
+                application_log.exception("Failed to compile ONT flowcell dataframe")
 
         return ont_flowcells, unfetched_runs
 
@@ -300,9 +299,7 @@ def search_flowcell_names(self, search_string=""):
                 if search_string in row_key.lower():
                     splitted_fc = row_key.split("_")
                     fc = {
-                        "url": "/flowcells/{}_{}".format(
-                            splitted_fc[0], splitted_fc[-1]
-                        ),
+                        "url": f"/flowcells/{splitted_fc[0]}_{splitted_fc[-1]}",
                         "name": row_key,
                     }
                     flowcells.append(fc)
@@ -325,9 +322,7 @@ def search_flowcell_names(self, search_string=""):
                 if search_string in row_key.lower():
                     splitted_fc = row_key.split("_")
                     fc = {
-                        "url": "/flowcells/{}_{}".format(
-                            splitted_fc[0], splitted_fc[-1]
-                        ),
+                        "url": f"/flowcells/{splitted_fc[0]}_{splitted_fc[-1]}",
                         "name": row_key,
                     }
                     flowcells.append(fc)
@@ -424,12 +419,12 @@ def get(self, flowcell):
         self.set_header("Content-type", "application/json")
         try:
             p = get_container_from_id(flowcell)
-        except (KeyError, IndexError) as e:
+        except (KeyError, IndexError):
             self.write("{}")
         else:
             try:
                 links = json.loads(p.udf["Links"]) if "Links" in p.udf else {}
-            except KeyError as e:
+            except KeyError:
                 links = {}
 
             # Sort by descending date, then hopefully have deviations on top
@@ -454,7 +449,7 @@ def post(self, flowcell):
         else:
             try:
                 p = get_container_from_id(flowcell)
-            except (KeyError, IndexError) as e:
+            except (KeyError, IndexError):
                 self.status(400)
                 self.write("Flowcell not found")
             else:
@@ -505,8 +500,8 @@ def get(self, query):
                 "info/summary", descending=True
             )
 
-            for row in xfc_view[query : "{}Z".format(query)]:
-                if not row.key in data:
+            for row in xfc_view[query : f"{query}Z"]:
+                if row.key not in data:
                     data[row.key] = []
                 # To add correct threshold values
                 fc_long_name = row.value["fcp"].split(":")[0]

diff --git a/status/instruments.py b/status/instruments.py
@@ -1,9 +1,10 @@
-from status.util import SafeHandler
-
 import datetime
+import json
+
 from dateutil import tz
 from dateutil.relativedelta import relativedelta
-import json
+
+from status.util import SafeHandler
 
 
 def recover_logs(handler, search_string=None, inst_type="bravo"):
@@ -43,7 +44,7 @@ def recover_logs(handler, search_string=None, inst_type="bravo"):
 
         for row in handler.application.biomek_errs_db.view("dates/timestamp", startkey=date_earlier, endkey=date_later):
             date = datetime.datetime.strptime(row.key, "%Y-%m-%dT%H:%M:%S.%fZ").replace(tzinfo=tz.tzutc()).astimezone(tz.tzlocal())
-            inst = f"{instruments_list[row.value["inst_id"]]}({row.value["inst_id"]})"
+            inst = f"{instruments_list[row.value['inst_id']]}({row.value['inst_id']})"
             method = row.value.get("method", 'diff')
             errs = row.value["errors"]
             valid_rows.append({"timestamp": f"{date}", "instrument_name": inst, "method": method, "message": errs})