Merge pull request #17 from galaxy-genome-annotation/ggasync

Move here some code from galaxy tool

.gitignore

@@ -45,3 +45,5 @@ docs/_build
 
 # test harness
 test_harness.py
+
+apollo_shared_dir

.travis.yml

@@ -1,25 +1,49 @@
 language: python
+os: linux
+
 python:
-- '2.7'
-- '3.5'
+  - '2.7'
+  - '3.6'
+
+jobs:
+  include:
+    - stage: lint
+      install:
+        - pip install -U pip flake8
+      script:
+        - flake8 apollo --ignore=E501,W503 --exclude=arrow/commands/,scripts/
+
+    - stage: deploy
+      install: skip
+      script: echo "Deploying to Pypi"
+      deploy:
+        provider: pypi
+        username: erasche
+        password:
+          secure: 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
+        on:
+          tags: true
+          distributions: "sdist bdist_wheel"
+          repo: galaxy-genome-annotation/python-apollo
+
+install:
+  - pip install -U pip setuptools nose
+
 script:
-- pip install -U pip setuptools
-- pip install -U flake8
-- flake8 apollo --ignore=E501,W504 --exclude=arrow/commands/,scripts/
-- python setup.py install
-deploy:
-  provider: pypi
-  user: erasche
-  password:
-    secure: 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
-  on:
-    tags: true
-    distributions: sdist bdist_wheel
-    repo: galaxy-genome-annotation/python-apollo
+  - python setup.py install
+  - export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/arrow.yml
+  - ./bootstrap_apollo.sh
+  - python setup.py nosetests
+
 notifications:
   webhooks:
     urls:
     - https://webhooks.gitter.im/e/dd56606ea08bece475e7
     on_success: change
     on_failure: always
     on_start: never
+
+stages:
+  - lint
+  - test
+  - deploy

README.rst

@@ -11,9 +11,18 @@ Apollo API Library
 Apollo is a Python library for interacting with
 `Apollo <https://github.com/gmod/apollo/>`__
 
+Installation
+------------
+
+.. code-block:: shell
+
+    pip install apollo
+
 Examples
 --------
 
+Example code to create a new organism and add yourself in the permission list:
+
 .. code:: python
 
     from apollo import ApolloInstance
@@ -39,7 +48,15 @@ Examples
         read=True,
     )
 
-Or with the new Arrow client:
+If you have already created an Arrow config file (with command `arrow init`),
+you can also get an ApolloInstance without writing credentials explicitely:
+
+.. code:: python
+
+    from arrow.apollo import get_apollo_instance
+    wa = get_apollo_instance()
+
+Or with the Arrow client:
 
 .. code-block:: shell
 
@@ -64,8 +81,10 @@ Or with the new Arrow client:
 History
 -------
 
-- 3.2
+- 4.0
     - Added support for remote creation/update/deletion of organisms/tracks
+    - Added support for adding GFF3 in the annotation track
+    - Added tests
 - 3.1
     - Added user activate/inactivate
     - Added get_creator for user, group and organisms

apollo/__init__.py

@@ -1,14 +1,13 @@
-import os
 import logging
-
-from cachetools import TTLCache
-from apollo.util import AssertUser
-from apollo.exceptions import UnknownUserException
+import os
 
 from apollo import (annotations, cannedcomments, cannedkeys,
                     cannedvalues, groups, io, metrics, organisms,
-                    status, users, remote)
+                    remote, status, users)
+from apollo.exceptions import UnknownUserException
+from apollo.util import AssertUser
 
+from cachetools import TTLCache
 
 cache = TTLCache(
     100,  # Up to 100 items
@@ -57,31 +56,39 @@ def require_user(wa, email):
         # If we hit a key error above, indicating that
         # we couldn't find the key, we'll simply re-request
         # the data
-        data = wa.users.loadUsers()
+        data = wa.users.get_users()
         userCache[cache_key] = data
 
     return AssertUser([x for x in data if x.username == email])
 
 
-def accessible_organisms(user, orgs):
+def accessible_organisms(user, orgs, permission=None):
     """Get the list of organisms accessible to a user, filtered by `orgs`"""
     permission_map = {
         x['organism']: x['permissions']
         for x in user.organismPermissions
-        if 'WRITE' in x['permissions'] or
-        'READ' in x['permissions'] or
-        'ADMINISTRATE' in x['permissions'] or
-        user.role == 'ADMIN'
+        if (permission is not None and permission in x['permissions'])
+        or (permission is None and ('WRITE' in x['permissions']
+                                    or 'READ' in x['permissions']
+                                    or 'ADMINISTRATE' in x['permissions']))
+        or user.role == 'ADMIN'
     }
 
     if 'error' in orgs:
+        if orgs['error'] == "Not authorized for any organisms":
+            return []
         raise Exception("Error received from Apollo server: \"%s\"" % orgs['error'])
 
-    return [
-        (org['commonName'], org['id'], False)
-        for org in sorted(orgs, key=lambda x: x['commonName'])
-        if org['commonName'] in permission_map
-    ]
+    if len(orgs) > 0 and isinstance(orgs[0], dict):
+        # Received complete org json
+        return [
+            org
+            for org in sorted(orgs, key=lambda x: x['commonName'])
+            if org['commonName'] in permission_map
+        ]
+    else:
+        # Received only a list of commonnames
+        return [org for org in sorted(orgs) if org in permission_map]
 
 
 def galaxy_list_groups(trans, *args, **kwargs):