Move the knowledge of the urls for the REST API to one new file

htsworkflow.util.api and then update some of the scripts that were
using the api to import from the new module.

Yes this increases the dependencies, but it does mean it'll be
easier to update the urls if we need to change them

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 0ef42a589fcdd06a90be00c4cdda4a48d10c7b02..fbd1187a5ca14e5517b4e8b455d3cf82c203a484 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -14,6 +14,7 @@ except ImportError, e:
     import simplejson as json
 
 from htsworkflow.frontend.auth import apidata
+from htsworkflow.util import api
 from htsworkflow.util.url import normalize_url
 from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
 from htsworkflow.pipelines.genome_mapper import constructMapperDict
@@ -36,7 +37,7 @@ def retrieve_flowcell_info(base_host_url, flowcell):
     """
     Return a dictionary describing a 
     """
-    url = base_host_url + '/experiments/config/%s/json' % (flowcell)
+    url = api.flowcell_url(base_host_url, flowcell)
   
     try:
         apipayload = urllib.urlencode(apidata)

diff --git a/htsworkflow/util/api.py b/htsworkflow/util/api.py
new file mode 100644 (file)
index 0000000..f6af79f
--- /dev/null
+++ b/htsworkflow/util/api.py
@@ -0,0 +1,94 @@
+"""
+Common functions for accessing the HTS Workflow REST API
+
+"""
+# try to deal with python <2.6
+try:
+  import json
+except ImportError:
+  import simplejson as json
+
+import urllib
+import urllib2
+import urlparse
+
+def library_url(root_url, library_id):
+    """
+    Return the url for retrieving information about a specific library.
+
+    Args:
+      library_id (str): the library id of interest
+      root_url (str): the root portion of the url, e.g. http://localhost
+
+    Returns:
+      str. The url to use for this REST api.
+
+    >>> print library_url('http://localhost', '12345')
+    http://localhost/samples/library/12345/json
+
+    """
+    url_fragment = '/samples/library/%s/json' % (library_id,)
+    url = urlparse.urljoin(root_url, url_fragment)
+
+    return url
+
+
+def flowcell_url(root_url, flowcell_id):
+    """
+    Return the url for retrieving information about a specific flowcell.
+
+    Args:
+      root_url (str): the root portion of the url, e.g. http://localhost
+      flowcell_id (str): the flowcell id of interest
+
+    Returns:
+      str. The url to use for this REST api.
+
+    >>> print flowcell_url('http://localhost', '1234AAXX')
+    http://localhost/experiments/config/1234AAXX/json
+    """
+    url_fragment = '/experiments/config/%s/json' % (flowcell_id,)
+    url = urlparse.urljoin(root_url, url_fragment)
+
+    return url
+
+
+def lanes_for_user_url(root_url, username):
+    """
+    Return the url for returning all the lanes associated with a username
+    
+    Args:
+      username (str): a username in your target filesystem
+      root_url (str): the root portion of the url, e.g. http://localhost
+
+    Returns:
+      str. The url to use for this REST api.
+
+    >>> print lanes_for_user_url('http://localhost', 'diane')
+    http://localhost/lanes_for/diane/json
+
+    """
+    url_fragment = '/lanes_for/%s/json' % (username,)
+    url = urlparse.urljoin(root_url, url_fragment)
+
+    return url
+
+def retrieve_info(url, apidata):
+    """
+    Return a dictionary from the HTSworkflow API
+    """
+    try:
+        apipayload = urllib.urlencode(apidata)
+        web = urllib2.urlopen(url, apipayload)
+    except urllib2.URLError, e:
+        if e.code == 404:
+            logging.info("%s was not found" % (url,))
+            return None
+        else:
+            errmsg = 'URLError: %d %s' % (e.code, e.msg)
+            raise IOError(errmsg)
+    
+    contents = web.read()
+    headers = web.info()
+
+    return json.loads(contents)

diff --git a/scripts/make-library-tree b/scripts/make-library-tree
index 822af4829e2be4f88c889c61791888cb730f869e..b6edb9311eddbd1680fab7bcd86c816ad11c94c9 100644 (file)
--- a/scripts/make-library-tree
+++ b/scripts/make-library-tree
@@ -1,11 +1,6 @@
 #!/usr/bin/env python
 
 from ConfigParser import SafeConfigParser
-# try to deal with python <2.6
-try:
-  import json
-except ImportError:
-  import simplejson as json
 
 import logging
 import os
@@ -13,9 +8,8 @@ from optparse import OptionParser
 import stat
 import re
 import shelve
-import urllib
-import urllib2
-import urlparse
+
+from htsworkflow.util import api
 
 eland_re = re.compile('s_(?P<lane>\d)(?P<read>_\d)?_eland_')
 raw_seq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Z]+')
@@ -127,25 +121,6 @@ def scan_for_sequences(dirs):
                     
     return sequences
 
-def retrieve_info(url, apidata):
-    """
-    Return a dictionary from the HTSworkflow API
-    """
-    try:
-        apipayload = urllib.urlencode(apidata)
-        web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
-        if e.code == 404:
-            logging.info("%s was not found" % (url,))
-            return None
-        else:
-            errmsg = 'URLError: %d %s' % (e.code, e.msg)
-            raise IOError(errmsg)
-    
-    contents = web.read()
-    headers = web.info()
-
-    return json.loads(contents)
 
 def build_flowcell_db(fcdb_filename, sequences, baseurl, apiid, apikey):
     """
@@ -161,8 +136,8 @@ def build_flowcell_db(fcdb_filename, sequences, baseurl, apiid, apikey):
 
         # get info about flowcell from server or shelf
         if not fcdb.has_key(flowcell):
-            url = urlparse.urljoin(baseurl, 'experiments/config/%s/json' % (flowcell,))
-            flowcell_info = retrieve_info(url, apidata)
+            url = api.flowcell_url(baseurl, flowcell)
+            flowcell_info = api.retrieve_info(url, apidata)
             if flowcell_info is not None:
                 fcdb[flowcell] = flowcell_info
         else:
@@ -273,6 +248,7 @@ def configure_opts(opts):
     if opts.sequence_archive is None and \
        config_file.has_option(SECTION_NAME, ARCHIVE_OPT):
         opts.sequence_archive = config_file.get(SECTION_NAME, ARCHIVE_OPT)
+        opts.sequence_archive = os.path.expanduser(opts.sequence_archive)
 
     opts.sequence_archive = os.path.abspath(opts.sequence_archive)
     opts.library_tree = os.path.join(opts.sequence_archive, 'libraries')