sample tracking web api cleaned up

- added a samples controller

lib/galaxy/model/__init__.py

@@ -1767,6 +1767,7 @@ class RequestTypePermissions( object ):
 class Sample( object ):
     bulk_operations = Bunch( CHANGE_STATE = 'Change state', 
                              SELECT_LIBRARY = 'Select data library and folder' )
+    api_collection_visible_keys = ( 'id', 'name' )
     def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None):
         self.name = name
         self.desc = desc
@@ -1818,6 +1819,18 @@ class Sample( object ):
                                           pexpect.TIMEOUT:print_ticks}, 
                                           timeout=10)
         return output.replace(filepath, '').strip()
+    def get_api_value( self, view='collection' ):
+        rval = {}
+        try:
+            visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' )
+        except AttributeError:
+            raise Exception( 'Unknown API view: %s' % view )
+        for key in visible_keys:
+            try:
+                rval[key] = self.__getattribute__( key )
+            except AttributeError:
+                rval[key] = None
+        return rval
 
 class SampleState( object ):
     def __init__(self, name=None, desc=None, request_type=None):

lib/galaxy/web/api/requests.py

@@ -22,23 +22,57 @@ class RequestsController( BaseController ):
         GET /api/requests
         Displays a collection (list) of sequencing requests.
         """
-        query = trans.sa_session.query( trans.app.model.Request )\
-                                .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \
-                                               and trans.app.model.Request.table.c.deleted == False ) ) \
-                                .all()
+        # if admin user then return all requests
+        if trans.user_is_admin():
+            query = trans.sa_session.query( trans.app.model.Request )\
+                                    .filter(  trans.app.model.Request.table.c.deleted == False )\
+                                    .all()
+        else:
+            query = trans.sa_session.query( trans.app.model.Request )\
+                                    .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \
+                                                   and trans.app.model.Request.table.c.deleted == False ) ) \
+                                    .all()
         rval = []
         for request in query:
             item = request.get_api_value()
             item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
             item['id'] = trans.security.encode_id( item['id'] )
+            if trans.user_is_admin():
+                item['user'] = request.user.email
             rval.append( item )
         return rval
-
+    
+    @web.expose_api
+    def show( self, trans, id, **kwd ):
+        """
+        GET /api/requests/{encoded_request_id}
+        Displays details of a sequencing request.
+        """
+        try:
+            request_id = trans.security.decode_id( id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed  %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( request_id )
+        except:
+            request = None
+        if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ):
+            trans.response.status = 400
+            return "Invalid request id ( %s ) specified." % str( request_id )
+        item = request.get_api_value()
+        item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) )
+        item['id'] = trans.security.encode_id( item['id'] )
+        item['user'] = request.user.email
+        item['num_of_samples'] = len(request.samples)
+        return item
+    
     @web.expose_api
     def update( self, trans, id, key, payload, **kwd ):
         """
         PUT /api/requests/{encoded_request_id}
-        Displays information about a sequencing request.
+        Updates a request state, sample state or sample dataset transfer status
+        depending on the update_type
         """
         params = util.Params( kwd )
         update_type = None
@@ -124,7 +158,3 @@ class RequestsController( BaseController ):
                                                                                new_status=new_status,
                                                                                error_msg=error_msg )
         return status, output
-                    
-    
-    
-    

lib/galaxy/web/api/samples.py

@@ -0,0 +1,44 @@
+"""
+API operations on a sample tracking system.
+"""
+import logging, os, string, shutil, urllib, re, socket
+from cgi import escape, FieldStorage
+from galaxy import util, datatypes, jobs, web, util
+from galaxy.web.base.controller import *
+from galaxy.util.sanitize_html import sanitize_html
+from galaxy.model.orm import *
+from galaxy.util.bunch import Bunch
+
+log = logging.getLogger( __name__ )
+
+class SamplesController( BaseController ):
+
+    @web.expose_api
+    def index( self, trans, **kwd ):
+        """
+        GET /api/requests/{encoded_request_id}/samples
+        Displays a collection (list) of sample of a sequencing request.
+        """
+        try:
+            request_id = trans.security.decode_id( kwd[ 'request_id' ] )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed  request id ( %s ) specified, unable to decode." % str( encoded_request_id )
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( request_id )
+        except:
+            request = None
+        if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ):
+            trans.response.status = 400
+            return "Invalid request id ( %s ) specified." % str( request_id )
+        rval = []
+        for sample in request.samples:
+            item = sample.get_api_value()
+            item['url'] = url_for( 'samples', 
+                                   request_id=trans.security.encode_id( request_id ), 
+                                   id=trans.security.encode_id( sample.id ) )
+            item['id'] = trans.security.encode_id( item['id'] )
+            rval.append( item )
+        return rval
+
+    

lib/galaxy/web/buildapp.py

@@ -104,8 +104,15 @@ def app_factory( global_conf, **kwargs ):
     # If enabled, add the web API
     if asbool( kwargs.get( 'enable_api', False ) ):
         add_api_controllers( webapp, app )
-        webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) )
+        webapp.api_mapper.resource( 'content', 
+                                    'contents', 
+                                    path_prefix='/api/libraries/:library_id', 
+                                    parent_resources=dict( member_name='library', collection_name='libraries' ) )
         webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' )
+        webapp.api_mapper.resource( 'sample', 
+                                    'samples', 
+                                    path_prefix='/api/requests/:request_id', 
+                                    parent_resources=dict( member_name='request', collection_name='requests' ) )
         webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' )
     webapp.finalize_config()
     # Wrap the webapp in some useful middleware