Merge pull request #38 from opentargets/cm_removed_unused_code

Remove unused code

config.yaml

@@ -111,28 +111,6 @@ efo:
       output_filename: ontology-mondo.jsonl
       resource: ontology-mondo
       owl_jq: '.["@graph"][] | @json'
-  efo_extra_downloads:
-    - uri: http://www.informatics.jax.org/downloads/reports/mp.owl
-      output_filename: ontology-mp-{suffix}.owl
-      resource: ontology-mp
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/ibd_2_pheno_associations.owl?format=raw
-      output_filename: ibd_2_pheno_associations-{suffix}.owl
-      resource: disease-phenotype
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/immune_disease_2_pheno.owl?format=raw
-      output_filename: immune_disease_2_pheno-{suffix}.owl
-      resource: disease-phenotype
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/rareAlbuminuria_associations_03Jun15.owl?format=raw
-      output_filename: rareAlbuminuria_associations-{suffix}.owl
-      resource: disease-phenotype
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/rareIBDpheno.owl?format=raw
-      output_filename: rareIBDpheno-{suffix}.owl
-      resource: disease-phenotype
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/ordo_hpo_mappings.owl?format=raw
-      output_filename: ordo_hpo_mappings-{suffix}.owl
-      resource: disease-phenotype
-    - uri: https://sourceforge.net/p/efo/code/HEAD/tree/trunk/src/efoassociations/charite_HP_ORDO_07Oct15.owl?format=raw
-      output_filename: charite_HP_ORDO-{suffix}.owl
-      resource: disease-phenotype
 chemical_probes:
   output_filename: chemicalprobes_portalprobes-{suffix}.tsv
   resource: chemical-probes-1

modules/EFO.py

@@ -40,14 +40,6 @@ def download_file_original(self, uri):
 
         return destination_filename
 
-    # This method will be soon obsolete. Legacy with data_pipeline
-    def download_extra_files(self,yaml):
-        for entry in yaml:
-            download = DownloadResource(self.local_output_dir)
-            destination_filename = download.execute_download(entry)
-            self.list_files_downloaded[destination_filename] = {'resource': entry.resource,
-                                                                'gs_output_dir': self.output_dir}
-        return destination_filename
 
     # This method download and convert the owl file into JSON using riot.
     # More details in the README
@@ -101,8 +93,6 @@ def get_ontology_EFO(self):
 
     def generate_efo(self):
         logger.info("Running EFO step ")
-        #Potentially obsolete soon! Legacy data_pipeline : TODO remove legacy
-        self.download_extra_files(self.yaml.efo_extra_downloads)
 
         # Generate the ontologies and the phenotype mapping file.
         self.get_hpo_phenotype()