Refactor run_wf (WIP)

phaeoexplorer_constants.py → phaeo_constants.py

@@ -4,6 +4,7 @@
 import constants
 
 ### Workflows
+# WARNING: Be very careful about how the workflow is "organized" (i.e the order of the steps/datasets, check the .ga if there is any error)
 
 WORKFLOWS_PATH = "workflows_phaeoexplorer/"
 WF_LOAD_GFF_JB = "load_fasta_gff_jbrowse"
@@ -20,6 +21,25 @@ WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
 WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
 WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
 
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v4.ga"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "0"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "1"
+WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "3"
+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_LOAD_GFF_ORG1 = "9"
+WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER = "10"
+WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_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_FEATURE_SYNC_ORG2 = "14"
+WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "15"
+WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "16"
+
 WORKFLOW_BLAST = "blast"
 WORKFLOW_INTERPRO = "interpro"
 WORKFLOW_VALID_TYPES = [WF_LOAD_GFF_JB, WORKFLOW_BLAST, WORKFLOW_INTERPRO]

speciesData.py

@@ -42,7 +42,12 @@ class SpeciesData:
 
     def clean_string(self, string):
         if not string is None and string != "":
-            clean_string = string.replace(" ", "_").replace("-", "_").replace("(", "").replace(")", "").replace("'", "").strip()
+            clean_string = string\
+                .replace(" ", "_")\
+                .replace("-", "_")\
+                .replace("(", "")\
+                .replace(")", "")\
+                .replace("'", "").strip()
             return clean_string
         else:
             return string