Merge pull request #14 from galaxy-genome-annotation/2.4

Various updates

Author: hexylena

.travis.yml

@@ -5,7 +5,7 @@ python:
 script:
 - pip install -U pip setuptools
 - pip install -U flake8
-- flake8 apollo --ignore=E501 --exclude=arrow/commands/,scripts/
+- flake8 apollo --ignore=E501,W504 --exclude=arrow/commands/,scripts/
 - python setup.py install
 deploy:
   provider: pypi

README.rst

@@ -9,7 +9,7 @@ Apollo API Library
     :alt: Documentation Status
 
 Apollo is a Python library for interacting with
-`WebApollo <https://github.com/gmod/apollo/>`__
+`Apollo <https://github.com/gmod/apollo/>`__
 
 Examples
 --------
@@ -27,7 +27,7 @@ Examples
         public=False
     )
 
-    # Give webapollo a second to process the uploaded organism.
+    # Give Apollo a second to process the uploaded organism.
     time.sleep(1)
 
     # Then add yourself to permission list
@@ -64,6 +64,12 @@ Or with the new Arrow client:
 History
 -------
 
+- 3.1
+    - Added user activate/inactivate
+    - Added get_creator for user, group and organisms
+    - Added omitEmptyOrganisms to get_users
+    - Added support for group admins
+    - Repaired GFF3/Fasta downloading
 - 3.0.4
     - `Fixed bug <https://github.com/galaxy-genome-annotation/python-apollo/issues/4>`__ in deleteFeatures (Thanks `@NeillGibson <https://github.com/NeillGibson>`__)
 - 3.0.3

apollo/client.py

@@ -1,8 +1,9 @@
 """Base apollo client
 """
 import json
-import requests
 import logging
+
+import requests
 try:
     from shlex import quote
 except ImportError:
@@ -63,7 +64,7 @@ def post(self, client_method, data, post_params=None, is_json=True):
         raise Exception("Unexpected response from apollo %s: %s" %
                         (resp.status_code, resp.text))
 
-    def get(self, client_method, get_params):
+    def get(self, client_method, get_params, is_json=True):
         """Make a GET request"""
         url = self._wa.apollo_url + self.CLIENT_BASE + client_method
         headers = {}
@@ -72,8 +73,11 @@ def get(self, client_method, get_params):
                                 verify=self.__verify, params=get_params,
                                 **self._request_args)
         if response.status_code == 200:
-            data = response.json()
-            return self._scrub_data(data)
+            if is_json:
+                data = response.json()
+                return self._scrub_data(data)
+            else:
+                return response.text
         # @see self.body for HTTP response body
         raise Exception("Unexpected response from apollo %s: %s" %
                         (response.status_code, response.text))

apollo/decorators.py

@@ -1,6 +1,9 @@
 from apollo.exceptions import APIErrorResponseException
 
+from decorator import decorator
 
+
+@decorator
 def raise_error_decorator(fn):
     def wrapper(*args, **kwargs):
         r = fn(*args, **kwargs)

apollo/groups/__init__.py

@@ -164,3 +164,54 @@ def update_membership(self, group_id, users=[]):
             'users': users,
         }
         return _fix_group(self.post('updateMembership', data))
+
+    def update_group_admin(self, group_id, users=[]):
+        """
+        Update the group's admins
+
+        :type group_id: int
+        :param group_id: Group ID Number
+
+        :type users: list of str
+        :param users: List of emails
+
+        :rtype: dict
+        :return: dictionary of group information
+        """
+        data = {
+            'groupId': group_id,
+            'users': users,
+        }
+        return _fix_group(self.post('updateGroupAdmin', data))
+
+    def get_group_admin(self, group):
+        """
+        Get the group's admins
+
+        :type group: str
+        :param group: group name
+
+        :rtype: list
+        :return: a list containing group admins
+        """
+        data = {
+            'name': group,
+        }
+        response = _fix_group(self.post('getGroupAdmin', data))
+        return response
+
+    def get_group_creator(self, group):
+        """
+        Get the group's creator
+
+        :type group: str
+        :param group: group name
+
+        :rtype: list
+        :return: creator userId
+        """
+        data = {
+            'name': group,
+        }
+        response = _fix_group(self.post('getGroupCreator', data))
+        return response

apollo/io/__init__.py

@@ -9,7 +9,7 @@ class IOClient(Client):
 
     def write_downloadable(self, organism, export_type='FASTA',
                            seq_type='peptide', export_format='text',
-                           export_gff3_fasta=False, sequences=[]):
+                           export_gff3_fasta=False, sequences=[], region=None):
         """
         Prepare a download for an organism
 
@@ -20,7 +20,7 @@ def write_downloadable(self, organism, export_type='FASTA',
         :param sequences: Names of references sequences to add (default is all)
 
         :type export_type: str
-        :param export_type: Export type. Choices: FASTA, GFF3
+        :param export_type: Export type. Choices: FASTA, GFF3, VCF
 
         :type seq_type: str
         :param seq_type: Export selection. Choices: peptide, cds, cdna, genomic
@@ -31,10 +31,19 @@ def write_downloadable(self, organism, export_type='FASTA',
         :type export_gff3_fasta: bool
         :param export_gff3_fasta: Export reference sequence when exporting GFF3 annotations.
 
+        :type region: str
+        :param region: Region to export in form sequence:min..max e.g., chr3:1001..1034
+
         :rtype: dict
         :return: a dictionary containing download information
         """
 
+        if export_format.lower() not in ('gzip', 'text'):
+            raise Exception("export_format must be one of file, text")
+
+        if export_type.lower() not in ('fasta', 'gff3', 'vcf'):
+            raise Exception("export_type must be one of FASTA, GFF3, VCF")
+
         data = {
             'type': export_type,
             'seq_type': seq_type,
@@ -46,13 +55,16 @@ def write_downloadable(self, organism, export_type='FASTA',
             'exportGff3Fasta': export_gff3_fasta,
         }
 
+        if region:
+            data['region'] = region
+
         return self.post('write', data)
 
     def write_text(self, organism, export_type='FASTA', seq_type='peptide',
                    export_format='text', export_gff3_fasta=False,
-                   sequences=[]):
+                   sequences=[], region=None):
         """
-        Download or prepare a download for an organism
+        [DEPRECATED, use write_downloadable] Download or prepare a download for an organism
 
         :type organism: str
         :param organism: organism common name
@@ -61,7 +73,7 @@ def write_text(self, organism, export_type='FASTA', seq_type='peptide',
         :param sequences: Names of references sequences to add (default is all)
 
         :type export_type: str
-        :param export_type: Export type. Choices: FASTA, GFF3
+        :param export_type: Export type. Choices: FASTA, GFF3, VCF
 
         :type seq_type: str
         :param seq_type: Export selection. Choices: peptide, cds, cdna, genomic
@@ -72,44 +84,36 @@ def write_text(self, organism, export_type='FASTA', seq_type='peptide',
         :type export_gff3_fasta: bool
         :param export_gff3_fasta: Export reference sequence when exporting GFF3 annotations.
 
+        :type region: str
+        :param region: Region to export in form sequence:min..max e.g., chr3:1001..1034
+
         :rtype: str
         :return: the exported data
         """
-        if sequences is None:
-            sequences = []
 
-        data = {
-            'type': export_type,
-            'seqType': seq_type,
-            'format': export_format,
-            'sequences': sequences,
-            'organism': organism,
-            'output': 'text',
-            'exportAllSequences': True if not sequences else len(sequences) == 0,
-            'exportGff3Fasta': export_gff3_fasta,
-        }
-
-        return self.post('write', data, is_json=False)
+        return self.write_downloadable(organism, export_type, seq_type,
+                                       export_format, export_gff3_fasta,
+                                       sequences, region)
 
     def download(self, uuid, output_format='gzip'):
         """
-        [CURRENTLY BROKEN] Download pre-prepared data by UUID
+        Download pre-prepared data by UUID
 
         :type uuid: str
         :param uuid: Data UUID
 
         :type output_format: str
         :param output_format: Output format of the data, either "gzip" or "text"
 
-        :rtype: dict
-        :return: a dictionary
+        :rtype: str
+        :return: The downloaded content
         """
 
         if output_format.lower() not in ('gzip', 'text'):
-            raise Exception("outputFormat must be one of file, text")
+            raise Exception("output_format must be one of file, text")
 
         data = {
             'format': output_format,
             'uuid': uuid,
         }
-        return self.post('write', data)
+        return self.get('download', get_params=data, is_json=False)

apollo/organisms/__init__.py

@@ -166,3 +166,15 @@ def get_sequences(self, organism_id):
         :return: The set of sequences associated with an organism
         """
         return self.post('getSequencesForOrganism', {'organism': organism_id})
+
+    def get_organism_creator(self, organism_id):
+        """
+        Get the creator of an organism
+
+        :type organism_id: str
+        :param organism_id: Organism ID Number
+
+        :rtype: dict
+        :return: a dictionary containing user information
+        """
+        return self.post('getOrganismCreator', {'organism': organism_id})

apollo/users/__init__.py

@@ -42,17 +42,27 @@ def _handle_empty(self, user, response):
         """Apollo likes to return empty user arrays, even when you REALLY
         want a user response back... like creating a user."""
         if len(response.keys()) == 0:
-            return self.show_user(user)
+            response = self.show_user(user)
+
+            # And sometimes show_user can return nothing. Ask again...
+            if len(response) == 0:
+                response = self.show_user(user)
         return response
 
-    def get_users(self):
+    def get_users(self, omit_empty_organisms=False):
         """
         Get all users known to this Apollo instance
 
+        :type omit_empty_organisms: bool
+        :param omit_empty_organisms: Will omit users having no access to any organism
+
         :rtype: list of dicts
         :return: list of user info dictionaries
         """
-        res = self.post('loadUsers', {})
+        payload = {}
+        if omit_empty_organisms:
+            payload['omitEmptyOrganisms'] = omit_empty_organisms
+        res = self.post('loadUsers', payload)
         data = [_fix_user(user) for user in res]
         return data
 
@@ -67,7 +77,7 @@ def show_user(self, user):
         :return: a dictionary containing user information
         """
         res = self.post('loadUsers', {'userId': user})
-        if isinstance(res, list):
+        if isinstance(res, list) and len(res) > 0:
             res = res[0]
         return _fix_user(res)
 
@@ -235,3 +245,39 @@ def update_user(self, email, first_name, last_name, password, metadata={}):
         }
         response = self.post('updateUser', data)
         return self._handle_empty(email, response)
+
+    def get_user_creator(self, user):
+        """
+        Get the creator of a user
+
+        :type user: str
+        :param user: User Email
+
+        :rtype: dict
+        :return: a dictionary containing user information
+        """
+        return self.post('getUserCreator', {'email': user})
+
+    def activate_user(self, user):
+        """
+        Activate a user
+
+        :type user: str
+        :param user: User's email
+
+        :rtype: dict
+        :return: an empty dictionary
+        """
+        return self.post('activateUser', {'userToActivate': user})
+
+    def inactivate_user(self, user):
+        """
+        Activate a user
+
+        :type user: str
+        :param user: User's email
+
+        :rtype: dict
+        :return: an empty dictionary
+        """
+        return self.post('inactivateUser', {'userToDelete': user})

apollo/util.py

@@ -104,8 +104,8 @@ def featuresToFeatureSchema(features):
     compiled = []
     for feature in features:
         # if feature.type != 'gene':
-            # log.warn("Not able to handle %s features just yet...", feature.type)
-            # continue
+        #     log.warn("Not able to handle %s features just yet...", feature.type)
+        #     continue
 
         for x in _yieldFeatData([feature]):
             compiled.append(x)

arrow/__init__.py

@@ -1 +1 @@
-__version__ = '3.0.4'
+__version__ = '3.1'