Add a picture in Tripal home page

Fix http://gitlab.sb-roscoff.fr/abims/e-infra/gga_load_data/issues/3

run_workflow_development

gga_init.py

@@ -76,6 +76,20 @@ 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)
+                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)
+                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:
@@ -111,11 +125,12 @@ 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}
+                          "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}
         if (len(self.config.keys()) == 0):
             logging.error("Empty config dictionary")
         # Merge the two dicts