Refactor relecov_documentation

relecov_dashboard/utils/met_sequencing.py

@@ -1,11 +1,9 @@
 # Generic imports
 from statistics import mean
-
 import pandas as pd
 
 # Local imports
-import relecov_core.utils.rest_api_handling
-import relecov_core.utils.schema_handling
+import relecov_core.utils.rest_api
 import relecov_dashboard.utils.generic_graphic_data
 import relecov_dashboard.utils.plotly
 import relecov_dashboard.utils.generic_process_data
@@ -60,7 +58,7 @@ def get_pre_proc_data(graphic_name, out_format):
 
     def fetch_sequencing_data(project_field, columns):
         # get stats utilization fields from LIMS
-        lims_data = relecov_core.utils.rest_api_handling.get_stats_data(
+        lims_data = relecov_core.utils.rest_api.get_stats_data(
             {
                 "sample_project_name": "Relecov",
                 "project_field": project_field,

relecov_documentation/apps.py

@@ -1,3 +1,4 @@
+# Generic imports
 from django.apps import AppConfig
 
 

relecov_documentation/urls.py

@@ -1,52 +1,55 @@
+# Generic imports
 from django.urls import path
 from django.conf import settings
-from relecov_documentation import views
 from django.conf.urls.static import static
 
+# Local imports
+import relecov_documentation
+
 urlpatterns = [
-    path("", views.index, name="index"),
-    path("description", views.description, name="description"),
-    path("relecovInstall/", views.relecov_install, name="relecov_install"),
-    path("configuration/", views.configuration, name="configuration"),
-    path("metadata/", views.metadata, name="metadata"),
-    path("metadataLabExcel/", views.metadata_lab_excel, name="metadata_lab_excel"),
-    path("relecovTools/", views.relecov_tools, name="relecov_tools"),
-    path("intranetOverview/", views.intranet_overview, name="intranet_overview"),
+    path("", relecov_documentation.views.index, name="index"),
+    path("description", relecov_documentation.views.description, name="description"),
+    path("relecovInstall/", relecov_documentation.views.relecov_install, name="relecov_install"),
+    path("configuration/", relecov_documentation.views.configuration, name="configuration"),
+    path("metadata/", relecov_documentation.views.metadata, name="metadata"),
+    path("metadataLabExcel/", relecov_documentation.views.metadata_lab_excel, name="metadata_lab_excel"),
+    path("relecovTools/", relecov_documentation.views.relecov_tools, name="relecov_tools"),
+    path("intranetOverview/", relecov_documentation.views.intranet_overview, name="intranet_overview"),
     path(
         "intranetContactData/",
-        views.intranet_contact_data,
+        relecov_documentation.views.intranet_contact_data,
         name="intranet_contact_data",
     ),
     path(
         "intranetSampleSearch/",
-        views.intranet_sample_search,
+        relecov_documentation.views.intranet_sample_search,
         name="intranet_sample_search",
     ),
     path(
         "intranetReceivedSamples/",
-        views.intranet_received_samples,
+        relecov_documentation.views.intranet_received_samples,
         name="intranet_received_samples",
     ),
     path(
         "intranetUploadMetadata/",
-        views.intranet_upload_metadata,
+        relecov_documentation.views.intranet_upload_metadata,
         name="intranet_upload_metadata",
     ),
-    path("variantDashboard/", views.variant_dashboard, name="variant_dashboard"),
+    path("variantDashboard/", relecov_documentation.views.variant_dashboard, name="variant_dashboard"),
     path(
         "methodologyDashboard/",
-        views.methodology_dashboard,
+        relecov_documentation.views.methodology_dashboard,
         name="methodology_dashboard",
     ),
-    path("nextstrainInstall/", views.nextstrain_install, name="nextstrain_install"),
-    path("howtoNextstrain/", views.howto_nextstrain, name="howto_nextstrain"),
-    path("uploadToEna/", views.upload_to_ena, name="upload_to_ena"),
-    path("uploadToGisaid/", views.upload_to_gisaid, name="upload_to_gisaid"),
-    path("apiSchema/", views.api_schema, name="api_schema"),
-    path("howtoApi/", views.howto_api, name="howto_api"),
+    path("nextstrainInstall/", relecov_documentation.views.nextstrain_install, name="nextstrain_install"),
+    path("howtoNextstrain/", relecov_documentation.views.howto_nextstrain, name="howto_nextstrain"),
+    path("uploadToEna/", relecov_documentation.views.upload_to_ena, name="upload_to_ena"),
+    path("uploadToGisaid/", relecov_documentation.views.upload_to_gisaid, name="upload_to_gisaid"),
+    path("apiSchema/", relecov_documentation.views.api_schema, name="api_schema"),
+    path("howtoApi/", relecov_documentation.views.howto_api, name="howto_api"),
     path(
         "createNewUser/",
-        views.create_new_user,
+        relecov_documentation.views.create_new_user,
         name="create_new_user",
     ),
 ]