Merge pull request #884 from kedhammar/ci-formatting

CI pt. 3: Formatting

setup.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
-"""Setup file and install script SciLife python scripts.
-"""
+"""Setup file and install script SciLife python scripts."""
+
 from setuptools import find_packages, setup
 
 try:

status/applications.py

@@ -1,5 +1,5 @@
-"""Handlers related to applications
-"""
+"""Handlers related to applications"""
+
 import json
 from collections import Counter
 
@@ -78,7 +78,7 @@ def list_applications_and_samples(self, start=None, end="z"):
         # Projects per application
         applications = Counter()
         view = self.application.projects_db.view("project/date_applications")
-        for row in view[[start, ""]:[end, "z"]]:
+        for row in view[[start, ""] : [end, "z"]]:
             if row.key[1] is None:
                 # This corresponds to StatusDB:s notation
                 # and avoids conflict with 'None'.
@@ -89,7 +89,7 @@ def list_applications_and_samples(self, start=None, end="z"):
         # Samples per application
         samples = Counter()
         view = self.application.projects_db.view("project/date_samples_applications")
-        for row in view[[start, ""]:[end, "z"]]:
+        for row in view[[start, ""] : [end, "z"]]:
             if row.key[1] is None:
                 samples["null"] += row.value
             else:

status/barcode.py

@@ -1,5 +1,4 @@
-"""Handlers related to test for barcode printing
-"""
+"""Handlers related to test for barcode printing"""
 
 import re
 import subprocess
@@ -52,9 +51,7 @@ def post(self):
                     for _ in range(copies):  # loops over copies to print
                         print_barcode(linesToPrint)
                 else:  # file submitted is a text file
-                    for (
-                        line
-                    ) in (
+                    for line in (
                         linesToPrint.splitlines()
                     ):  # split into the different lines of the text file
                         if self.get_argument(
@@ -112,9 +109,7 @@ def post(self):
                 if re.compile(r"^P\d+$").search(user_project_ID):
                     projectNo_only_extracted = re.search(
                         "P(.*)", user_project_ID
-                    ).group(
-                        1
-                    )  # have only the number of the project ID
+                    ).group(1)  # have only the number of the project ID
                     for projects in range(0, int(projectNo)):
                         new_projectNo = int(projectNo_only_extracted) + projects
                         new_projectID = "P" + str(new_projectNo)

status/bioinfo_analysis.py

@@ -28,7 +28,7 @@ def post(self, project_id):
         assert_project_id(project_id)
         # Fetching documents one by one generates too many requests to statusdb
         # Hopefully fetching all documents at once doesn't require too much memory
-        view = v[[project_id, "", "", ""]:[project_id, "Z", "Z", "Z"]]
+        view = v[[project_id, "", "", ""] : [project_id, "Z", "Z", "Z"]]
         cached_view = {}
         for row in view.rows:
             if tuple(row.key) in cached_view:
@@ -117,9 +117,9 @@ def get(self, project_id):
                     "lanes": {lane_id: bioinfo_qc}
                 }
             elif lane_id not in bioinfo1[sample_id]["flowcells"][flowcell_id]["lanes"]:
-                bioinfo1[sample_id]["flowcells"][flowcell_id]["lanes"][
-                    lane_id
-                ] = bioinfo_qc
+                bioinfo1[sample_id]["flowcells"][flowcell_id]["lanes"][lane_id] = (
+                    bioinfo_qc
+                )
             else:
                 bioinfo1[sample_id]["flowcells"][flowcell_id]["lanes"][lane_id].update(
                     bioinfo_qc
@@ -136,9 +136,9 @@ def get(self, project_id):
                     "samples": {sample_id: bioinfo_qc}
                 }
             elif sample_id not in bioinfo2[flowcell_id]["lanes"][lane_id]["samples"]:
-                bioinfo2[flowcell_id]["lanes"][lane_id]["samples"][
-                    sample_id
-                ] = bioinfo_qc
+                bioinfo2[flowcell_id]["lanes"][lane_id]["samples"][sample_id] = (
+                    bioinfo_qc
+                )
             else:
                 bioinfo2[flowcell_id]["lanes"][lane_id]["samples"][sample_id].update(
                     bioinfo_qc

status/clone_project.py

@@ -1,5 +1,3 @@
-
-
 import requests
 from genologics import lims
 from genologics.config import BASEURI, PASSWORD, USERNAME
@@ -21,58 +19,86 @@ def get(self):
             )
         )
 
+
 class LIMSProjectCloningHandler(SafeHandler):
     """Gets and posts the project data from LIMS for cloning it
     URL: /api/v1/lims_project_data/([^/]*)$
     """
 
     def get(self, projectid):
-
-        proj_values = self.get_project_data(projectid, 'get')
+        proj_values = self.get_project_data(projectid, "get")
         if not proj_values:
             self.set_status(404)
             self.write({"error": "Project not found"})
             return
         self.set_header("Content-type", "application/json")
         self.write(proj_values)
-    
+
     def post(self, projectid):
-
-        if not (self.get_current_user().is_proj_coord or self.get_current_user().is_any_admin):
+        if not (
+            self.get_current_user().is_proj_coord
+            or self.get_current_user().is_any_admin
+        ):
             self.set_status(401)
             return self.write(
                 "Error: You do not have the permissions for this operation!"
             )
-        
-        new_proj = self.get_project_data(projectid, 'post')
-        if 'error' in new_proj:
+
+        new_proj = self.get_project_data(projectid, "post")
+        if "error" in new_proj:
             self.set_status(400)
-            self.write({"error": new_proj['error']})
+            self.write({"error": new_proj["error"]})
             return
-        
+
         self.set_status(201)
         self.write(new_proj)
-    
+
     def get_project_data(self, projectid, type):
         copy_udfs = {
-                      "Customer project reference", "Project Comment", "Type", "Application", "Reference genome",
-                      "Library construction method", "Sequencing setup", "Accredited (Data Analysis)", 
-                      "Accredited (Data Processing)", "Accredited (Library Preparation)", "Accredited (Sequencing)", "Delivery type",
-                      "Agreement cost", "Invoice Reference", "Customer Project Description", "Project category", "Sample type",
-                      "Sample units ordered", "Library type (ready-made libraries)", "Sequence units ordered (lanes)", "Sequencing platform",
-                      "Flowcell", "Custom Primer", "Low Diversity", "Best practice bioinformatics", "Funding agency", "Project coordinator",
-                      "Library prep option", "Flowcell", "Organism", "PhiX spike-in (percent)", "Flowcell option", "Ethics permit number"
-                      }
+            "Customer project reference",
+            "Project Comment",
+            "Type",
+            "Application",
+            "Reference genome",
+            "Library construction method",
+            "Sequencing setup",
+            "Accredited (Data Analysis)",
+            "Accredited (Data Processing)",
+            "Accredited (Library Preparation)",
+            "Accredited (Sequencing)",
+            "Delivery type",
+            "Agreement cost",
+            "Invoice Reference",
+            "Customer Project Description",
+            "Project category",
+            "Sample type",
+            "Sample units ordered",
+            "Library type (ready-made libraries)",
+            "Sequence units ordered (lanes)",
+            "Sequencing platform",
+            "Flowcell",
+            "Custom Primer",
+            "Low Diversity",
+            "Best practice bioinformatics",
+            "Funding agency",
+            "Project coordinator",
+            "Library prep option",
+            "Flowcell",
+            "Organism",
+            "PhiX spike-in (percent)",
+            "Flowcell option",
+            "Ethics permit number",
+        }
 
         lims_instance = lims.Lims(BASEURI, USERNAME, PASSWORD)
         uri = lims_instance.get_uri(f"projects/{projectid}")
         existing_project = Project(lims=lims_instance, uri=uri)
         proj_values = {}
         try:
-            proj_values['name'] = existing_project.name
+            proj_values["name"] = existing_project.name
         except requests.exceptions.HTTPError:
             return {}
-        
+
         proj_values["researcher_id"] = existing_project.researcher.id
         proj_values["Client"] = existing_project.researcher.name
         proj_values["Account"] = existing_project.researcher.lab.name
@@ -81,25 +107,26 @@ def get_project_data(self, projectid, type):
         for udf in copy_udfs:
             if udf in existing_project.udf:
                 udfs[udf] = existing_project.udf[udf]
-        proj_values['udfs'] = udfs
+        proj_values["udfs"] = udfs
 
-        if type=='get':
+        if type == "get":
             return proj_values
-        
+
         else:
-            new_name = existing_project.name + '_CLONE'
+            new_name = existing_project.name + "_CLONE"
             check_if_new_name_exists = lims_instance.get_projects(name=new_name)
 
             if check_if_new_name_exists:
-                return {'error': f'A project with the name {new_name} already exists'}
-            
+                return {"error": f"A project with the name {new_name} already exists"}
+
             try:
-                new_project = Project.create(lims_instance, udfs=proj_values['udfs'], name=new_name,
-                                                researcher=existing_project.researcher)
+                new_project = Project.create(
+                    lims_instance,
+                    udfs=proj_values["udfs"],
+                    name=new_name,
+                    researcher=existing_project.researcher,
+                )
             except requests.exceptions.HTTPError as e:
-                return {'error': e.message}
-
-            return {'project_id': new_project.id, 'project_name': new_project.name}
-
-
+                return {"error": e.message}
 
+            return {"project_id": new_project.id, "project_name": new_project.name}