returnAllOrganisms parameter for add_organism (#41)

* added apollo3 link * Exposed returnAllOrganisms option to the Organisms.addOrganisms API call * param name fix * rebuilt arrow properly * fixed call * added delete organisms * arrow/docs rebuild Co-authored-by: Nathan Dunn <[email protected]> Co-authored-by: Cory Maughmer <[email protected]>
galaxy-genome-annotation · Aug 25, 2020 · cddf637 · cddf637
1 parent 3733712
commit cddf637
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Showing 8 changed files with 59 additions and 14 deletions.
diff --git a/README.rst b/README.rst
@@ -85,6 +85,8 @@ Or with the Arrow client:
 History
 -------
 
+- 4.2.6
+    - Prevent from displaying login/password in the logs
 - 4.2.5
     - Prevent from displaying login/password in the logs
 - 4.2.4

diff --git a/apollo/organisms/__init__.py b/apollo/organisms/__init__.py
@@ -12,7 +12,7 @@ class OrganismsClient(Client):
 
     @raise_error_decorator
     def add_organism(self, common_name, directory, blatdb=None, genus=None,
-                     species=None, public=False, metadata=None):
+                     species=None, public=False, metadata=None, return_all=None):
         """
         Add an organism
 
@@ -37,6 +37,9 @@ def add_organism(self, common_name, directory, blatdb=None, genus=None,
         :type metadata: str
         :param metadata: JSON formatted arbitrary metadata
 
+        :type return_all: bool
+        :param return_all: Return all organisms (true / false) (default true)
+
         :rtype: dict
         :return: a dictionary with information about the new organism
         """
@@ -57,13 +60,18 @@ def add_organism(self, common_name, directory, blatdb=None, genus=None,
                 # Apollo wants a string
                 metadata = json.dumps(metadata)
             data['metadata'] = metadata
+        if return_all is not None:
+            data['returnAllOrganisms'] = return_all
 
         response = self.post('addOrganism', data)
         # Apollo decides here that it would be nice to return information about
         # EVERY organism. LMAO.
         if type(response) is not list:
             return response
-        return [x for x in response if x['commonName'] == common_name][0]
+        if len(response) > 0:
+            return [x for x in response if x['commonName'] == common_name][0]
+        else:
+            return data
 
     def update_organism(self, organism_id, common_name, directory, blatdb=None, species=None, genus=None, public=False,
                         no_reload_sequences=False):
@@ -149,17 +157,27 @@ def show_organism(self, common_name):
             orgs = orgs[0]
         return orgs
 
-    def delete_organism(self, organism_id):
+    def delete_organism(self, organism_id, return_all=None):
         """
-        Delete an organim
+        Delete an organism
 
         :type organism_id: str
         :param organism_id: Organism ID Number
 
+        :type return_all: bool
+        :param return_all: Return all organisms (true / false) (default true)
+
         :rtype: list
         :return: A list of all remaining organisms
+
         """
-        return self.post('deleteOrganism', {'id': organism_id})
+        data = {
+            'id': organism_id,
+        }
+        if return_all is not None:
+            data['returnAllOrganisms'] = return_all
+
+        return self.post('deleteOrganism', data)
 
     def delete_features(self, organism_id):
         """

diff --git a/arrow/commands/organisms/add_organism.py b/arrow/commands/organisms/add_organism.py
@@ -31,14 +31,19 @@
     help="JSON formatted arbitrary metadata",
     type=str
 )
+@click.option(
+    "--return_all",
+    help="Return all organisms (true / false) (default true)",
+    is_flag=True
+)
 @pass_context
 @custom_exception
 @dict_output
-def cli(ctx, common_name, directory, blatdb="", genus="", species="", public=False, metadata=""):
+def cli(ctx, common_name, directory, blatdb="", genus="", species="", public=False, metadata="", return_all=""):
     """Add an organism
 
 Output:
 
     a dictionary with information about the new organism
     """
-    return ctx.gi.organisms.add_organism(common_name, directory, blatdb=blatdb, genus=genus, species=species, public=public, metadata=metadata)
+    return ctx.gi.organisms.add_organism(common_name, directory, blatdb=blatdb, genus=genus, species=species, public=public, metadata=metadata, return_all=return_all)
diff --git a/arrow/commands/organisms/delete_organism.py b/arrow/commands/organisms/delete_organism.py
@@ -5,14 +5,19 @@
 
 @click.command('delete_organism')
 @click.argument("organism_id", type=str)
+@click.option(
+    "--return_all",
+    help="Return all organisms (true / false) (default true)",
+    is_flag=True
+)
 @pass_context
 @custom_exception
 @list_output
-def cli(ctx, organism_id):
-    """Delete an organim
+def cli(ctx, organism_id, return_all=""):
+    """Delete an organism
 
 Output:
 
     A list of all remaining organisms
     """
-    return ctx.gi.organisms.delete_organism(organism_id)
+    return ctx.gi.organisms.delete_organism(organism_id, return_all=return_all)
diff --git a/arrow/commands/remote/add_organism.py b/arrow/commands/remote/add_organism.py
@@ -46,4 +46,9 @@ def cli(ctx, common_name, organism_data, blatdb="", genus="", species="", public
 
     a dictionary with information about the new organism
     """
-    return ctx.gi.remote.add_organism(common_name, organism_data, blatdb=blatdb, genus=genus, species=species, public=public, non_default_translation_table=non_default_translation_table, metadata=metadata)
+    print("running the add organism command ")
+    return_all = return_no_organisms is None or return_no_organisms is True
+    print("return all is: "+str(return_all))
+    return ctx.gi.remote.add_organism(common_name, organism_data, blatdb=blatdb, genus=genus, species=species,
+                                      public=public, non_default_translation_table=non_default_translation_table,
+                                      metadata=metadata, return_all=return_all)
diff --git a/bootstrap_apollo.sh b/bootstrap_apollo.sh
@@ -14,6 +14,13 @@ do
         mkdir -p $APOLLO_DATA_DIRECTORY
         shift
         ;;
+        --apollo3)
+        SHOULD_LAUNCH_DOCKER=0
+        ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo3-arrow.yml
+        APOLLO_DATA_DIRECTORY=$GALAXY_SHARED_DIR
+        mkdir -p $APOLLO_DATA_DIRECTORY
+        shift
+        ;;
         *)
         shift
         ;;

diff --git a/docs/commands/organisms.rst b/docs/commands/organisms.rst
@@ -30,6 +30,7 @@ Add an organism
       --species TEXT   Species
       --public         Should the organism be public or not
       --metadata TEXT  JSON formatted arbitrary metadata
+      --return_all     Return all organisms (true / false) (default true)
       -h, --help       Show this message and exit.
     
 
@@ -65,7 +66,7 @@ Remove features of an organism
 
 **Help**
 
-Delete an organim
+Delete an organism
 
 
 **Output**
@@ -76,7 +77,8 @@ Delete an organim
 **Options**::
 
 
-      -h, --help  Show this message and exit.
+      --return_all  Return all organisms (true / false) (default true)
+      -h, --help    Show this message and exit.
     
 
 ``get_organism_creator`` command
@@ -221,5 +223,6 @@ Update an organism
       --public               User's email
       --no_reload_sequences  Set this if you don't want Apollo to reload genome
                              sequences (no change in genome sequence)
+    
       -h, --help             Show this message and exit.
     
diff --git a/setup.py b/setup.py
@@ -16,7 +16,7 @@
 
 setup(
     name="apollo",
-    version='4.2.5',
+    version='4.2.6',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau;Nathan Dunn",
-Original file line number
+Diff line change
@@ Expand Up / @@ -85,6 +85,8 @@ Or with the Arrow client: @@
     History
     -------
+    - 4.2.6
+        - Prevent from displaying login/password in the logs
     - 4.2.5
         - Prevent from displaying login/password in the logs
     - 4.2.4
@@ Expand Down @@