コード例 #1
0
ファイル: __init__.py プロジェクト: maikenp/galaxy
    def to_xml_file(self,
                    shed_tool_data_table_config,
                    new_elems=None,
                    remove_elems=None):
        """
        Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.
        remove_elems are removed before new_elems are added.
        """
        if not (new_elems or remove_elems):
            log.debug(
                'ToolDataTableManager.to_xml_file called without any elements to add or remove.'
            )
            return  # no changes provided, no need to persist any changes
        if not new_elems:
            new_elems = []
        if not remove_elems:
            remove_elems = []
        full_path = os.path.abspath(shed_tool_data_table_config)
        # FIXME: we should lock changing this file by other threads / head nodes
        try:
            try:
                tree = util.parse_xml(full_path)
            except OSError as e:
                if e.errno == errno.ENOENT:
                    with open(full_path, 'w') as fh:
                        fh.write(TOOL_DATA_TABLE_CONF_XML)
                    tree = util.parse_xml(full_path)
                else:
                    raise
            root = tree.getroot()
            out_elems = [elem for elem in root]
        except Exception as e:
            out_elems = []
            log.debug(
                'Could not parse existing tool data table config, assume no existing elements: %s',
                e)
        for elem in remove_elems:
            # handle multiple occurrences of remove elem in existing elems
            while elem in out_elems:
                remove_elems.remove(elem)
        # add new elems
        out_elems.extend(new_elems)
        out_path_is_new = not os.path.exists(full_path)

        root = util.parse_xml_string(
            '<?xml version="1.0"?>\n<tables></tables>')
        for elem in out_elems:
            root.append(elem)
        with RenamedTemporaryFile(full_path, mode='w') as out:
            out.write(util.xml_to_string(root, pretty=True))
        os.chmod(full_path, RW_R__R__)
        if out_path_is_new:
            self.tool_data_path_files.update_files()
コード例 #2
0
 def config_elems_to_xml_file(self, config_elems, config_filename, tool_path):
     """
     Persist the current in-memory list of config_elems to a file named by the
     value of config_filename.
     """
     try:
         root = parse_xml_string('<?xml version="1.0"?>\n<toolbox tool_path="%s"></toolbox>' % str(tool_path))
         for elem in config_elems:
             root.append(elem)
         with RenamedTemporaryFile(config_filename, mode='w') as fh:
             fh.write(xml_to_string(root, pretty=True))
     except Exception:
         log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
コード例 #3
0
 def config_elems_to_xml_file(self, config_elems, config_filename, tool_path, tool_cache_data_dir=None):
     """
     Persist the current in-memory list of config_elems to a file named by the
     value of config_filename.
     """
     try:
         tool_cache_data_dir = f' tool_cache_data_dir="{tool_cache_data_dir}"' if tool_cache_data_dir else ''
         root = parse_xml_string(f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"{tool_cache_data_dir}></toolbox>')
         for elem in config_elems:
             root.append(elem)
         with RenamedTemporaryFile(config_filename, mode='w') as fh:
             fh.write(xml_to_string(root, pretty=True))
     except Exception:
         log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
コード例 #4
0
ファイル: data_manager.py プロジェクト: xingyongma/galaxy
 def data_manager_config_elems_to_xml_file(self, config_elems, config_filename):
     """
     Persist the current in-memory list of config_elems to a file named by the value
     of config_filename.
     """
     data_managers_path = self.data_managers_path
     if data_managers_path:
         root_str = '<?xml version="1.0"?><data_managers tool_path="%s"></data_managers>' % data_managers_path
     else:
         root_str = '<?xml version="1.0"?><data_managers></data_managers>'
     root = ElementTree.fromstring(root_str)
     for elem in config_elems:
         root.append(elem)
     try:
         with RenamedTemporaryFile(config_filename, mode='w') as fh:
             fh.write(xml_to_string(root))
     except Exception:
         log.exception("Exception in DataManagerHandler.data_manager_config_elems_to_xml_file")
コード例 #5
0
    def _write_integrated_tool_panel_config_file(self):
        """
        Write the current in-memory version of the integrated_tool_panel.xml file to disk.  Since Galaxy administrators
        use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
        """
        destination = os.path.abspath(self._integrated_tool_panel_config)
        log.debug("Writing integrated tool panel config file to '%s'",
                  destination)
        tracking_directory = self._integrated_tool_panel_tracking_directory
        if tracking_directory:
            if not os.path.exists(tracking_directory):
                os.makedirs(tracking_directory)
            name = "integrated_tool_panel_%.10f.xml" % time.time()
            filename = os.path.join(tracking_directory, name)
        else:
            filename = destination
        template = string.Template("""<?xml version="1.0"?>
<toolbox>
    <!--
    $INTEGRATED_TOOL_PANEL_DESCRIPTION
    -->
$INTEGRATED_TOOL_PANEL
</toolbox>
""")
        integrated_tool_panel = []
        for key, item_type, item in self._integrated_tool_panel.panel_items_iter(
        ):
            if item:
                if item_type == panel_item_types.TOOL:
                    integrated_tool_panel.append('    <tool id="%s" />\n' %
                                                 item.id)
                elif item_type == panel_item_types.WORKFLOW:
                    integrated_tool_panel.append('    <workflow id="%s" />\n' %
                                                 item.id)
                elif item_type == panel_item_types.LABEL:
                    label_id = item.id or ''
                    label_text = item.text or ''
                    label_version = item.version or ''
                    integrated_tool_panel.append(
                        '    <label id="%s" text="%s" version="%s" />\n' %
                        (label_id, label_text, label_version))
                elif item_type == panel_item_types.SECTION:
                    section_id = item.id or ''
                    section_name = item.name or ''
                    section_version = item.version or ''
                    integrated_tool_panel.append(
                        '    <section id="%s" name="%s" version="%s">\n' %
                        (escape(section_id), escape(section_name),
                         section_version))
                    for section_key, section_item_type, section_item in item.panel_items_iter(
                    ):
                        if section_item_type == panel_item_types.TOOL:
                            if section_item:
                                integrated_tool_panel.append(
                                    '        <tool id="%s" />\n' %
                                    section_item.id)
                        elif section_item_type == panel_item_types.WORKFLOW:
                            if section_item:
                                integrated_tool_panel.append(
                                    '        <workflow id="%s" />\n' %
                                    section_item.id)
                        elif section_item_type == panel_item_types.LABEL:
                            if section_item:
                                label_id = section_item.id or ''
                                label_text = section_item.text or ''
                                label_version = section_item.version or ''
                                integrated_tool_panel.append(
                                    '        <label id="%s" text="%s" version="%s" />\n'
                                    % (label_id, label_text, label_version))
                    integrated_tool_panel.append('    </section>\n')
        tool_panel_description = '\n    '.join(
            [l for l in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if l])
        tp_string = template.substitute(
            INTEGRATED_TOOL_PANEL_DESCRIPTION=tool_panel_description,
            INTEGRATED_TOOL_PANEL='\n'.join(integrated_tool_panel))
        with RenamedTemporaryFile(filename, mode='w') as f:
            f.write(tp_string)
        if tracking_directory:
            with open(filename + ".stack", "w") as f:
                f.write(''.join(traceback.format_stack()))
            shutil.copy(filename, filename + ".copy")
            shutil.move(filename + ".copy", destination)
        try:
            os.chmod(destination, 0o644)
        except OSError:
            # That can happen if multiple threads are simultaneously moving/chmod'ing this file
            # Should be harmless, though this race condition should be avoided.
            pass