Merged in jdlogicman/galaxy-central-illumina-api-enhancements (pull request #6)

lib/galaxy/web/api/histories.py

@@ -7,6 +7,9 @@ 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.model import Dataset
+import galaxy.datatypes
+from galaxy.util.bunch import Bunch
 
 log = logging.getLogger( __name__ )
 
@@ -17,20 +20,19 @@ class HistoriesController( BaseController ):
         """
         GET /api/histories
         Displays a collection (list) of histories.
-        """
-        try:
-            query = trans.sa_session.query( trans.app.model.History ).filter( trans.app.model.History.table.c.deleted == False )
-            current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ]
-            user = trans.get_user()
-            query = query.filter_by( user=user, deleted=False )
+        """               
+        try:            
+            query = trans.sa_session.query( trans.app.model.History ).filter_by( user=trans.user, deleted=False ).order_by(
+                desc(trans.app.model.History.table.c.update_time)).all()           
         except Exception, e:
             log.debug("Error in history API: %s" % str(e))
+            
         rval = []
         try:
             for history in query:
-                item = history.get_api_value()
+                item = history.get_api_value(value_mapper={'id':trans.security.encode_id})
                 item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
-                item['id'] = trans.security.encode_id( item['id'] )
+                # item['id'] = trans.security.encode_id( item['id'] )
                 rval.append( item )
         except Exception, e:
             log.debug("Error in history API at constructing return list: %s" % str(e))
@@ -39,26 +41,63 @@ class HistoriesController( BaseController ):
     @web.expose_api
     def show( self, trans, id, **kwd ):
         """
-        GET /api/histories/{encoded_library_id}
+        GET /api/histories/{encoded_history_id}
         Displays information about a history.
         """
         history_id = id
         params = util.Params( kwd )
+        
+        def traverse( datasets ):
+            rval = {}
+            states = Dataset.states
+            for key, state in states.items():
+                rval[state] = 0
+            #log.debug("History API: Init rval %s" % rval)
+            for dataset in datasets:
+                item = dataset.get_api_value( view='element' )
+                #log.debug("History API: Set rval %s" % item['state'])
+                if not item['deleted']:
+                    rval[item['state']] = rval[item['state']] + 1
+            return rval            
+            
         try:
             decoded_history_id = trans.security.decode_id( history_id )
         except TypeError:
             trans.response.status = 400
-            return "Malformed history id ( %s ) specified, unable to decode." % str( library_id )
+            return "Malformed history id ( %s ) specified, unable to decode." % str( history_id )
         try:
-            history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id )
+            history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+            if history.user != trans.user and not trans.user_is_admin():
+                if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                    trans.response.status = 400
+                    return("History is not owned by or shared with current user")
         except:
-            history = None
+            trans.response.status = 400
+            return "That history does not exist."
+            
         try:
-            if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( trans.get_current_user_roles(), history ) ):
-                trans.response.status = 400
-                return "Invalid history id ( %s ) specified." % str( history_id )
-            item = history.get_api_value( view='element' )
+            item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id})
+            num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] )            
+            states = Dataset.states
+            state = states.ERROR
+            if num_sets == 0:            
+                state = states.NEW
+            else:
+                summary = traverse(history.datasets)
+                #log.debug("History API: Status summary %s" % summary)                
+                if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0:
+                    state = states.ERROR
+                elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0:
+                    state = states.RUNNING
+                elif summary[states.QUEUED] > 0:
+                    state = states.QUEUED
+                elif summary[states.OK] == num_sets:
+                    state = states.OK                       
+            #item['user'] = item['user'].username
             item['contents_url'] = url_for( 'history_contents', history_id=history_id )
+            #item['datasets'] = len( item['datasets'] )
+            item['state'] = state
+            #log.debug("History API: State %s for %d datasets" % (state, num_sets))
         except Exception, e:
             log.debug("Error in history API at showing history detail: %s" % str(e))
         return item
@@ -69,5 +108,48 @@ class HistoriesController( BaseController ):
         POST /api/histories
         Creates a new history.
         """
-        trans.response.status = 403
-        return "Not implemented."
+        params = util.Params( payload )
+        hist_name = util.restore_text( params.get( 'name', None ) )        
+        new_history = trans.app.model.History( user=trans.user, name=hist_name )
+        
+        trans.sa_session.add( new_history )
+        trans.sa_session.flush()
+        item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id})
+        return item
+    @web.expose_api
+    def delete( self, trans, id, **kwd ):
+        """
+        DELETE /api/histories/{encoded_history_id}
+        Deletes a history
+        """
+        history_id = id
+        params = util.Params( kwd )
+        
+        try:
+            decoded_history_id = trans.security.decode_id( history_id )
+        except TypeError:
+            trans.response.status = 400
+            return "Malformed history id ( %s ) specified, unable to decode." % str( history_id )
+        try:
+            history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+            if history.user != trans.user and not trans.user_is_admin():
+                if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                    trans.response.status = 400
+                    return("History is not owned by or shared with current user")
+        except:
+            trans.response.status = 400
+            return "That history does not exist."
+        history.deleted = True
+        # If deleting the current history, make a new current.
+        if history == trans.get_history():
+            trans.new_history()
+        if trans.app.config.allow_user_dataset_purge:
+            for hda in history.datasets:
+                hda.purged = True
+                trans.sa_session.add( hda )
+                if hda.dataset.user_can_purge:
+                    try:
+                        hda.dataset.full_delete()
+                        trans.sa_session.add( hda.dataset )
+                    except:
+                        trans.sa_session.flush()

lib/galaxy/web/api/history_contents.py

@@ -21,42 +21,23 @@ class HistoryContentsController( BaseController ):
         """
         GET /api/histories/{encoded_history_id}/contents
         Displays a collection (list) of history contents
-        """
-        rval = []
-        current_user_roles = trans.get_current_user_roles()
-        def traverse( folder ):
-            admin = trans.user_is_admin()
-            rval = []
-            for subfolder in folder.active_folders:
-                if not admin:
-                    can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder )
-                if (admin or can_access) and not subfolder.deleted:
-                    subfolder.api_path = folder.api_path + '/' + subfolder.name
-                    subfolder.api_type = 'folder'
-                    rval.append( subfolder )
-                    rval.extend( traverse( subfolder ) )
-            for ld in folder.datasets:
-                if not admin:
-                    can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset )
-                if (admin or can_access) and not ld.deleted:
-                    ld.api_path = folder.api_path + '/' + ld.name
-                    ld.api_type = 'file'
-                    rval.append( ld )
-            return rval
-        #log.debug("Entering Content API for history with %s" % str(history_id))
+        """        
         try:
             decoded_history_id = trans.security.decode_id( history_id )
         except TypeError:
             trans.response.status = 400
             return "Malformed history id ( %s ) specified, unable to decode." % str( history_id )
         try:
-            history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id )
+            history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+            if history.user != trans.user and not trans.user_is_admin():
+                if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                    trans.response.status = 400
+                    return("History is not owned by or shared with current user")
         except:
-            history = None
-        if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( current_user_roles, history ) ):
             trans.response.status = 400
-            return "Invalid history id ( %s ) specified." % str( history_id )
-        #log.debug("History item %s" % str(history))
+            return "That history does not exist."
+                       
+        rval = []
         try:
             for dataset in history.datasets:
                 api_type = "file"
@@ -93,10 +74,12 @@ class HistoryContentsController( BaseController ):
             try:
                 content = trans.sa_session.query( model_class ).get( decoded_content_id )
             except:
-                content = None
-            if not content or ( not trans.user_is_admin() and not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), content, trans.user ) ):
                 trans.response.status = 400
                 return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) )
+            if content.history.user != trans.user and not trans.user_is_admin():
+                if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                    trans.response.status = 400
+                    return("History is not owned by or shared with current user")                      
             item = content.get_api_value( view='element' )
             if not item['deleted']:
                 # Problem: Method url_for cannot use the dataset controller
@@ -106,14 +89,21 @@ class HistoryContentsController( BaseController ):
                 # url_for is being phased out, so new applications should use url
                 item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(decoded_content_id), to_ext=content.ext)
         except Exception, e:
-            log.debug("Error in history API at listing dataset: %s" % str(e))
+            log.debug("Error in history API at listing dataset: %s" % str(e))               
         return item
 
     @web.expose_api
     def create( self, trans, history_id, payload, **kwd ):
         """
-        POST /api/libraries/{encoded_library_id}/contents
-        Creates a new history content item (file or folder).
-        """
-        trans.response.status = 403
-        return "Not implemented."
+        POST /api/libraries/{encoded_history_id}/contents
+        Creates a new history content item.        """          
+        params = util.Params( payload )
+        history_id = util.restore_text( params.get( 'history_id', None ) )
+        ldda_id = util.restore_text( params.get( 'ldda_id', None ) )
+        add_to_history = True               
+        decoded_history_id = trans.security.decode_id( history_id )
+        ld_t, ld_id = trans.security.decode_string_id(ldda_id).split('.')
+        history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+        ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get(ld_id)
+        hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history)        
+        history.add_dataset(hda)