Removed commented code

gga_init.py

@@ -89,21 +89,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
                     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))
-
-        # if self.picture_path is not None:
-        #     if self.picture_path.endswith("png"):
-        #         species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.png"))
-        #         try:
-        #             os.symlink(os.path.abspath(self.picture_path), species_picture_dest_path)
-        #         except FileNotFoundError:
-        #             logging.info("Specified organism picture ({0}) not found for {1}".format(self.picture_path, self.genus_uppercase + " " + self.species))
-        #     elif self.picture_path.endswith("jpg"):
-        #         species_picture_dest_path = os.path.join(self.species_dir, os.path.abspath("species.jpg"))
-        #         try:
-        #             os.symlink(os.path.abspath(self.picture_path), species_picture_dest_path)
-        #         except FileNotFoundError:
-        #             logging.info("Specified organism picture ({0}) not found 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:

run_workflow_phaeoexplorer.py

@@ -71,40 +71,6 @@ class RunWorkflow(speciesData.SpeciesData):
         logging.debug("Library ID: %s" % self.library_id)
         instance_source_data_folders = self.instance.libraries.get_folders(library_id=library_id)
 
-        # # Access folders via their absolute path
-        # genome_folder = self.instance.libraries.get_folders(library_id=library_id, name="/genome/" + str(self.species_folder_name) + "/v" + str(self.genome_version))
-        # annotation_folder = self.instance.libraries.get_folders(library_id=library_id, name="/annotation/" + str(self.species_folder_name) + "/OGS" + str(self.ogs_version))
-        
-        # # Get their IDs
-        # genome_folder_id = genome_folder[0]["id"]
-        # annotation_folder_id = annotation_folder[0]["id"]
-
-        # # Get the content of the folders
-        # genome_folder_content = self.instance.folders.show_folder(folder_id=genome_folder_id, contents=True)
-        # annotation_folder_content = self.instance.folders.show_folder(folder_id=annotation_folder_id, contents=True)
-
-        # # Find genome folder datasets
-        # genome_fasta_ldda_id = genome_folder_content["folder_contents"][0]["ldda_id"]
-
-        # annotation_gff_ldda_id, annotation_proteins_ldda_id, annotation_transcripts_ldda_id = None, None, None
-
-        # # Several dicts in the annotation folder content (one dict = one file)
-        # for k, v in annotation_folder_content.items():
-        #     if k == "folder_contents":
-        #         for d in v:
-        #             if "proteins" in d["name"]:
-        #                 annotation_proteins_ldda_id = d["ldda_id"]
-        #             if "transcripts" in d["name"]:
-        #                 annotation_transcripts_ldda_id = d["ldda_id"]
-        #             if ".gff" in d["name"]:
-        #                 annotation_gff_ldda_id = d["ldda_id"]
-
-        # # Minimum datasets to populate tripal views --> will not work if these files are not assigned in the input file
-        # self.datasets["genome_file"] = genome_fasta_ldda_id
-        # self.datasets["gff_file"] = annotation_gff_ldda_id
-        # self.datasets["proteins_file"] = annotation_proteins_ldda_id
-        # self.datasets["transcripts_file"] = annotation_transcripts_ldda_id
-
         return {"history_id": self.history_id, "library_id": library_id}