Add project_url env variable in tripal service

constants.py

@@ -25,6 +25,7 @@ ORG_PARAM_DATA_BLASTX_PATH = "blastx_path"
 ORG_PARAM_DATA_GENOME_VERSION = "genome_version"
 ORG_PARAM_DATA_OGS_VERSION = "ogs_version"
 ORG_PARAM_SERVICES = "services"
+ORG_PARAM_SERVICES_PROJECT_URL = "project_url"
 ORG_PARAM_SERVICES_BLAST = "blast"
 ORG_PARAM_SERVICES_GO = "go"
 

gga_init.py

@@ -135,7 +135,7 @@ class DeploySpeciesStack(species_data.SpeciesData):
                         "genus_species": self.genus_species, "jbrowse_dataset_id": self.species_folder_name, "jbrowse_links": self.jbrowse_links,
                         "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lowercase, self.sex),
                         "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lowercase),
-                        "blast": self.blast, "go": self.go, "picture_path": self.picture_path}
+                        "blast": self.blast, "go": self.go, "project_url": self.project_url, "picture_path": self.picture_path}
         if len(self.config.keys()) == 0:
             logging.error("Empty config dictionary")
         # Merge the two dicts

species_data.py

@@ -107,6 +107,7 @@ class SpeciesData:
 
         self.blast = set_service_attribute(constants.ORG_PARAM_SERVICES_BLAST, parameters_dictionary)
         self.go = set_service_attribute(constants.ORG_PARAM_SERVICES_GO, parameters_dictionary)
+        self.project_url = set_service_attribute(constants.ORG_PARAM_SERVICES_PROJECT_URL, parameters_dictionary)
 
         self.genus_lowercase = self.genus.lower()
         self.species_lowercase = self.species.lower()

templates/gspecies_compose.yml.j2

@@ -75,6 +75,9 @@ services:
             ENABLE_GO: {{ go }}
             ENABLE_ORTHOLOGY: 0
             ENABLE_ORTHOLOGY_LINKS: 0
+            {% if (project_url is defined and project_url) and (project_url != "0") %}
+            PROJECT_URL: {{ project_url }}
+            {% endif %}
             THEME: "{{ tripal_theme_name }}"  # Use this to use another theme
             THEME_GIT_CLONE: "{{ tripal_theme_git_clone }}"  # Use this to install another theme
             ADMIN_PASSWORD: {{ tripal_password }}  # You need to define it and update it in galaxy config below

templates/organisms.yml.j2

@@ -23,5 +23,6 @@
     {{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }}
     {{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }}
   {{ org_param_services }}:
+    {{ org_param_services_project_url }}: {{ org_param_services_project_url_value }}
     {{ org_param_services_blast }}: {{ org_param_services_blast_value }}
     {{ org_param_services_go }}: {{ org_param_services_go_value }}
\ No newline at end of file

utilities.py

@@ -224,5 +224,6 @@ def create_org_param_dict_from_constants():
     org_param_dict["org_param_services"] = constants.ORG_PARAM_SERVICES
     org_param_dict["org_param_services_blast"] = constants.ORG_PARAM_SERVICES_BLAST
     org_param_dict["org_param_services_go"] = constants.ORG_PARAM_SERVICES_GO
+    org_param_dict["org_param_services_project_url"] = constants.ORG_PARAM_SERVICES_PROJECT_URL
 
     return org_param_dict