Remove option for url

galaxyproject · Oct 30, 2020 · e506ebf · e506ebf
1 parent 646b133
commit e506ebf
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Showing 4 changed files with 4 additions and 24 deletions.
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
@@ -3199,17 +3199,7 @@
     Sets the path to EDAM ontology file.
     The value of this option will be resolved with respect to
     <data_dir>.
-:Default: ``EDAM_1.23.tsv``
-:Type: str
-
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-``beta_edam_ontology_url``
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Sets the url to the EDAM ontology file.
-:Default: ``https://edamontology.org/EDAM_1.23.tsv``
+:Default: ``EDAM.tsv``
 :Type: str
 
 

diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1596,10 +1596,7 @@ galaxy:
   # Sets the path to EDAM ontology file.
   # The value of this option will be resolved with respect to
   # <data_dir>.
-  #beta_edam_toolbox_ontology_path: EDAM_1.23.tsv
-
-  # Sets the url to the EDAM ontology file.
-  #beta_edam_ontology_url: https://edamontology.org/EDAM_1.23.tsv
+  #beta_edam_toolbox_ontology_path: EDAM.tsv
 
   # Default format for the export of workflows. Possible values are 'ga'
   # or 'format2'.

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
@@ -140,7 +140,7 @@ def _load_edam(self):
         if not os.path.exists(self.app.config.beta_edam_toolbox_ontology_path):
             log.debug('EDAM ontology file not present, downloading')
 
-            page = urllib.request.urlopen(self.app.config.beta_edam_ontology_url)
+            page = urllib.request.urlopen('https://edamontology.org/EDAM.tsv')
             sniff.stream_to_open_named_file(page, os.open(self.app.config.beta_edam_toolbox_ontology_path, os.O_WRONLY | os.O_CREAT), None, source_encoding=get_charset_from_http_headers(page.headers))
 
         log.debug('Processing EDAM Terms')

diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2333,19 +2333,12 @@ mapping:
 
       beta_edam_toolbox_ontology_path:
         type: str
-        default: EDAM_1.23.tsv
+        default: EDAM.tsv
         path_resolves_to: data_dir
         required: false
         desc: |
           Sets the path to EDAM ontology file.
 
-      beta_edam_ontology_url:
-        type: str
-        default: 'https://edamontology.org/EDAM_1.23.tsv'
-        required: false
-        desc: |
-          Sets the url to the EDAM ontology file.
-
       default_workflow_export_format:
         type: str
         default: ga