Merge branch 'picture' into 'dev'

fixes

See merge request !16

gga_init.py

@@ -38,7 +38,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
 
     """
 
-    def make_directory_tree(self):
+    def make_directory_tree(self, picture_path):
         """
         Generate the directory tree for an organism
 
@@ -76,19 +76,19 @@ 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 one was specified in the input species
-        if self.picture_path is not None:
-            if os.path.isfile(self.picture_path):
-                picture_path_basename = os.path.basename(self.picture_path)
+        # Copy the organism picture for tripal
+        if picture_path is not None:
+            if os.path.isfile(picture_path):
+                picture_path_basename = os.path.basename(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)
+                    shutil.copy(picture_path, picture_dest_path)
                 else:
-                    logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(self.picture_path))
+                    logging.error("Specified organism picture has wrong extension (must be '.png' or '.jpg'): {0}".format(picture_path))
             else:
-                logging.error("Specified organism picture not found {0} for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
+                logging.error("Specified organism picture not found {0} for {1}".format(picture_path, self.genus_uppercase + " " + self.species))
                 
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
@@ -127,10 +127,10 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # 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, "picture_path": self.picture_path}
+                        "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": "{0} {1}".format(self.genus_uppercase, self.species_lower()),
+                        "blast": self.blast, "picture_path": self.picture_path}
         if (len(self.config.keys()) == 0):
             logging.error("Empty config dictionary")
         # Merge the two dicts
@@ -402,6 +402,7 @@ if __name__ == "__main__":
         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)
 
     logging.info("Deploying stacks for organisms in input file %s" % args.input)
     for sp_dict in unique_sp_dict_list:
@@ -422,7 +423,8 @@ 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.make_directory_tree()
+        picture_path = sp_picture_dict[deploy_stack_for_current_organism.genus_species]
+        deploy_stack_for_current_organism.make_directory_tree(picture_path)
         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

speciesData.py

@@ -93,20 +93,25 @@ class SpeciesData:
         else:
             self.picture_path = None
 
-        self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
-        self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
+        self.genus_lowercase = self.genus.lower()
+        self.species_lower = self.species.lower()
+        self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:]
+        self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lower)
+
         self.chado_species_name = "{0} {1}".format(self.species, self.sex)
         self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"])
-
         self.full_name_lowercase = self.full_name.lower()
         self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
-        
-        self.genus_species = "{0}_{1}".format(self.genus.lower(), self.species.lower())
+
+        self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
+            [self.genus_lowercase, self.species_lower(), self.strain.lower(),
+             self.sex.lower()])["not_empty"])
+
         self.dataset_prefix = None
         if self.sex is not None or self.sex != "":
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species.lower() + "_" + self.sex[0].lower()
+            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower + "_" + self.sex[0].lower()
         else:
-            self.dataset_prefix = self.genus[0].lower() + "_" + self.species.lower()
+            self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower
 
         # Bioblend/Chado IDs for an organism analyses/organisms/datasets/history/library
         self.org_id = None
@@ -131,6 +136,3 @@ class SpeciesData:
         self.api_key = None  # API key used to communicate with the galaxy instance. Cannot be used to do user-tied actions
         self.datasets = dict()
         self.config = None  # Custom config used to set environment variables inside containers
-        self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items(
-            [self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(),
-             self.sex.lower()])["not_empty"])

templates/gspecies_compose.yml.j2

@@ -38,18 +38,18 @@ services:
             - ./docker_data/galaxy/:/export/:ro
             - ./src_data/:/project_data/:ro
             - ./src_data:/data:ro
-          {% if 'tripal_banner_path' is defined %}
+            {% if 'tripal_banner_path' is defined %}
             - ./banner.png:/var/www/html/banner.png:ro
-          {% endif %}
+            {% endif %}
             #- /groups/XXX/:/groups/XXX/:ro  # We do this when we have symlinks in src_data pointing to /groups/XXX/...
-          {% if 'picture_path' is defined %}
-            {% if 'png' in picture_path %}
+            {% if 'picture_path' is defined %}
+                {% if 'png' in picture_path %}
             - ./species.png:/var/www/html/species.png:ro
-            {% endif %}
-            {% if 'jpg' in picture_path %}
+                {% endif %}
+                {% if 'jpg' in picture_path %}
             - ./species.jpg:/var/www/html/species.jpg:ro
+                {% endif %}
             {% endif %}
-          {% endif %}
         environment:
             DB_HOST: tripal-db.{{ genus_species }}
             BASE_URL_PATH: /sp/{{ genus_species }}

utilities.py

@@ -162,14 +162,28 @@ def get_unique_species_dict_list(sp_dict_list):
         if gspecies not in unique_species_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
                                                            sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
             unique_species_dict[gspecies] = sp
-        else:
-            continue
 
     for k, v in unique_species_dict.items():
         unique_species_list_of_dict.append(v)
 
     return unique_species_list_of_dict
 
+def get_sp_picture(sp_dict_list):
+    """
+    Get the picture for each species: the picture of the main strain if exists, other strain if not
+    """
+
+    sp_picture_dict = {}
+
+    for sp in sp_dict_list:
+        gspecies = get_gspecies_string_from_sp_dict(sp)
+        if gspecies not in sp_picture_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
+                                                           sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ):
+            if sp[constants.ORG_PARAM_DESC_PICTURE_PATH] != "":
+                sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC_PICTURE_PATH]
+
+    return sp_picture_dict
+
 def run_tool(instance, tool_id, history_id, tool_inputs):
 
     output_dict = None
@@ -223,4 +237,4 @@ 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
 
-    return org_param_dict
\ No newline at end of file
+    return org_param_dict