add suppress_output to update_organism

README.rst

@@ -85,6 +85,8 @@ Or with the Arrow client:
 History
 -------
 
+- 4.2.8
+    - Added --suppress_output to update_organism
 - 4.2.7
     - Renamed --return_all option to --suppress_output
 - 4.2.6

apollo/organisms/__init__.py

@@ -74,7 +74,7 @@ def add_organism(self, common_name, directory, blatdb=None, genus=None,
             return data
 
     def update_organism(self, organism_id, common_name, directory, blatdb=None, species=None, genus=None, public=False,
-                        no_reload_sequences=False):
+                        no_reload_sequences=False, suppress_output=False):
         """
         Update an organism
 
@@ -102,6 +102,9 @@ def update_organism(self, organism_id, common_name, directory, blatdb=None, spec
         :type no_reload_sequences: bool
         :param no_reload_sequences: Set this if you don't want Apollo to reload genome sequences (no change in genome sequence)
 
+        :type suppress_output: bool
+        :param suppress_output: Suppress output of all organisms (true / false) (default false)
+
         :rtype: dict
         :return: a dictionary with information about the updated organism
         """
@@ -119,6 +122,8 @@ def update_organism(self, organism_id, common_name, directory, blatdb=None, spec
             data['genus'] = genus
         if species is not None:
             data['species'] = species
+        if suppress_output is not None and suppress_output is True:
+            data['returnAllOrganisms'] = False
 
         response = self.post('updateOrganismInfo', data)[0]
 

arrow/commands/organisms/update_organism.py

@@ -32,14 +32,19 @@
     help="Set this if you don't want Apollo to reload genome sequences (no change in genome sequence)",
     is_flag=True
 )
+@click.option(
+    "--suppress_output",
+    help="Suppress output of all organisms (true / false) (default false)",
+    is_flag=True
+)
 @pass_context
 @custom_exception
 @dict_output
-def cli(ctx, organism_id, common_name, directory, blatdb="", species="", genus="", public=False, no_reload_sequences=False):
+def cli(ctx, organism_id, common_name, directory, blatdb="", species="", genus="", public=False, no_reload_sequences=False, suppress_output=False):
     """Update an organism
 
 Output:
 
     a dictionary with information about the updated organism
     """
-    return ctx.gi.organisms.update_organism(organism_id, common_name, directory, blatdb=blatdb, species=species, genus=genus, public=public, no_reload_sequences=no_reload_sequences)
+    return ctx.gi.organisms.update_organism(organism_id, common_name, directory, blatdb=blatdb, species=species, genus=genus, public=public, no_reload_sequences=no_reload_sequences, suppress_output=suppress_output)

docs/commands/organisms.rst

@@ -228,5 +228,8 @@ Update an organism
       --no_reload_sequences  Set this if you don't want Apollo to reload genome
                              sequences (no change in genome sequence)
     
+      --suppress_output      Suppress output of all organisms (true / false)
+                             (default false)
+    
       -h, --help             Show this message and exit.
     

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="apollo",
-    version='4.2.7',
+    version='4.2.8',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau;Nathan Dunn",