Fix for rendering multiple readme files contained within a tool shed repository.

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -1,16 +1,17 @@
 import logging
 from galaxy.web.framework.helpers import time_ago
+from galaxy import eggs
 from galaxy import web
 from galaxy import util
 from galaxy.web.base.controller import BaseAPIController
 import tool_shed.util.shed_util_common as suc
 from tool_shed.galaxy_install import repository_util
 
-from galaxy import eggs
-import pkg_resources
+eggs.require( 'mercurial' )
 
-pkg_resources.require( 'mercurial' )
-from mercurial import hg, ui, commands
+from mercurial import commands
+from mercurial import hg
+from mercurial import ui 
 
 log = logging.getLogger( __name__ )
 

lib/tool_shed/grids/admin_grids.py

@@ -1,15 +1,19 @@
-import os, logging
-from galaxy.web.framework.helpers import time_ago, grids
+import logging
+import os
+from galaxy.web.framework.helpers import grids
+from galaxy.web.framework.helpers import time_ago
 from galaxy.webapps.tool_shed import model
 from galaxy.model.orm import and_
 import tool_shed.util.shed_util_common as suc
-from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid
+from tool_shed.grids.repository_grids import CategoryGrid
+from tool_shed.grids.repository_grids import RepositoryGrid
 
 from galaxy import eggs
-import pkg_resources
+eggs.require( 'mercurial' )
 
-pkg_resources.require( 'mercurial' )
-from mercurial import hg, ui, commands
+from mercurial import commands
+from mercurial import hg
+from mercurial import ui
 
 log = logging.getLogger( __name__ )
 

lib/tool_shed/util/container_util.py

@@ -573,27 +573,23 @@ def build_invalid_tools_folder( trans, folder_id, invalid_tool_configs, changese
 def build_readme_files_folder( trans, folder_id, readme_files_dict, label='Readme files' ):
     """Return a folder hierarchy containing readme text files."""
     if readme_files_dict:
-        multiple_readme_files = len( readme_files_dict ) > 1
         readme_id = 0
         folder_id += 1
         readme_files_root_folder = Folder( id=folder_id, key='root', label='root', parent=None )
-        if multiple_readme_files:
-            folder_id += 1
-            readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder )
-            readme_files_root_folder.folders.append( readme_files_folder )
+        folder_id += 1
+        readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder )
+        multiple_readme_files = len( readme_files_dict ) > 1
+        readme_files_root_folder.folders.append( readme_files_folder )
         for readme_file_name, readme_file_text in readme_files_dict.items():
             readme_id += 1
             readme = ReadMe( id=readme_id, name=readme_file_name, text=readme_file_text )
             if multiple_readme_files:
                 folder_id += 1
-                folder = Folder( id=folder_id, key=readme.name, label=readme.name, parent=readme_files_folder )
+                folder = Folder( id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder )
                 folder.readme_files.append( readme )
                 readme_files_folder.folders.append( folder )
             else:
-                folder_id += 1
-                readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name, parent=readme_files_root_folder )
                 readme_files_folder.readme_files.append( readme )
-                readme_files_root_folder.folders.append( readme_files_folder )
     else:
         readme_files_root_folder = None
     return folder_id, readme_files_root_folder

lib/tool_shed/util/metadata_util.py

@@ -589,7 +589,7 @@ def generate_metadata_for_changeset_revision( app, repository, changeset_revisio
         original_repository_metadata = repository.metadata
     else:
         original_repository_metadata = None
-    readme_file_names = get_readme_file_names( repository.name )
+    readme_file_names = readme_util.get_readme_file_names( str( repository.name ) )
     if app.name == 'galaxy':
         # Shed related tool panel configs are only relevant to Galaxy.
         metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) }
@@ -1046,16 +1046,6 @@ def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
         # The tool did not change through all of the changeset revisions.
         return old_id
 
-def get_readme_file_names( repository_name ):
-    """Creates a list of valid filenames."""
-    readme_files = [ 'readme', 'read_me', 'install' ]
-    valid_filenames = map( lambda f: '%s.txt' % f, readme_files )
-    valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) )
-    valid_filenames.extend( readme_files )
-    valid_filenames.append( '%s.txt' % repository_name )
-    valid_filenames.append( '%s.rst' % repository_name )
-    return valid_filenames
-
 def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ):
     if resetting_all_metadata_on_repository:
         full_path_to_file = os.path.join( root, name )

lib/tool_shed/util/readme_util.py

@@ -70,3 +70,13 @@ def get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ):
     raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
     readme_files_dict = json.from_json_string( raw_text )
     return readme_files_dict
+
+def get_readme_file_names( repository_name ):
+    """Return a list of file names that will be categorized as README files for the received repository_name."""
+    readme_files = [ 'readme', 'read_me', 'install' ]
+    valid_filenames = map( lambda f: '%s.txt' % f, readme_files )
+    valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) )
+    valid_filenames.extend( readme_files )
+    valid_filenames.append( '%s.txt' % repository_name )
+    valid_filenames.append( '%s.rst' % repository_name )
+    return valid_filenames

templates/webapps/tool_shed/repository/common.mako

@@ -425,7 +425,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rd-${encoded_id}">
         <${cell_type} style="padding-left: ${pad+20}px;">${datatype.extension | h}</${cell_type}>
         <${cell_type}>${datatype.type | h}</${cell_type}>
         <${cell_type}>${datatype.mimetype | h}</${cell_type}>
@@ -446,7 +446,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rft-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="failed_test_table" class="tool_test_results">
                 <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr>
@@ -475,7 +475,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-ridm-${encoded_id}">
         <${cell_type} style="padding-left: ${pad+20}px;">${data_manager.index | h}</${cell_type}>
         <${cell_type}>${data_manager.error | h}</${cell_type}>
     </tr>
@@ -493,7 +493,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rird-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             ${ invalid_repository_dependency.error | h }
         </td>
@@ -510,7 +510,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rit-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             %if trans.webapp.name == 'tool_shed' and invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision:
                 <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision, render_repository_actions_for=render_repository_actions_for )}">
@@ -545,7 +545,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-ritd-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="invalid_td_table">
                 <tr><td>${ invalid_tool_dependency.error | h }</td></tr>
@@ -564,7 +564,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rmtc-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="missing_table" class="tool_test_results">
                 <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr>
@@ -587,27 +587,17 @@
         encoded_id = trans.security.encode_id( readme.id )
         render_rst = readme.name.endswith( '.rst' )
     %>
-    <style type="text/css">
-        #readme_table{ table-layout:fixed;
-                       width:100%;
-                       overflow-wrap:normal;
-                       overflow:hidden;
-                       border:0px; 
-                       word-break:keep-all;
-                       word-wrap:break-word;
-                       line-break:strict; }
-    </style>
     <tr class="datasetRow"
         %if parent is not None:
-            parent="${parent}"
+            parent="${parent}" 
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rr-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
-            <table id="readme_table">
+            <table id="readme_files">
                 %if render_rst:
                     <tr><td>${ rst_to_html( readme.text ) }</td></tr>
                 %else:
-                    <tr><td>${readme.name}<br/>${ to_html_string( readme.text ) }</td></tr>
+                    <tr><td>${ to_html_string( readme.text ) }</td></tr>
                 %endif
             </table>
         </td>
@@ -652,7 +642,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rrd-${encoded_id}">
         %if trans.webapp.name == 'galaxy':
             <${cell_type} style="padding-left: ${pad+20}px;">
                 %if row_is_header:
@@ -684,6 +674,19 @@
     %>
 </%def>
 
+<%def name="render_readme_files_css()">
+    <style type="text/css">
+        table.readme_files{ table-layout:fixed;
+                            width:100%;
+                            overflow-wrap:normal;
+                            overflow:hidden;
+                            border:0px; 
+                            word-break:keep-all;
+                            word-wrap:break-word;
+                            line-break:strict; }
+    </style>
+</%def>
+
 <%def name="render_tool_test_results_css()">
     <style type="text/css">
         table.tool_test_results{ table-layout:fixed;
@@ -703,7 +706,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rtdie-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="td_install_error_table" class="tool_test_results">
                 <tr bgcolor="#FFFFCC">
@@ -731,7 +734,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rrie-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="rd_install_error_table" class="tool_test_results">
                 %if not is_current_repository:
@@ -762,7 +765,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rnt-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="not_tested_table" class="tool_test_results">
                 <tr><td>${not_tested.reason | h}</td></tr>
@@ -781,7 +784,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rpt-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
             <table id="passed_tests_table" class="tool_test_results">
                 <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr>
@@ -808,7 +811,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rt-${encoded_id}">
         %if row_is_header:
             <th style="padding-left: ${pad+20}px;">${tool.name | h}</th>
         %else:
@@ -857,7 +860,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rtd-${encoded_id}">
         <${cell_type} style="padding-left: ${pad+20}px;">
             %if row_is_header:
                 ${tool_dependency.name | h}
@@ -913,13 +916,23 @@
 
 <%def name="render_test_environment( test_environment, pad, parent, row_counter, row_is_header=False )">
     <% encoded_id = trans.security.encode_id( test_environment.id ) %>
+    <style type="text/css">
+        #test_environment_table{ table-layout:fixed;
+                                 width:100%;
+                                 overflow-wrap:normal;
+                                 overflow:hidden;
+                                 border:0px; 
+                                 word-break:keep-all;
+                                 word-wrap:break-word;
+                                 line-break:strict; }
+    </style>
     <tr class="datasetRow"
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rte-${encoded_id}">
         <td style="padding-left: ${pad+20}px;">
-            <table class="grid" id="readme_table">
+            <table class="grid" id="test_environment_table">
                 <tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr>
                 <tr><td><b>System:</b> ${test_environment.system | h}</td></tr>
                 <tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr>
@@ -950,7 +963,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rvdm-${encoded_id}">
         <${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}>
         <${cell_type}>${data_manager.version | h}</${cell_type}>
         <${cell_type}>${data_manager.data_tables | h}</${cell_type}>
@@ -981,7 +994,7 @@
         %if parent is not None:
             parent="${parent}"
         %endif
-        id="libraryItem-${encoded_id}">
+        id="libraryItem-rw-${encoded_id}">
         <${cell_type} style="padding-left: ${pad+20}px;">
             %if row_is_header:
                 ${workflow.workflow_name | h}
@@ -1045,6 +1058,8 @@
                 return str( self.count )
     %>
     %if readme_files_root_folder:
+        ${render_readme_files_css()}
+        <p/>
         <div class="toolForm">
             <div class="toolFormTitle">Repository README files - may contain important installation or license information</div>
             <div class="toolFormBody">
@@ -1161,11 +1176,11 @@
         <div class="toolForm">
             <div class="toolFormTitle">Automated tool test results</div>
             <div class="toolFormBody">
-                    <p/>
-                    <% row_counter = RowCounter() %>
-                    <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment">
-                        ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
-                    </table>
+                <p/>
+                <% row_counter = RowCounter() %>
+                <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment">
+                    ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+                </table>
             </div>
         </div>
     %endif