fix time_sleep and common_name for org. Change dataset_prefix

gga_run_workflow_phaeo_jbrowse.py

@@ -68,7 +68,9 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
 
         self.common = self.name
         if not self.common_name is None and self.common_name != "":
-            self.common = self.common_name
+            # common_name only is not sufficient as may not be unique between the different strains of the species and
+            # galaxy will throw error "Found a preexisting organism with the same attributes in the database"
+            self.common = self.common_name + "(" + self.name + ")"
 
         self.genome_analysis_name = "genome v{0} of {1}".format(self.genome_version, self.full_name)
         self.genome_analysis_programversion = "genome v{0}".format(self.genome_version)
@@ -156,7 +158,9 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
                 tool_inputs={"abbr": self.abbreviation,
                              "genus": self.genus_uppercase,
                              "species": self.chado_species_name,
-                             "common": self.common})
+                             "common": self.common},
+                time_sleep=30
+            )
             organism_dict = json.loads(add_organism_tool_dataset)
             org_id = str(organism_dict["organism_id"])  # id needs to be a str to be recognized by chado tools
 
@@ -194,7 +198,8 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
         if len(prj_lib) == 1:
             library_id = prj_lib[0].id
         else:
-            logging.error("Multiple (or no one) libraries '%s' exist" % constants.GALAXY_LIBRARY_NAME)
+            logging.critical("Multiple (or no one) libraries '%s' exist" % constants.GALAXY_LIBRARY_NAME)
+            sys.exit()
         folder_dict_list = self.instance.libraries.get_folders(library_id=str(library_id))
 
         folders_id_dict = {}

runWorkflowPhaeo.py

@@ -78,7 +78,9 @@ class RunWorkflow(speciesData.SpeciesData):
                          "program": constants_phaeo.ADD_ANALYSIS_TOOL_PARAM_PROGRAM,
                          "programversion": programversion,
                          "sourcename": sourcename,
-                         "date_executed": constants_phaeo.ADD_ANALYSIS_TOOL_PARAM_DATE})
+                         "date_executed": constants_phaeo.ADD_ANALYSIS_TOOL_PARAM_DATE},
+            time_sleep = 30
+        )
         analysis_dict = json.loads(add_analysis_tool_dataset)
         analysis_id = str(analysis_dict["analysis_id"])
 

speciesData.py

@@ -106,7 +106,7 @@ class SpeciesData:
 
         self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:]
         self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lowercase)
-        self.strain_sex = "{0}_{1}".format(self.strain_lowercase, self.sex_lowercase)
+        self.strain_sex = '_'.join(utilities.filter_empty_not_empty_items([self.strain_lowercase, self.sex_lowercase])["not_empty"])
 
         self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"])
         self.full_name_lowercase = self.full_name.lower()
@@ -115,11 +115,7 @@ class SpeciesData:
             [self.genus_lowercase, self.species_lowercase, self.strain.lower(),
              self.sex.lower()])["not_empty"])
 
-        self.dataset_prefix = None
-        if self.sex is not None or self.sex != "":
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase + "_" + self.sex[0].lower()
-        else:
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase
+        self.dataset_prefix = self.strain_sex
 
         self.genome_filename = "{0}_v{1}.fasta".format(self.dataset_prefix, self.genome_version)
         self.gff_filename = "{0}_OGS{1}_{2}.gff".format(self.dataset_prefix, self.ogs_version, constants.DATA_DATE)