Merge pull request #59 from bgruening/dev

merge dev into master

Dockerfile

@@ -16,7 +16,7 @@ RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
     libfreetype6-dev libpng-dev net-tools procps r-base libreadline-dev && \
     pip install distribute --upgrade && \
     pip install pyzmq ipython==2.4 jinja2 tornado pygments numpy biopython scikit-learn pandas \
-        scipy sklearn-pandas bioblend matplotlib patsy pysam khmer dendropy ggplot mpld3 sympy rpy2 && \
+        scipy sklearn-pandas bioblend matplotlib patsy pysam khmer ggplot mpld3 sympy rpy2 && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ADD ./startup.sh /startup.sh

galaxy.py

@@ -1,28 +1,16 @@
-from bioblend import galaxy
-from bioblend.galaxy.tools import ToolClient
-from bioblend.galaxy.histories import HistoryClient
-from bioblend.galaxy.datasets import DatasetClient
+#!/usr/bin/env python
 from bioblend.galaxy import objects
 import subprocess
 import argparse
 import os
 from string import Template
 import logging
-logging.getLogger("bioblend").setLevel(logging.WARNING)
+DEBUG = os.environ.get('DEBUG', "False").lower() == 'true'
+if DEBUG:
+    logging.basicConfig(level=logging.DEBUG)
+logging.getLogger("bioblend").setLevel(logging.CRITICAL)
+log = logging.getLogger()
 
-# Consider not using objects deprecated.
-DEFAULT_USE_OBJECTS = True
-ENV_KEYS = ('DEBUG', 'GALAXY_WEB_PORT', 'NOTEBOOK_PASSWORD', 'CORS_ORIGIN',
-            'DOCKER_PORT', 'API_KEY', 'HISTORY_ID', 'REMOTE_HOST',
-            'GALAXY_URL')
-
-
-def _get_conf():
-    conf = {}
-    for key in ENV_KEYS:
-        conf[key.lower()] = os.environ.get(key, None)
-    conf['galaxy_paster_port'] = conf['galaxy_web_port']
-    return conf
 
 
 def _get_ip():
@@ -35,25 +23,23 @@ def _get_ip():
     cmd_awk = ['awk', '{ print $2 }']
     p3 = subprocess.Popen(cmd_awk, stdin=p2.stdout, stdout=subprocess.PIPE)
     galaxy_ip = p3.stdout.read()
+    log.debug('Host IP determined to be %s', galaxy_ip)
     return galaxy_ip
 
 
-def _test_url(url, key, history_id, use_objects=False):
+def _test_url(url, key, history_id):
     """Test the functionality of a given galaxy URL, to ensure we can connect
     on that address."""
     try:
-        if use_objects:
-            gi = objects.GalaxyInstance(url, key)
-            gi.histories.get(history_id)
-        else:
-            gi = galaxy.GalaxyInstance(url=url, key=key)
-            gi.histories.get_histories()
+        gi = objects.GalaxyInstance(url, key)
+        gi.histories.get(history_id)
+        log.debug('Galaxy URL %s is functional', url)
         return gi
     except Exception:
         return None
 
 
-def get_galaxy_connection( use_objects=DEFAULT_USE_OBJECTS ):
+def get_galaxy_connection(history_id=None):
     """
         Given access to the configuration dict that galaxy passed us, we try and connect to galaxy's API.
 
@@ -69,97 +55,76 @@ def get_galaxy_connection( use_objects=DEFAULT_USE_OBJECTS ):
         through. This will succeed where the previous connection fails under
         the conditions of REMOTE_USER and galaxy running under uWSGI.
     """
-    conf = _get_conf()
-    key = conf['api_key']
+    history_id = history_id or os.environ['HISTORY_ID']
+    key = os.environ['API_KEY']
 
     ### Customised/Raw galaxy_url ###
     galaxy_ip = _get_ip()
     # Substitute $DOCKER_HOST with real IP
-    url = Template(conf['galaxy_url']).safe_substitute({'DOCKER_HOST': galaxy_ip})
-    gi = _test_url(url, key, history_id, use_objects=use_objects)
+    url = Template(os.environ['GALAXY_URL']).safe_substitute({'DOCKER_HOST': galaxy_ip})
+    gi = _test_url(url, key, history_id)
     if gi is not None:
         return gi
 
     ### Failover, fully auto-detected URL ###
     # Remove trailing slashes
-    app_path = conf['galaxy_url'].rstrip('/')
+    app_path = os.environ['GALAXY_URL'].rstrip('/')
     # Remove protocol+host:port if included
     app_path = ''.join(app_path.split('/')[3:])
 
-    if 'galaxy_paster_port' not in conf:
+    if 'GALAXY_WEB_PORT' not in os.environ:
         # We've failed to detect a port in the config we were given by
         # galaxy, so we won't be able to construct a valid URL
         raise Exception("No port")
     else:
         # We should be able to find a port to connect to galaxy on via this
         # conf var: galaxy_paster_port
-        galaxy_port = conf['galaxy_paster_port']
+        galaxy_port = os.environ['GALAXY_WEB_PORT']
 
     built_galaxy_url = 'http://%s:%s/%s' %  (galaxy_ip.strip(), galaxy_port, app_path.strip())
     url = built_galaxy_url.rstrip('/')
 
-    gi = _test_url(url, key, history_id, use_objects=use_objects)
+    gi = _test_url(url, key, history_id)
     if gi is not None:
         return gi
 
     ### Fail ###
-    raise Exception("Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error")
-
-
-def _get_history_id():
-    """
-    Extract the history ID from the config file.
-    """
-    conf = _get_conf()
-    return conf['history_id']
+    msg = "Could not connect to a galaxy instance. Please contact your SysAdmin for help with this error"
+    raise Exception(msg)
 
 
-def put(filename, file_type='auto', history_id=None, use_objects=DEFAULT_USE_OBJECTS):
+def put(filename, file_type='auto', history_id=None):
     """
         Given a filename of any file accessible to the docker instance, this
         function will upload that file to galaxy using the current history.
         Does not return anything.
     """
-    conf = _get_conf()
-    gi = get_galaxy_connection(use_objects)
-    history_id = history_id or _get_history_id()
-    if use_objects:
-        history = gi.histories.get( history_id )
-        history.upload_dataset(filename, file_type=file_type)
-    else:
-        tc = ToolClient( gi )
-        tc.upload_file(filename, history_id, file_type=file_type)
+    gi = get_galaxy_connection(history_id=history_id)
+    history_id = history_id or os.environ['HISTORY_ID']
+    history = gi.histories.get( history_id )
+    history.upload_dataset(filename, file_type=file_type)
 
 
-def get(dataset_id, history_id=None, use_objects=DEFAULT_USE_OBJECTS):
+def get(dataset_id, history_id=None):
     """
         Given the history_id that is displayed to the user, this function will
         download the file from the history and stores it under /import/
         Return value is the path to the dataset stored under /import/
     """
-    conf = _get_conf()
-    gi = get_galaxy_connection(use_objects)
+    history_id = history_id or os.environ['HISTORY_ID']
+
+    gi = get_galaxy_connection(history_id=history_id)
 
     file_path = '/import/%s' % dataset_id
-    history_id = history_id or _get_history_id()
 
     # Cache the file requests. E.g. in the example of someone doing something
     # silly like a get() for a Galaxy file in a for-loop, wouldn't want to
     # re-download every time and add that overhead.
     if not os.path.exists(file_path):
-        if use_objects:
-            history = gi.histories.get(history_id)
-            datasets = dict([( d.wrapped["hid"], d.id ) for d in history.get_datasets()])
-            dataset = history.get_dataset( datasets[dataset_id] )
-            dataset.download( open(file_path, 'wb') )
-        else:
-            hc = HistoryClient(gi)
-            dc = DatasetClient(gi)
-            dataset_mapping = dict([(dataset['hid'], dataset['id']) for dataset in hc.show_history(history_id, contents=True)])
-            try:
-                hc.download_dataset(history_id, dataset_mapping[dataset_id], file_path, use_default_filename=False, to_ext=None)
-            except:
-                dc.download_dataset(dataset_mapping[dataset_id], file_path, use_default_filename=False)
+        history = gi.histories.get(history_id)
+        datasets = dict([( d.wrapped["hid"], d.id ) for d in history.get_datasets()])
+        dataset = history.get_dataset( datasets[dataset_id] )
+        dataset.download( open(file_path, 'wb') )
 
     return file_path
 
@@ -175,6 +140,6 @@ def get(dataset_id, history_id=None, use_objects=DEFAULT_USE_OBJECTS):
 
     if args.action == 'get':
         # Ensure it's a numerical value
-        get(int(args.argument))
+        get(int(args.argument), history_id=args.history_id)
     elif args.action == 'put':
-        put(args.argument, file_type=args.filetype)
+        put(args.argument, file_type=args.filetype, history_id=args.history_id)