Improve error message handling when setting metadata on tool shed repositories. Display the repository owner in the table grid when displaying invalid tools in the tool shed.

2026-09-24 16:30:27 +08:00 · 2012-08-15 14:50:38 -04:00
parent cdd15be456
commit c0898c6882
4 changed files with 65 additions and 30 deletions
@@ -696,9 +696,14 @@ class AdminController( BaseUIController, Admin ):
                    owner = repository_name_owner_list[ 1 ]
                    repository = get_repository_by_name_and_owner( trans, name, owner )
                    try:
-                        reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
-                        log.debug( "Successfully reset metadata on repository %s" % repository.name )
-                        successful_count += 1
+                        invalid_file_tups = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
+                        if invalid_file_tups:
+                            message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False )
+                            log.debug( message )
+                            unsuccessful_count += 1
+                        else:
+                            log.debug( "Successfully reset metadata on repository %s" % repository.name )
+                            successful_count += 1
                    except Exception, e:
                        log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
                        unsuccessful_count += 1
@@ -277,6 +277,41 @@ def generate_clone_url( trans, repository_id ):
        return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
    else:
        return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name )
+def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True ):
+    if as_html:
+        new_line = '<br/>'
+        bold_start = '<b>'
+        bold_end = '</b>'
+    else:
+        new_line = '\n'
+        bold_start = ''
+        bold_end = ''
+    message = ''
+    if metadata_dict:
+        message += "Metadata was defined for some items in revision '%s'.  " % str( repository.tip )
+        message += "Correct the following problems if necessary and reset metadata.%s" % new_line
+    else:
+        message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip )
+        message += "installed into a local Galaxy instance.  Correct the following problems and reset metadata.%s" % new_line
+    for itc_tup in invalid_file_tups:
+        tool_file, exception_msg = itc_tup
+        if exception_msg.find( 'No such file or directory' ) >= 0:
+            exception_items = exception_msg.split()
+            missing_file_items = exception_items[ 7 ].split( '/' )
+            missing_file = missing_file_items[ -1 ].rstrip( '\'' )
+            if missing_file.endswith( '.loc' ):
+                sample_ext = '%s.sample' % missing_file
+            else:
+                sample_ext = missing_file
+            correction_msg = "This file refers to a missing file %s%s%s.  " % ( bold_start, str( missing_file ), bold_end )
+            correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end )
+        else:
+            if as_html:
+                correction_msg = exception_msg
+            else:
+                correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end )
+        message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line )
+    return message
 def generate_tool_guid( trans, repository, tool ):
    """
    Generate a guid for the received tool.  The form of the guid is    
@@ -854,6 +889,7 @@ def reset_all_metadata_on_repository( trans, id, **kwd ):
    clean_repository_metadata( trans, id, changeset_revisions )
    # Set tool version information for all downloadable changeset revisions.  Get the list of changeset revisions from the changelog.
    reset_all_tool_versions( trans, id, repo )
+    return invalid_file_tups
 def set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
    """
    Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset
@@ -931,27 +967,7 @@ def set_repository_metadata( trans, repository, content_alert_str='', **kwd ):
        message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
        status = "error"
    if invalid_file_tups:
-        if metadata_dict:
-            message += "Metadata was defined for some items in revision '%s'.  " % str( repository.tip )
-            message += "Correct the following problems if necessary and reset metadata.<br/>"
-        else:
-            message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip )
-            message += "installed into a local Galaxy instance.  Correct the following problems and reset metadata.<br/>"
-        for itc_tup in invalid_file_tups:
-            tool_file, exception_msg = itc_tup
-            if exception_msg.find( 'No such file or directory' ) >= 0:
-                exception_items = exception_msg.split()
-                missing_file_items = exception_items[ 7 ].split( '/' )
-                missing_file = missing_file_items[ -1 ].rstrip( '\'' )
-                if missing_file.endswith( '.loc' ):
-                    sample_ext = '%s.sample' % missing_file
-                else:
-                    sample_ext = missing_file
-                correction_msg = "This file refers to a missing file <b>%s</b>.  " % str( missing_file )
-                correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % sample_ext
-            else:
-               correction_msg = exception_msg
-            message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg )            
+        message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict )
        status = 'error'
    return message, status
 def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ):
@@ -458,7 +458,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
                    metadata = downloadable_revision.metadata
                    invalid_tools = metadata.get( 'invalid_tools', [] )
                    for invalid_tool_config in invalid_tools:
-                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id,
+                                                                      repository.name,
+                                                                      repository.user.username,
+                                                                      downloadable_revision.changeset_revision )
        else:
            for repository in trans.sa_session.query( trans.model.Repository ) \
                                              .filter( and_( trans.model.Repository.table.c.deleted == False,
@@ -468,7 +471,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
                    metadata = downloadable_revision.metadata
                    invalid_tools = metadata.get( 'invalid_tools', [] )
                    for invalid_tool_config in invalid_tools:
-                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
+                        invalid_tools_dict[ invalid_tool_config ] = ( repository.id,
+                                                                      repository.name,
+                                                                      repository.user.username,
+                                                                      downloadable_revision.changeset_revision )
        return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako',
                                    cntrller=cntrller,
                                    invalid_tools_dict=invalid_tools_dict,
@@ -1373,6 +1379,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
        return trans.response.send_redirect( url )
    @web.expose
    def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
+        # FIXME: loading an invalid tool should display an appropriate message as to why the tool is invalid.  This worked until recently.
        params = util.Params( kwd )
        message = util.restore_text( params.get( 'message', ''  ) )
        status = params.get( 'status', 'error' )
@@ -1752,9 +1759,14 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                    status=status )
    @web.expose
    def reset_all_metadata( self, trans, id, **kwd ):
-        reset_all_metadata_on_repository( trans, id, **kwd )
-        message = "All repository metadata has been reset."
-        status = 'done'
+        invalid_file_tups = reset_all_metadata_on_repository( trans, id, **kwd )
+        if invalid_file_tups:
+            repository = get_repository( trans, id )
+            message = generate_message_for_invalid_tools( invalid_file_tups, repository, None )
+            status = 'error'
+        else:
+            message = "All repository metadata has been reset."
+            status = 'done'
        return trans.response.send_redirect( web.url_for( controller='repository',
                                                          action='manage_repository',
                                                          id=id,
@@ -13,10 +13,11 @@
                    <tr>
                        <th>Tool config</th>
                        <th>Repository name</th>
+                        <th>Repository owner</th>
                        <th>Changeset revision</th>
                    </tr>
                    %for invalid_tool_config, repository_tup in invalid_tools_dict.items():
-                        <% repository_id, repository_name, changeset_revision = repository_tup %>
+                        <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %>
                        <tr>
                            <td>
                                <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}">
@@ -24,6 +25,7 @@
                                </a>
                            </td>
                            <td>${repository_name}</td>
+                            <td>${repository_owner}</td>
                            <td>${changeset_revision}</td>
                        </tr>
                    %endfor