Release v2.1.0

General

• Bump cryptography requirement version to 3.2
• Create tools to handle multiple docker stacks in docker_tools repository (toggl galaxy state, update service)

Input config.yml file

• Fix typo in parameter galaxy_default_admin_user
• Add parameter galaxy_default_admin_key (required to create the admin user galaxy_default_admin_user in Galaxy)
• Check that all required parameters are not empty

Input organisms.yml file

• Add the parameter picture_path in the description section to add this picture in the Tripal homepage
• Add parameter contig_prefix in the data section to list the prefixes used for contig names. Required when they are multiple strains from the same species to map the contig name prefix to the right JBrowse dataset ID in Tripal (see Step "init")
• Add the go summary functionality in Tripal. This functionality can be activated with parameter go set to 1 in the services section
• Remove unused performed_by parameter
• Fix code for empty strain and/or sex

Step "init"

• Add a picture of the species in the Tripal homepage (the picture of the main strain if exists, the picture of another strain if not)
• Fix Tripal site name
• Add env variable JBROWSE_LINKS in the Tripal service, to map the contig name prefix to the right JBrowse dataset ID in Tripal (for Tripal hyperlinks to JBrowse)

Step "get data"

• Change data file names: use prefix strain_sex

Step "run workflow Phaeoexplorer"

• Create a parent module run_workflow_phaeo.py, with classes and methods used by the workflow scripts
• Create file constants_phaeo.py to store constants used in step "run workflow Phaeoexplorer" (workflows and galaxy tools details)
• Script gga_run_workflow_phaeo_jbrowse.py: runs a Galaxy workflow to load the genome, the annotations and the proteins to Chado, Tripal and JBrowse, for one or two strains of the same species
• Work in progress: workflows to load blast and interpro results

gga_init.py

@@ -13,7 +13,7 @@ from pathlib import Path
 from jinja2 import Environment, FileSystemLoader
 
 import utilities
-import speciesData
+import species_data
 import constants
 
 
@@ -29,7 +29,7 @@ TODO
 
 """
 
-class DeploySpeciesStack(speciesData.SpeciesData):
+class DeploySpeciesStack(species_data.SpeciesData):
     """
     Child of SpeciesData
 
@@ -37,6 +37,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
     the organism's directory tree to create the required docker-compose files and stack deployment
 
     """
+    def __init__(self, parameters_dictionary):
+        self.picture_path = None
+        self.jbrowse_links = None
+        super().__init__(parameters_dictionary)
 
     def make_directory_tree(self):
         """
@@ -76,6 +80,21 @@ class DeploySpeciesStack(speciesData.SpeciesData):
             logging.debug("Using default banner for Tripal pages")
             self.config.pop(constants.CONF_TRIPAL_BANNER_PATH, None)
 
+        # Copy the organism picture for tripal
+        if self.picture_path is not None:
+            if os.path.isfile(self.picture_path):
+                picture_path_basename = os.path.basename(self.picture_path)
+                picture_path_filename, picture_path_extension = os.path.splitext(picture_path_basename)
+                if picture_path_extension == ".png" or picture_path_extension == ".jpg":
+                    picture_dest_name = "species%s" % picture_path_extension
+                    picture_dest_path = os.path.join(self.species_dir, picture_dest_name)
+                    shutil.copy(self.picture_path, picture_dest_path)
+                    logging.info("Add picture %s" % self.picture_path)
+                else:
+                    logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
+            else:
+                logging.error("Specified organism picture not found {0} for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
+                
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
         try:
@@ -111,12 +130,13 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # We need a dict holding all key (variables) - values that needs to be replaced in the template as our rendering dict
         # To do so we need both input file vars and config vars
         # Create input file vars dict
+
         input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
-                      "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
-                      "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species.lower(), self.sex),
-                      "strain": self.strain, "sex": self.sex, "Genus_species": self.genus_species[0].upper() + self.genus_species[1:],
-                      "blast": self.blast}
-        if (len(self.config.keys()) == 0):
+                        "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}
+        if len(self.config.keys()) == 0:
             logging.error("Empty config dictionary")
         # Merge the two dicts
         render_vars = {**self.config, **input_vars}
@@ -146,19 +166,6 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         os.chdir(self.main_dir)
 
 
-    def make_orthology_compose_files(self):
-        """
-        Create/update orthology compose files
-
-        :return:
-        """
-
-        os.chdir(self.main_dir)
-
-        make_dirs["./orthology", "./orthology/src_data", "./orthology/src_data/genomes", 
-                       "./orthology/src_data/gff", "./orthology/src_data/newicks", "./orthology/src_data/proteomes"]
-
-
 def make_dirs(dir_paths_li):
     """
     Recursively create directories from a list of paths with a try-catch condition
@@ -334,6 +341,7 @@ def deploy_stacks(input_list, main_dir, deploy_traefik):
     logging.info("Updating traefik stack")
     run_docker_stack_deploy("traefik", traefik_dir)
 
+    #TODO: add test to check that the network/name resolution is fine in each galaxy container
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Deploy GGA containers")
@@ -371,7 +379,7 @@ if __name__ == "__main__":
     else:
         config_file = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])), constants.DEFAULT_CONFIG)
     config = utilities.parse_config(config_file)
-    if (len(config.keys()) == 0):
+    if len(config.keys()) == 0:
         logging.error("Empty config dictionary")
 
     main_dir = None
@@ -382,11 +390,19 @@ if __name__ == "__main__":
 
     sp_dict_list = utilities.parse_input(os.path.abspath(args.input))
 
+    #TODO: create SpeciesData objects in utilities.parse_input()
+    org_list = []
+    for sp_dict in sp_dict_list:
+        org = DeploySpeciesStack(parameters_dictionary=sp_dict)
+        org_list.append(org)
+
     # Create traefik directory and compose files if needed or specified
     if args.force_traefik or not os.path.isdir(os.path.join(os.path.abspath(main_dir), "traefik")):
         make_traefik_compose_files(config=config, main_dir=main_dir)
 
     unique_sp_dict_list = utilities.get_unique_species_dict_list(sp_dict_list=sp_dict_list)
+    sp_picture_dict = utilities.get_sp_picture(sp_dict_list=sp_dict_list)
+    sp_jbrowse_links_dict = utilities.get_sp_jbrowse_links(org_list=org_list)
 
     logging.info("Deploying stacks for organisms in input file %s" % args.input)
     for sp_dict in unique_sp_dict_list:
@@ -407,10 +423,12 @@ if __name__ == "__main__":
         logging.info("gga_init.py called for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 
         # Make/update directory tree
+        deploy_stack_for_current_organism.picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
         deploy_stack_for_current_organism.make_directory_tree()
         logging.info("Successfully generated the directory tree for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 
         # Make compose files
+        deploy_stack_for_current_organism.jbrowse_links = sp_jbrowse_links_dict[deploy_stack_for_current_organism.genus_species]
         deploy_stack_for_current_organism.make_compose_files()
         logging.info("Successfully generated the docker-compose files for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)