Fix tripal page organism picture

constants.py

@@ -7,6 +7,7 @@ ORG_PARAM_DESC_SEX = "sex"
 ORG_PARAM_DESC_STRAIN = "strain"
 ORG_PARAM_DESC_COMMON_NAME = "common_name"
 ORG_PARAM_DESC_ORIGIN = "origin"
+ORG_PARAM_DESC_PICTURE_PATH = "tripal_species_picture"
 ORG_PARAM_DESC_MAIN_SPECIES = "main_species"
 ORG_PARAM_DATA = "data"
 ORG_PARAM_DATA_GENOME_PATH = "genome_path"
@@ -23,6 +24,7 @@ ORG_PARAM_DATA_PERFORMED_BY = "performed_by"
 ORG_PARAM_SERVICES = "services"
 ORG_PARAM_SERVICES_BLAST = "blast"
 
+
 # Constants used in the config yaml file
 CONF_ALL_HOSTNAME = "hostname"
 CONF_ALL_HTTP_PORT = "http_port"

gga_init.py

@@ -76,6 +76,21 @@ 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 one was specified in the input species
+        if self.tripal_species_picture is not None:
+            if self.tripal_species_picture.endswith("png"):
+                species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.png"))
+                try:
+                    os.symlink(os.path.abspath(self.tripal_species_picture, species_picture_dest_path))
+                except FileNotFoundError:
+                    logging.info("Specified organism picture ({0}) not found for {1}".format(self.tripal_species_picture, self.genus_upper + " " + self.species))
+            elif self.tripal_species_picture.endswith("jpg"):
+                species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.jpg"))
+                try:
+                    os.symlink(os.path.abspath(self.tripal_species_picture, species_picture_dest_path))
+                except FileNotFoundError:
+                    logging.info("Specified organism picture ({0}) not found for {1}".format(self.tripal_species_picture, self.genus_upper + " " + self.species))
+
         # Create nginx dirs and write/re-write nginx conf
         make_dirs(dir_paths_li=["./nginx", "./nginx/conf"])
         try:
@@ -111,11 +126,20 @@ 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}
+
+        input_vars = {}
+        if self.tripal_species_picture is not None:
+            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, "tripal_species_picture": self.tripal_species_picture}
+        else:
+            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):
             logging.error("Empty config dictionary")
         # Merge the two dicts

speciesData.py

@@ -91,7 +91,7 @@ class SpeciesData:
         if constants.ORG_PARAM_DESC_PICTURE_PATH in parameters_dictionary_description.keys():
             self.tripal_species_picture = parameters_dictionary_services[constants.ORG_PARAM_DESC_PICTURE_PATH]
         else:
-            self.tripal_species_picture = ""
+            self.tripal_species_picture = None
 
         self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
         self.genus_uppercase = self.genus[0].upper() + self.genus[1:]