Update to wf_v7: sync in wf

constants_phaeo.py

@@ -32,19 +32,19 @@ WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "4"
 WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2 = "5"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1 = "6"
 WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "7"
-WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2 = "8"
+WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2 = "8"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1 = "9"
 WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER = "10"
 WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1 = "11"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG2 = "12"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG2 = "13"
 WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2 = "14"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG1 = "15"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG2 = "16"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1 = "17"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1 = "18"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2 = "19"
-WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2 = "20"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG1 = "15"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG2 = "16"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1 = "17"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1 = "18"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2 = "19"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2 = "20"
 WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "21"
 WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "22"
 

gga_run_workflow_phaeo.py

@@ -136,7 +136,7 @@ class RunWorkflow(species_data.SpeciesData):
         :return:
         """
 
-        self.add_analysis_if_needed(analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename)
+        analysis_id = self.add_analysis_if_needed(analyses_dict_list, analysis_name, analysis_programversion, analysis_sourcename)
 
         # Synchronize analysis in Tripal
         logging.info("Synchronizing analysis %s in Tripal" % analysis_name)

gga_run_workflow_phaeo_jbrowse.py

@@ -131,7 +131,7 @@ class RunWorkflowJbrowse(gga_run_workflow_phaeo.RunWorkflow):
 
         logging.info("Success: individual tools versions and changesets validated")
 
-    def add_organism_and_sync(self):
+    def add_organism_if_needed(self):
 
         get_organisms_tool_dataset = utilities_bioblend.run_tool_and_download_single_output_dataset(
             instance=self.instance,
@@ -283,7 +283,7 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
 
             analyses_dict_list = run_workflow_for_current_organism.get_analyses()
 
-            org_id = run_workflow_for_current_organism.add_organism_and_sync()
+            org_id = run_workflow_for_current_organism.add_organism_if_needed()
             genome_analysis_id = run_workflow_for_current_organism.add_analysis_if_needed(
                 analyses_dict_list=analyses_dict_list,
                 analysis_name=run_workflow_for_current_organism.genome_analysis_name,
@@ -405,17 +405,28 @@ if __name__ == "__main__":
 
             # Set the workflow parameters (individual tools runtime parameters in the workflow)
             workflow_parameters = {}
-            # Input files have no parameters (they are set via assigning the hda IDs in the datamap parameter of the bioblend method)
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_FASTA] = {
                 "organism": org_wf_param.org_id,
                 "analysis_id": org_wf_param.genome_analysis_id,
-                "do_update": "true"}
+                "do_update": "true"
+            }
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE] = {}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF] = {
                 "organism": org_wf_param.org_id,
-                "analysis_id": org_wf_param.ogs_analysis_id}
+                "analysis_id": org_wf_param.ogs_analysis_id
+            }
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE] = {
-                "organism_id": org_wf_param.org_id}
+                "organism_id": org_wf_param.org_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG] = {
+                "organism_id": org_wf_param.org_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS] = {
+                "analysis_id": org_wf_param.genome_analysis_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS] = {
+                "analysis_id": org_wf_param.ogs_analysis_id
+            }
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS] = {}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_INDEX] = {}
 
@@ -485,50 +496,67 @@ if __name__ == "__main__":
             logging.info("Input organism %s: 2 species detected in input dictionary" % genus_species)
             strain_sex_org1 = strains_list[0]
             strain_sex_org2 = strains_list[1]
-            sp_wf_param_org1 = strains[strain_sex_org1]
-            sp_wf_param_org2 = strains[strain_sex_org2]
+            org_wf_param_org1 = strains[strain_sex_org1]
+            org_wf_param_org2 = strains[strain_sex_org2]
 
             # Set workflow path (2 organisms)
             workflow_path = os.path.join(os.path.abspath(script_dir), constants_phaeo.WORKFLOWS_PATH, constants_phaeo.WF_LOAD_GFF_JB_2_ORG_FILE)
 
             # Check if the versions of tools specified in the workflow are installed in galaxy
-            utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=sp_wf_param_org1.instance)
+            utilities_bioblend.install_workflow_tools(workflow_path=workflow_path, instance=org_wf_param_org1.instance)
 
             # Set the workflow parameters (individual tools runtime parameters in the workflow)
             workflow_parameters = {}
-            # Input files have no parameters (they are set via assigning the hda IDs in the datamap parameter of the bioblend method)
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1] = {}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1] = {}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1] = {}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2] = {}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2] = {}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2] = {}
             # Organism 1
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1] = {
-                "organism": sp_wf_param_org1.org_id,
-                "analysis_id": sp_wf_param_org1.genome_analysis_id,
-                "do_update": "true"}
+                "organism": org_wf_param_org1.org_id,
+                "analysis_id": org_wf_param_org1.genome_analysis_id,
+                "do_update": "true"
+            }
             # workflow_parameters[JBROWSE_ORG1] = {"jbrowse_menu_url": jbrowse_menu_url_org1}
+            # workflow_parameters[JRBOWSE_ORG2] = {"jbrowse_menu_url": jbrowse_menu_url_org2}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1] = {}
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2] = {}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1] = {
-                "organism": sp_wf_param_org1.org_id,
-                "analysis_id": sp_wf_param_org1.ogs_analysis_id}
+                "organism": org_wf_param_org1.org_id,
+                "analysis_id": org_wf_param_org1.ogs_analysis_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER] = {}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1] = {
-                "organism_id": sp_wf_param_org1.org_id}
+                "organism_id": org_wf_param_org1.org_id
+            }
             # workflow_parameters[JBROWSE_CONTAINER] = {"organisms": [{"name": org1_full_name, "unique_id": org1_species_folder_name, }, {"name": org2_full_name, "unique_id": org2_species_folder_name}]}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER] = {}
             # Organism 2
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG2] = {
-                "organism": sp_wf_param_org2.org_id,
-                "analysis_id": sp_wf_param_org2.genome_analysis_id,
-                "do_update": "true"}
+                "organism": org_wf_param_org2.org_id,
+                "analysis_id": org_wf_param_org2.genome_analysis_id,
+                "do_update": "true"
+            }
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG2] = {
-                "organism": sp_wf_param_org2.org_id,
-                "analysis_id": sp_wf_param_org2.ogs_analysis_id}
-            # workflow_parameters[JRBOWSE_ORG2] = {"jbrowse_menu_url": jbrowse_menu_url_org2}
-            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2] = {}
+                "organism": org_wf_param_org2.org_id,
+                "analysis_id": org_wf_param_org2.ogs_analysis_id
+            }
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2] = {
-                "organism_id": sp_wf_param_org2.org_id}
+                "organism_id": org_wf_param_org2.org_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG1] = {
+                "organism_id": org_wf_param_org1.org_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG2] = {
+                "organism_id": org_wf_param_org2.org_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1] = {
+                "analysis_id": org_wf_param_org1.genome_analysis_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1] = {
+                "analysis_id": org_wf_param_org1.ogs_analysis_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2] = {
+                "analysis_id": org_wf_param_org2.genome_analysis_id
+            }
+            workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2] = {
+                "analysis_id": org_wf_param_org2.ogs_analysis_id
+            }
             # POPULATE + INDEX DATA
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS] = {}
             workflow_parameters[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_INDEX] = {}
@@ -536,13 +564,13 @@ if __name__ == "__main__":
             # Set datamap (mapping of input files in the workflow)
             datamap = {}
             # Organism 1
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1] = {"src": "hda", "id": sp_wf_param_org1.genome_hda_id}
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1] = {"src": "hda", "id": sp_wf_param_org1.gff_hda_id}
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1] = {"src": "hda", "id": sp_wf_param_org1.proteins_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1] = {"src": "hda", "id": org_wf_param_org1.genome_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1] = {"src": "hda", "id": org_wf_param_org1.gff_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1] = {"src": "hda", "id": org_wf_param_org1.proteins_hda_id}
             # Organism 2
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2] = {"src": "hda", "id": sp_wf_param_org2.genome_hda_id}
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2] = {"src": "hda", "id": sp_wf_param_org2.gff_hda_id}
-            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2] = {"src": "hda", "id": sp_wf_param_org2.proteins_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2] = {"src": "hda", "id": org_wf_param_org2.genome_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2] = {"src": "hda", "id": org_wf_param_org2.gff_hda_id}
+            datamap[constants_phaeo.WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2] = {"src": "hda", "id": org_wf_param_org2.proteins_hda_id}
 
             with open(workflow_path, 'r') as ga_in_file:
 
@@ -559,54 +587,54 @@ if __name__ == "__main__":
                 else:
                     root_url = config[constants.CONF_JBROWSE_MENU_URL]
                 # Set "Genus" and "species" as they are given in the add_organism tool (with spaces replaced by "_")
-                species_strain_sex_org1 = sp_wf_param_org1.chado_species_name.replace(" ", "-")
-                species_strain_sex_org2 = sp_wf_param_org2.chado_species_name.replace(" ", "-")
+                species_strain_sex_org1 = org_wf_param_org1.chado_species_name.replace(" ", "-")
+                species_strain_sex_org2 = org_wf_param_org2.chado_species_name.replace(" ", "-")
                 jbrowse_menu_url_org1 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
                     root_url=root_url,
                     genus_sp=genus_species,
-                    Genus=sp_wf_param_org1.genus_uppercase,
+                    Genus=org_wf_param_org1.genus_uppercase,
                     species=species_strain_sex_org1,
                     id="{id}")
                 jbrowse_menu_url_org2 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
                     root_url=root_url,
                     genus_sp=genus_species,
-                    Genus=sp_wf_param_org2.genus_uppercase,
+                    Genus=org_wf_param_org2.genus_uppercase,
                     species=species_strain_sex_org2,
                     id="{id}")
                 # Replace values in the workflow dictionary
                 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"]\
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_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"] = \
                     workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER]["tool_state"]\
-                    .replace("__DISPLAY_NAME_ORG1__", sp_wf_param_org1.full_name)\
-                    .replace("__UNIQUE_ID_ORG1__", sp_wf_param_org1.species_folder_name)\
-                    .replace("__DISPLAY_NAME_ORG2__", sp_wf_param_org2.full_name)\
-                    .replace("__UNIQUE_ID_ORG2__", sp_wf_param_org2.species_folder_name)
+                    .replace("__DISPLAY_NAME_ORG1__", org_wf_param_org1.full_name)\
+                    .replace("__UNIQUE_ID_ORG1__", org_wf_param_org1.species_folder_name)\
+                    .replace("__DISPLAY_NAME_ORG2__", org_wf_param_org2.full_name)\
+                    .replace("__UNIQUE_ID_ORG2__", org_wf_param_org2.species_folder_name)
 
                 # Import the workflow in galaxy as a dict
-                sp_wf_param_org1.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
+                org_wf_param_org1.instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
 
                 # Get its attributes
-                workflow_dict_list = sp_wf_param_org1.instance.workflows.get_workflows(name=workflow_name)
+                workflow_dict_list = org_wf_param_org1.instance.workflows.get_workflows(name=workflow_name)
                 # Then get its ID (required to invoke the workflow)
                 workflow_id = workflow_dict_list[0]["id"]  # Index 0 is the most recently imported workflow (the one we want)
                 logging.debug("Workflow ID: %s" % workflow_id)
                 # Check if the workflow is found
                 try:
-                    show_workflow = sp_wf_param_org1.instance.workflows.show_workflow(workflow_id=workflow_id)
+                    show_workflow = org_wf_param_org1.instance.workflows.show_workflow(workflow_id=workflow_id)
                 except bioblend.ConnectionError:
                     logging.warning("Error finding workflow %s" % workflow_name)
 
                 # Finally, invoke the workflow alogn with its datamap, parameters and the history in which to invoke it
-                sp_wf_param_org1.instance.workflows.invoke_workflow(
+                org_wf_param_org1.instance.workflows.invoke_workflow(
                     workflow_id=workflow_id,
-                    history_id=sp_wf_param_org1.history_id,
+                    history_id=org_wf_param_org1.history_id,
                     params=workflow_parameters,
                     inputs=datamap,
                     allow_tool_state_corrections=True)