Streamline history sharing, add a "Manage shared histories" section to the History options menu. Also use a better approach to setting peek on datasets.

lib/galaxy/datatypes/data.py

@@ -416,8 +416,9 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5 ):
     count = 0
     file_type = None
     data_checked = False
-    for line in file( file_name ):
-        line = line[:WIDTH]
+    temp = open( file_name, "U" )
+    while count <= LINE_COUNT:
+        line = temp.readline( WIDTH )
         if line and not is_multi_byte and not data_checked:
             # See if we have a compressed or binary file
             if line[0:2] == util.gzip_magic:
@@ -432,9 +433,8 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5 ):
         if file_type in [ 'gzipped', 'binary' ]:
             break
         lines.append( line )
-        if count == LINE_COUNT: 
-            break
         count += 1
+    temp.close()
     if file_type in [ 'gzipped', 'binary' ]: 
         text = "%s file" % file_type 
     else: 

lib/galaxy/web/controllers/history.py

@@ -4,7 +4,7 @@ from galaxy import util
 from galaxy.model.mapping import desc
 from galaxy.model.orm import *
 from galaxy.util.json import *
-import webhelpers, logging
+import webhelpers, logging, operator
 from datetime import datetime
 from cgi import escape
 
@@ -31,10 +31,12 @@ class HistoryListGrid( grids.Grid ):
                 return "deleted"
             elif history.users_shared_with:
                 return "shared"
+            elif history.importable:
+                return "importable"
             return ""
         def get_link( self, trans, grid, item ):
-            if item.users_shared_with:
-                return dict( operation="sharing", id=item.id )
+            if item.users_shared_with or item.importable:
+                return dict( operation="sharing" )
             return None
     # Grid definition
     title = "Stored histories"
@@ -55,9 +57,12 @@ class HistoryListGrid( grids.Grid ):
     operations = [
         grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
         grids.GridOperation( "Share", condition=( lambda item: not item.deleted )  ),
+        grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted )  ),
         grids.GridOperation( "Rename", condition=( lambda item: not item.deleted )  ),
         grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
-        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) )
+        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
+        grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ),
+        grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) )
     ]
     standard_filters = [
         grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
@@ -99,7 +104,9 @@ class SharedHistoryListGrid( grids.Grid ):
     ]
     operations = [
         grids.GridOperation( "Clone" ),
-        grids.GridOperation( "Unshare" )
+        grids.GridOperation( "Unshare" ),
+        grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ),
+        grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) )
     ]
     standard_filters = []
     def build_initial_query( self, session ):
@@ -126,19 +133,19 @@ class HistoryController( BaseController ):
         current_history = trans.get_history()
         status = message = None
         if 'operation' in kwargs:
-            history_ids = util.listify( kwargs.get( 'id', [] ) )
-            histories = []
             operation = kwargs['operation'].lower()
             if operation == "share":
                 return self.share( trans, **kwargs )
-            elif operation == "rename":
+            if operation == "rename":
                 return self.rename( trans, **kwargs )
-            elif operation == 'sharing':
-                return self.sharing( trans, id=kwargs['id'] )
+            history_ids = util.listify( kwargs.get( 'id', [] ) )
+            if operation == "sharing":
+                return self.sharing( trans, id=history_ids )
             # Display no message by default
             status, message = None, None
             refresh_history = False
             # Load the histories and ensure they all belong to the current user
+            histories = []
             for history_id in history_ids:      
                 history = get_history( trans, history_id )
                 if history:
@@ -161,6 +168,21 @@ class HistoryController( BaseController ):
                         trans.template_context['refresh_frames'] = ['history']
                 elif operation == "undelete":
                     status, message = self._list_undelete( trans, histories )
+                elif operation == "unshare":
+                    for history in histories:
+                        husas = trans.app.model.HistoryUserShareAssociation.filter_by( history=history ).all()
+                        for husa in husas:
+                            husa.delete()
+                elif operation == "enable import via link":
+                    for history in histories:
+                        if not history.importable:
+                            history.importable = True
+                elif operation == "disable import via link":
+                    if history_ids:
+                        histories = [ get_history( trans, history_id ) for history_id in history_ids ]
+                        for history in histories:
+                            if history.importable:
+                                history.importable = False
                 trans.sa_session.flush()
         # Render the list view
         return self.stored_list_grid( trans, status=status, message=message, **kwargs )
@@ -237,24 +259,20 @@ class HistoryController( BaseController ):
         msg = util.restore_text( kwargs.get( 'msg', '' ) )
         status = message = None
         if 'operation' in kwargs:
-            id = kwargs.get( 'id', None )
+            ids = util.listify( kwargs.get( 'id', [] ) )
             operation = kwargs['operation'].lower()
             if operation == "clone":
-                if not id:
+                if not ids:
                     message = "Select a history to clone"
                     return self.shared_list_grid( trans, status='error', message=message, **kwargs )
                 # When cloning shared histories, only copy active datasets
                 new_kwargs = { 'clone_choice' : 'active' }
                 return self.clone( trans, id, **new_kwargs )
             elif operation == 'unshare':
-                if not id:
+                if not ids:
                     message = "Select a history to unshare"
                     return self.shared_list_grid( trans, status='error', message=message, **kwargs )
-                ids = util.listify( id )
-                histories = []
-                for history_id in ids:
-                    history = get_history( trans, history_id, check_ownership=False )
-                    histories.append( history )
+                histories = [ get_history( trans, history_id ) for history_id in ids ]
                 for history in histories:
                     # Current user is the user with which the histories were shared
                     association = trans.app.model.HistoryUserShareAssociation.filter_by( user=trans.user, history=history ).one()
@@ -262,6 +280,20 @@ class HistoryController( BaseController ):
                     association.flush()
                 message = "Unshared %d shared histories" % len( ids )
                 status = 'done'
+            elif operation == "enable import via link":
+                if ids:
+                    histories = [ get_history( trans, id ) for id in ids ]
+                    for history in histories:
+                        if not history.importable:
+                            history.importable = True
+                            history.flush()
+            elif operation == "disable import via link":
+                if ids:
+                    histories = [ get_history( trans, id ) for id in ids ]
+                    for history in histories:
+                        if history.importable:
+                            history.importable = False
+                            history.flush()
         # Render the list view
         return self.shared_list_grid( trans, status=status, message=message, **kwargs )
     @web.expose
@@ -622,7 +654,9 @@ class HistoryController( BaseController ):
         params = util.Params( kwd )
         msg = util.restore_text ( params.get( 'msg', '' ) )
         if id:
-            histories = [ get_history( trans, id ) ]
+            ids = util.listify( id )
+            if ids:
+                histories = [ get_history( trans, history_id ) for history_id in ids ]
         for history in histories:
             if params.get( 'enable_import_via_link', False ):
                 history.importable = True
@@ -635,14 +669,34 @@ class HistoryController( BaseController ):
                 if not user:
                     msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email )
                     return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' )
-                association = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).one()
-                association.delete()
-                association.flush()
-            if not id:
-                shared_msg = "History (%s) now shared with: %d users.  " % ( history.name, len( history.users_shared_with ) )
-                msg = '%s%s' % ( shared_msg, msg )
+                husas = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).all()
+                if husas:
+                    for husa in husas:
+                        husa.delete()
+                        husa.flush()
+        histories = []
+        # Get all histories that have been shared with others
+        husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+                                .join( "history" ) \
+                                .filter( and_( trans.app.model.History.user == trans.user,
+                                               trans.app.model.History.deleted == False ) ) \
+                                .order_by( trans.app.model.History.table.c.name ) \
+                                .all()
+        for husa in husas:
+            history = husa.history
+            if history not in histories:
+                histories.append( history )
+        # Get all histories that are importable
+        importables = trans.sa_session.query( trans.app.model.History ) \
+                                      .filter_by( user=trans.user, importable=True, deleted=False ) \
+                                      .order_by( trans.app.model.History.table.c.name ) \
+                                      .all()
+        for importable in importables:
+            if importable not in histories:
+                histories.append( importable )
+        # Sort the list of histories by history.name
+        histories.sort( key=operator.attrgetter( 'name') )
         return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='done' )
-
     @web.expose
     @web.require_login( "rename histories" )
     def rename( self, trans, id=None, name=None, **kwd ):

templates/history/sharing.mako

@@ -1,75 +1,63 @@
 <%inherit file="/base.mako"/>
 <%namespace file="/message.mako" import="render_msg" />
 
-<h2>Public access via link</h2>
+##<h2>Import via link</h2>
 
 %if msg:
     ${render_msg( msg, messagetype )}
 %endif
 
-%for history in histories:
-    <p>
-        %if history.importable:
-            Send the following URL to users as an easy way for them to import the history, making a copy of their own:
-            <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %>
-            <blockquote>
-                <a href="${url}">${url}</a>
-            </blockquote>
-            <br/>
-            <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST">
-                <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link">
-            </form>
-        %else:
-            This history is currently restricted (only you and the users listed below
-            can access it). Enabling the following option will generate a URL that you
-            can give to a user to allow them to import this history.
-            <br/>
-            <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST">
-                <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link">
-            </form>
-        %endif
-    </p>
-    <h2>Sharing with specific users</h2>
-    %if history.users_shared_with:
-        <ul class="manage-table-actions">
-            <li>
-                <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}">
-                    <span>Share with another user</span>
-                </a>
-            </li>
-        </ul>
-        <p>
-            The following users will see this history in their list of histories 
-            shared with them by others, and they will be able to create their own copy of it:
-        </p>
-        <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-            <tr class="header">
-                <th>History '${history.name}' currently shared with</th>
-                <th></th>
-            </tr>
-            %for i, association in enumerate( history.users_shared_with ):
-                <% user = association.user %>
-                <tr>
-                    <td>
-                        ${user.email}
-                        <a id="user-${i}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-                    </td>
-                    <td>
-                        %if len( histories ) == 1:
-                            ## Only allow unsharing if we're dealing with 1 history, otherwise
-                            ## page refreshes screw things up
-                            <div popupmenu="user-${i}-popup">
-                                <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a>
+<h2>Histories that you've shared with others or enabled to be imported</h2>
+
+%if not histories:
+    You have no histories that you've shared with others or enabled to be imported
+%else:
+    %for history in histories:
+        <div class="toolForm">
+            <div class="toolFormTitle">History '${history.name}' shared with</div>
+            <div class="toolFormBody">
+                <div class="form-row">
+                    <div style="float: right;">
+                        <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}">
+                            <span>Share with another user</span>
+                        </a>
+                    </div>
+                </div>
+                %if history.users_shared_with:
+                    %for i, association in enumerate( history.users_shared_with ):
+                        <% user = association.user %>
+                        <div class="form-row">
+                            <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a>
+                            ${user.email}
+                        </div>
+                    %endfor
+                %endif
+                %if history.importable:
+                    <div class="form-row">
+                        <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %>
+                        <a href="${url}">${url}</a>
+                        <div class="toolParamHelp" style="clear: both;">
+                            Send the above URL to users as an easy way for them to import the history, making a copy of their own
+                        </div>
+                    </div>
+                    <div class="form-row">
+                        <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST">
+                            <div class="form-row">
+                                <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link">
                             </div>
-                        %endif
-                    </td>
-                </tr>    
-            %endfor
-        </table>
-    %else:
-        <p>You have not shared this history with any users.</p>
-        <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id(history.id) )}">
-            <span>Share with another user</span>
-        </a>
-    %endif
-%endfor
+                        </form>
+                    </div>
+                %else:
+                    <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST">
+                        <div class="form-row">
+                            <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link">
+                            <div class="toolParamHelp" style="clear: both;">
+                                Click to generate a URL that you can give to a user to allow them to import this history, making a copy of their own
+                            </div>
+                        </div>
+                    </form>
+                %endif
+            </div>
+        </div>
+    %endfor
+%endif

templates/root/index.mako

@@ -10,9 +10,6 @@
             "Stored by you": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='list')}";
             },
-            "Shared with you": function() {
-                galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}";
-            },
             "Current History": null,
             "Create new": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history_new' )}";
@@ -32,10 +29,19 @@
             "Show deleted datasets": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}";
             },
-            "Delete": function() {
-                if ( confirm( "Really delete the current history?" ) ) {
+            "Delete": function()
+            {
+                if ( confirm( "Really delete the current history?" ) )
+                {
                     galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}";
                 }
+            },
+            "Manage shared histories": null,
+            "Shared by you": function() {
+                galaxy_main.location = "${h.url_for( controller='history', action='list', operation='sharing' )}";
+            },
+            "Shared with you": function() {
+                galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}";
             }
         });
     });

test/functional/test_history_functions.py

@@ -141,14 +141,13 @@ class TestHistory( TwillTestCase ):
                                     check_str_after_submit='You cannot send histories to yourself.' )
         # Share history3 with 1 valid user
         self.share_current_history( regular_user1.email,
-                                    check_str=history3.name,
-                                    check_str_after_submit='History (%s) now shared with: 1 users' % history3.name )
+                                    check_str=history3.name )
         # Check out list of histories to make sure history3 was shared
-        self.view_stored_active_histories( check_str='operation=sharing&id=%s">shared' % self.security.encode_id( history3.id ) )
+        self.view_stored_active_histories( check_str='operation=sharing">shared' )
         # Enable importing history3 via a URL
         self.enable_import_via_link( self.security.encode_id( history3.id ),
                                      check_str='Unshare',
-                                     check_str_after_submit='Send the following URL to users' )
+                                     check_str_after_submit='Send the above URL to users' )
         # Make sure history3 is now import-able
         history3.refresh()
         if not history3.importable:
@@ -159,7 +158,7 @@ class TestHistory( TwillTestCase ):
                                      check_str_after_submit='You cannot import your own history.' )
         # Disable the import link for history3
         self.disable_import_via_link( self.security.encode_id( history3.id ),
-                                     check_str='Send the following URL to users',
+                                     check_str='Send the above URL to users',
                                      check_str_after_submit='Enable import via link' )
         # Try importing history3 after disabling the URL
         self.import_history_via_url( self.security.encode_id( history3.id ),
@@ -274,12 +273,10 @@ class TestHistory( TwillTestCase ):
         self.upload_file( '2.bed', dbkey='hg18' )
         ids = '%s,%s' % ( self.security.encode_id( history3.id ), self.security.encode_id( history4.id ) )
         emails = '%s,%s' % ( regular_user2.email, regular_user3.email )
-        check_str_after_submit = 'History (%s) now shared with: 3 users.' % history3.name
         self.share_histories_with_users( ids,
                                          emails,
                                          check_str1='Share 2 histories',
-                                         check_str2=history4.name,
-                                         check_str_after_submit=check_str_after_submit )
+                                         check_str2=history4.name )
         self.logout()
         self.login( email=regular_user2.email )
         # Shared history3 should be in regular_user2's list of shared histories
@@ -342,12 +339,10 @@ class TestHistory( TwillTestCase ):
         """Testing sharing a restricted history by making the datasets public"""
         # Logged in as admin_user
         action_check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email
-        action_check_str_after_submit = 'History (%s) now shared with: 1 users.' % history5.name
         # Current history is history5
         self.share_current_history( regular_user1.email,
                                     action='public',
-                                    action_check_str=action_check_str,
-                                    action_check_str_after_submit=action_check_str_after_submit )
+                                    action_check_str=action_check_str )
         self.logout()
         self.login( email=regular_user1.email )
         # Shared history5 should be in regular_user1's list of shared histories
@@ -375,12 +370,10 @@ class TestHistory( TwillTestCase ):
         self.upload_file( '2.bed', dbkey='hg18' )
         check_str_after_submit = 'The following datasets can be shared with %s with no changes' % regular_user2.email
         check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % regular_user2.email
-        action_check_str_after_submit = 'History (%s) now shared with: 2 users.' % history5.name
         self.share_current_history( regular_user2.email,
                                     check_str_after_submit=check_str_after_submit,
                                     check_str_after_submit2=check_str_after_submit2,
-                                    action='private',
-                                    action_check_str_after_submit=action_check_str_after_submit )        
+                                    action='private' )        
         # We should now have a new sharing role
         global sharing_role
         role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user2.email )
@@ -470,12 +463,10 @@ class TestHistory( TwillTestCase ):
         check_str_after_submit = 'The following datasets can be shared with %s with no changes' % email
         check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % email
         # history5 will be shared with regular_user1, regular_user2 and regular_user3
-        action_check_str_after_submit = 'History (%s) now shared with: 3 users.' % history5.name
         self.share_current_history( email,
                                     check_str_after_submit=check_str_after_submit,
                                     check_str_after_submit2=check_str_after_submit2,
-                                    action='share_anyway',
-                                    action_check_str_after_submit=action_check_str_after_submit )
+                                    action='share_anyway' )
         # Check security on clone of history5 for regular_user2
         self.logout()
         self.login( email=regular_user2.email )