fix replace workflow values. Add time sleep before sync analysis. Change full_name

gga_run_workflow_phaeo_jbrowse.py

@@ -583,10 +583,12 @@ if __name__ == "__main__":
                     species_strain_sex=species_strain_sex_org2,
                     id="{id}")
                 # Replace values in the workflow dictionary
-                jbrowse_tool_state_org1 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]
-                jbrowse_tool_state_org1 = jbrowse_tool_state_org1.replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
-                jbrowse_tool_state_org2 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]
-                jbrowse_tool_state_org2 = jbrowse_tool_state_org2.replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]\
+                    .replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]\
+                    .replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
                 # The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
                 # in galaxy --> define a naming method for these workflows
                 workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER]["tool_state"] = \

runWorkflowPhaeo.py

@@ -3,6 +3,7 @@
 
 import logging
 import json
+import time
 
 import utilities_bioblend
 import speciesData
@@ -116,6 +117,7 @@ class RunWorkflow(speciesData.SpeciesData):
 
         # Synchronize analysis in Tripal
         logging.info("Synchronizing analysis %s in Tripal" % analysis_name)
+        time.sleep(10)
         self.sync_analysis(analysis_id=analysis_id)
 
         return analysis_id

speciesData.py

@@ -108,7 +108,7 @@ class SpeciesData:
         self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_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 = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species_lowercase, self.strain, self.sex])["not_empty"])
         self.full_name_lowercase = self.full_name.lower()
 
         self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
@@ -118,7 +118,7 @@ class SpeciesData:
         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)
+        self.gff_filename = "{0}_OGS{1}_{2}.gff".format(self.dataset_prefix, self.ogs_version, constants.DATA_DATE.replace("-",""))
         self.transcripts_filename = "{0}_OGS{1}_{2}".format(self.dataset_prefix, self.ogs_version, constants.FILENAME_SUFFIX_TRANSCRIPTS)
         self.proteins_filename = "{0}_OGS{1}_{2}".format(self.dataset_prefix, self.ogs_version, constants.FILENAME_SUFFIX_PROTEINS)
         self.interpro_filename = "{0}_OGS{1}_{2}".format(self.dataset_prefix, self.ogs_version, constants.FILENAME_SUFFIX_INTERPRO)