Get input yml keys from constants

examples/citrus_sinensis.yml

@@ -33,6 +33,4 @@
   services:
   # List the optional services to be deploy in the stack
   # By default, only tripal, tripaldb, galaxy, jbrowse and elasticsearch services will be deployed
-    blast: "False"
-    wiki: "False"
-    apollo: "False"
\ No newline at end of file
+    blast: "False"
\ No newline at end of file

templates/organisms.yml.j2

-- name: {{ name }}
-  description:
-    genus: {{ genus }}
-    species: {{ species }}
-    sex: {{ sex }}
-    strain: {{ strain }}
-    common_name: {{ common_name }}
-    origin: {{ origin }}
-    {% if main_species is defined and main_species is sameas true %}
-    main_species: yes
+- {{ org_param_name  }}: {{ org_param_name_value }}
+  {{ org_param_desc }}:
+    {{ org_param_desc_genus }}: {{ org_param_desc_genus_value }}
+    {{ org_param_desc_species }}: {{ org_param_desc_species_value }}
+    {{ org_param_desc_sex }}: {{ org_param_desc_sex_value }}
+    {{ org_param_desc_strain }}: {{ org_param_desc_strain_value }}
+    {{ org_param_desc_common_name }}: {{ org_param_desc_common_name_value }}
+    {{ org_param_desc_origin }}: {{ org_param_desc_origin_value }}
+    {% if org_param_desc_main_species_value is defined and org_param_desc_main_species_value is same as true %}
+    {{ org_param_desc_main_species }}: yes
     {% endif %}
-  data:
-    genome_path: {{ genome_path }}
-    transcripts_path: {{ transcripts_path }}
-    proteins_path: {{ proteins_path }}
-    gff_path: {{ gff_path }}
-    interpro_path: {{ interpro_path }}
-    orthofinder_path: {{ orthofinder_path }}
-    blastp_path: {{ blastp_path }}
-    blastx_path: {{ blastx_path }}
-    genome_version: {{ genome_version }}
-    ogs_version: {{ ogs_version }}
-    performed_by: {{ performed_by }}
-  services:
-    blast: {{ blast }}
\ No newline at end of file
+  {{ org_param_data }}:
+    {{ org_param_data_genome_path }}: {{ org_param_data_genome_path_value }}
+    {{ org_param_data_transcripts_path }}: {{ org_param_data_transcripts_path_value }}
+    {{ org_param_data_proteins_path }}: {{ org_param_data_proteins_path_value }}
+    {{ org_param_data_gff_path }}: {{ org_param_data_gff_path_value }}
+    {{ org_param_data_interpro_path }}: {{ org_param_data_interpro_path_value }}
+    {{ org_param_data_orthofinder_path }}: {{ org_param_data_orthofinder_path_value }}
+    {{ org_param_data_blastp_path }}: {{ org_param_data_blastp_path_value }}
+    {{ org_param_data_blastx_path }}: {{ org_param_data_blastx_path_value }}
+    {{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }}
+    {{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
+    {{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }}
+  {{ org_param_services }}:
+    {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
\ No newline at end of file

utilities.py

@@ -187,4 +187,37 @@ def run_tool_and_get_single_output_dataset_id(instance, tool_id, history_id, too
     output_dict = run_tool(instance, tool_id, history_id, tool_inputs)
     single_output_dataset_id = output_dict["outputs"][0]["id"]
 
-    return single_output_dataset_id
\ No newline at end of file
+    return single_output_dataset_id
+
+def create_org_param_dict_from_constants():
+    """
+    Create a dictionary of variables containing the keys needed to render the organisms.yml.j2 (NOT the values)
+    Created from the constants
+    """
+
+    org_param_dict={}
+    org_param_dict[constants.ORG_PARAM_NAME] = constants.ORG_PARAM_NAME
+    org_param_dict[constants.ORG_PARAM_DESC] = constants.ORG_PARAM_DESC
+    org_param_dict[constants.ORG_PARAM_DESC_GENUS] = constants.ORG_PARAM_DESC_GENUS
+    org_param_dict[constants.ORG_PARAM_DESC_SPECIES] = constants.ORG_PARAM_DESC_SPECIES
+    org_param_dict[constants.ORG_PARAM_DESC_SEX] = constants.ORG_PARAM_DESC_SEX
+    org_param_dict[constants.ORG_PARAM_DESC_STRAIN] = constants.ORG_PARAM_DESC_STRAIN
+    org_param_dict[constants.ORG_PARAM_DESC_COMMON_NAME] = constants.ORG_PARAM_DESC_COMMON_NAME
+    org_param_dict[constants.ORG_PARAM_DESC_ORIGIN] = constants.ORG_PARAM_DESC_ORIGIN
+    org_param_dict[constants.ORG_PARAM_DESC_MAIN_SPECIES] = constants.ORG_PARAM_DESC_MAIN_SPECIES
+    org_param_dict[constants.ORG_PARAM_DATA] = constants.ORG_PARAM_DATA
+    org_param_dict[constants.ORG_PARAM_DATA_GENOME_PATH] = constants.ORG_PARAM_DATA_GENOME_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH] = constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_PROTEINS_PATH] = constants.ORG_PARAM_DATA_PROTEINS_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_GFF_PATH] = constants.ORG_PARAM_DATA_GFF_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_INTERPRO_PATH] = constants.ORG_PARAM_DATA_INTERPRO_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_ORTHOFINDER_PATH] = constants.ORG_PARAM_DATA_ORTHOFINDER_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_BLASTP_PATH] = constants.ORG_PARAM_DATA_BLASTP_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_BLASTX_PATH] = constants.ORG_PARAM_DATA_BLASTX_PATH
+    org_param_dict[constants.ORG_PARAM_DATA_GENOME_VERSION] = constants.ORG_PARAM_DATA_GENOME_VERSION
+    org_param_dict[constants.ORG_PARAM_DATA_OGS_VERSION] = constants.ORG_PARAM_DATA_GENOME_VERSION
+    org_param_dict[constants.ORG_PARAM_DATA_PERFORMED_BY] = constants.ORG_PARAM_DATA_PERFORMED_BY
+    org_param_dict[constants.ORG_PARAM_SERVICES] = constants.ORG_PARAM_SERVICES
+    org_param_dict[constants.ORG_PARAM_SERVICES_BLAST] = constants.ORG_PARAM_SERVICES_BLAST
+
+    return org_param_dict
\ No newline at end of file