Do not allow to import sample sheet if not library kits are defined

test/test_data.json

@@ -9165,7 +9165,7 @@
         "model": "wetlab.runstates",
         "pk": 2,
         "fields": {
-            "run_state_name": "Recorded"
+            "run_state_name": "recorded"
         }
     },
     {

wetlab/admin.py

@@ -60,6 +60,12 @@ class AdditionaKitsLibraryPreparationAdmin(admin.ModelAdmin):
     list_display = ["kit_name", "protocol_id", "commercial_kit_id"]
 
 
+class LibraryKitAdmin(admin.ModelAdmin):
+    list_display = [
+        "library_name",
+    ]
+
+
 class AdditionalUserLotKitAdmin(admin.ModelAdmin):
     list_display = ["lib_prep_id", "additional_lot_kits", "user_lot_kit_id"]
 
@@ -290,6 +296,7 @@ class RunConfigurationTestAdmin(admin.ModelAdmin):
 admin.site.register(wetlab.models.RunErrors, RunErrorsAdmin)
 admin.site.register(wetlab.models.RunStates, RunStatesAdmin)
 admin.site.register(wetlab.models.LibPrepareStates, StatesForLibraryPreparationAdmin)
+admin.site.register(wetlab.models.LibraryKit, LibraryKitAdmin)
 admin.site.register(wetlab.models.PoolStates, StatesForPoolAdmin)
 admin.site.register(wetlab.models.SamplesInProject, SamplesInProjectAdmin)
 admin.site.register(wetlab.models.StatsRunSummary, StatsRunSummaryAdmin)

wetlab/config.py

@@ -164,6 +164,7 @@
     "[Settings]",
     "[I7]",
 ]
+ERROR_NO_LIBRARY_KIT_DEFINED = ["Library Kits are not defined yet"]
 ##############################################################
 
 MIGRATION_DIRECTORY_FILES = "wetlab/BaseSpaceMigrationFiles/"

wetlab/models.py

@@ -152,7 +152,7 @@ def get_run_state_name(self):
 
 class RunProcessManager(models.Manager):
     def create_new_run_from_crontab(self, run_data):
-        run_state = RunStates.objects.get(run_state_name__exact="Recorded")
+        run_state = RunStates.objects.get(run_state_name__exact="recorded")
         new_run = self.create(state=run_state, run_name=run_data["experiment_name"])
         return new_run
 

wetlab/utils/crontab_update_run.py

@@ -228,7 +228,7 @@ def search_update_new_runs(request_reason):
             logger.debug(
                 "%s : Found the experiment name called : %s", new_run, experiment_name
             )
-            exclude_states = ["Error", "Recorded"]
+            exclude_states = ["Error", "recorded"]
             if (
                 wetlab.models.RunProcess.objects.filter(run_name__exact=experiment_name)
                 .exclude(state__run_state_name__in=exclude_states)
@@ -417,9 +417,9 @@ def handle_not_completed_run():
     runs_to_handle = {}
 
     # state_list_be_processed = ['Sample Sent','Processing Run','Processed Run', 'Processing Bcl2fastq',
-    #                                'Processed Bcl2fastq', 'Recorded']
+    #                                'Processed Bcl2fastq', 'recorded']
     state_list_be_processed = [
-        "Recorded",
+        "recorded",
         "Sample Sent",
         "Processing Run",
         "Processed Run",
@@ -442,7 +442,7 @@ def handle_not_completed_run():
 
     for state in runs_to_handle.keys():
         logger.info("Start processing the run found for state %s", state)
-        if state == "Recorded":
+        if state == "recorded":
             manage_run_in_recorded_state(conn, runs_to_handle[state])
 
         elif state == "Sample Sent":

wetlab/utils/fetch_info.py

@@ -207,7 +207,7 @@ def graphics_state(state):
     """
     state_list = [
         "Error",
-        "Recorded",
+        "recorded",
         "Sample Sent",
         "Processing Run",
         "Processed Run",
@@ -512,7 +512,7 @@ def get_information_for_incompleted_run():
     """
     Description:
         The function will get the information from the runs that are incompleted.
-        It creates a 4 groups. Recorded, Error, Canceled and rest of the states.
+        It creates a 4 groups. recorded, Error, Canceled and rest of the states.
         Creates a pie graphic
     Functions:
         graphic_3D_pie      # located at wetlab/utils/stats_graphics
@@ -522,11 +522,11 @@ def get_information_for_incompleted_run():
     run_information = {}
     today = datetime.today().date()
     if wetlab.models.RunProcess.objects.filter(
-        state__run_state_name="Recorded"
+        state__run_state_name="recorded"
     ).exists():
         run_information["recorded"] = []
         run_objs = wetlab.models.RunProcess.objects.filter(
-            state__run_state_name="Recorded"
+            state__run_state_name="recorded"
         ).order_by("run_name")
         for run_obj in run_objs:
             data = []
@@ -577,7 +577,7 @@ def get_information_for_incompleted_run():
             data.append(str((today - run_date).days))
             run_information["cancelled"].append(data)
 
-    exclude_state = ["Recorded", "Error", "Cancelled", "Completed", "pre_recorded"]
+    exclude_state = ["recorded", "Error", "Cancelled", "Completed", "pre_recorded"]
 
     if (
         wetlab.models.RunProcess.objects.all()
@@ -685,7 +685,7 @@ def get_information_run(run_object):
         return info_dict
 
     # allow to change the run name in case that run state was recorded or Sample Sent
-    if run_state == "Recorded" or run_state == "Sample Sent":
+    if run_state == "recorded" or run_state == "Sample Sent":
         info_dict["change_run_name"] = [
             [run_object.get_run_name(), run_object.get_run_id()]
         ]

wetlab/utils/samplesheet.py

@@ -373,35 +373,37 @@ def get_projects_in_run(in_file: str) -> dict:
     """
     header_found = False
     projects = {}
-    fh = open(in_file, "r")
-    for line in fh:
-        line = line.rstrip()
-        if line == "":
-            continue
-        found_header = re.search("^Sample_ID,Sample_Name", line)
-        if found_header:
-            # found the index for projects and description
-            if not "Sample_Project" and "Description" not in line:
-                break
-            split_line = line.split(",")
-            p_index = split_line.index("Sample_Project")
-            description_index = split_line(",").index("Description")
-            header_found = True
-            continue
-        if header_found:
-            # ignore the empty lines separated by commas
-            valid_line = re.search("^\w+", line)
-            if not valid_line:
+    with open(in_file, "r") as fh:
+        for line in fh:
+            line = line.rstrip()
+            if line == "":
                 continue
-            # store the project name and the user name (Description) inside projects dict
-            projects[line.split(",")[p_index]] = line.split(",")[description_index]
-    fh.close()
-    if not found_header:
+            if not header_found:
+                header = re.search("^Sample_ID,Sample_Name", line)
+                if header:
+                    # match line with the header
+                    # look for projects and description indexes
+                    if not "Sample_Project" and "Description" not in line:
+                        break
+                    split_line = line.split(",")
+                    p_index = split_line.index("Sample_Project")
+                    description_index = split_line.index("Description")
+                    header_found = True
+                    continue
+            else:
+                # ignore the empty lines separated by commas
+                valid_line = re.search("^\w+", line)
+                if not valid_line:
+                    continue
+                # store the project name and the user name (Description) inside projects dict
+                projects[line.split(",")[p_index]] = line.split(",")[description_index]
+
+    if not header_found:
         return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING}
     if not projects:
         return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS}
 
-    return {"projects": projects}
+    return projects
 
 
 def get_index_library_name(in_file):

wetlab/views.py

@@ -427,7 +427,6 @@ def create_nextseq_run(request):
 
         # Check if the projects are already defined on database.
         # Error page is showed if projects are already defined on database
-
         project_already_defined = []
         project_in_several_runs = wetlab.utils.common.get_configuration_value(
             "PROJECTS_ALLOWED_IN_MULTIPLE_RUNS"
@@ -448,7 +447,7 @@ def create_nextseq_run(request):
             return render(
                 request,
                 "wetlab/create_next_seq_run.html",
-                {"error_message": display_project + " already defined"},
+                {"error_message": [display_project, " already defined"]},
             )
 
         # Once the information looks good. it will be stores in runProcess and projects table
@@ -607,7 +606,16 @@ def create_nextseq_run(request):
             "wetlab/create_next_seq_run.html",
             {"completed_form": results},
         )
-
+    # check if library kit is already defined
+    if len(wetlab.models.LibraryKit.objects.all()) == 0:
+        return render(
+            request,
+            "wetlab/create_next_seq_run.html",
+            {
+                "error_message": wetlab.config.ERROR_NO_LIBRARY_KIT_DEFINED,
+                "disable_submit_form": True,
+            },
+        )
     return render(request, "wetlab/create_next_seq_run.html")