1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/f640c7bd6ffc/ changeset: f640c7bd6ffc user: greg date: 2011-11-14 22:19:56 summary: Add baseline support for handling data types included in tool shed repositories, add the ability to upload files to tool shed repositories by entering a URL in the upload form, provide much better file content checking when uploading either single files or archives to a tool shed repository (niether html content nor images are currently allowed), enhance error messaging when tool config parameter tags are not functionally correct. affected #: 11 files

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -164,9 +164,14 @@ @classmethod def build( cls, tool, param ): """Factory method to create parameter of correct type""" + param_name = param.get( "name" ) + if not param_name: + raise ValueError( "Tool parameters require a 'name'" ) param_type = param.get("type") - if not param_type or param_type not in parameter_types: - raise ValueError( "Unknown tool parameter type '%s'" % param_type ) + if not param_type: + raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) ) + elif param_type not in parameter_types: + raise ValueError( "Tool parameter '%s' uses an unknown type '%s'" % ( param_name, param_type ) ) else: return parameter_types[param_type]( tool, param )

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -6,6 +6,7 @@ from time import strftime from galaxy import config, tools, web, util from galaxy.util.hash_util import * +from galaxy.util.json import json_fix from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import *

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -4,12 +4,14 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch from galaxy.tools import ToolSection, json_fix +from galaxy.util import inflector import logging log = logging.getLogger( __name__ )

from galaxy.actions.admin import AdminActions from galaxy.web.params import QuotaParamParser from galaxy.exceptions import * +import galaxy.datatypes.registry

class UserListGrid( grids.Grid ): class EmailColumn( grids.TextColumn ): @@ -871,6 +873,10 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: + # Load data types required by tools. + # TODO: uncomment the following when we're ready... + #self.__load_datatypes( trans, repo_files_dir ) + # Load tools and tool data files required by them. sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. @@ -920,8 +926,9 @@ status = 'error' if installed_repository_names: installed_repository_names.sort() - message += 'These %d repositories were installed and all tools were loaded into tool panel section <b>%s</b>:<br/>' % \ - ( len( installed_repository_names ), tool_section.name ) + num_repositories_installed = len( installed_repository_names ) + message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \ + ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name ) for i, repo_name in enumerate( installed_repository_names ): if i == len( installed_repository_names ) -1: message += '%s.<br/>' % repo_name @@ -1171,6 +1178,45 @@ error = tmp_stderr.read() tmp_stderr.close() log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + def __load_datatypes( self, trans, repo_files_dir ): + # Find datatypes_conf.xml if it exists. + datatypes_config = None + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + # Parse datatypes_config. + tree = ElementTree.parse( datatypes_config ) + root = tree.getroot() + ElementInclude.include( root ) + datatype_files = root.find( 'datatype_files' ) + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + relative_path = None + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + relative_path = os.path.join( root, name ) + break + relative_head, relative_tail = os.path.split( relative_path ) + # TODO: get the import_module by parsing the <registration><datatype> tags + if datatype_file_name.find( '.' ) > 0: + import_module = datatype_file_name.split( '.' )[ 0 ] + else: + import_module = datatype_file_name + try: + sys.path.insert( 0, relative_head ) + module = __import__( import_module ) + sys.path.pop( 0 ) + except Exception, e: + log.debug( "Execption importing datatypes code file included in installed repository: %s" % str( e ) ) + trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config ) def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): # The sample_files list contains all files whose name ends in .sample sample_files = []

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -124,34 +124,6 @@ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() -def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): - """ - Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything in the database. - """ - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( exported_workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] - return metadata_dict -def new_workflow_metadata_required( trans, id, metadata_dict ): - """ - Currently everything about an exported workflow except the name is hard-coded, so there's - no real way to differentiate versions of exported workflows. If this changes at some future - time, this method should be enhanced accordingly. - """ - if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - if repository_metadata.metadata: - # The repository has metadata, so update the workflows value - no new record is needed. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table - # record is not needed. - return False def generate_clone_url( trans, repository_id ): repository = get_repository( trans, repository_id ) protocol, base = trans.request.base.split( '://' ) @@ -313,6 +285,62 @@ # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False +def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied + to the received exported_workflow_dict. Store everything in the database. + """ + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( exported_workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] + return metadata_dict +def new_workflow_metadata_required( trans, id, metadata_dict ): + """ + Currently everything about an exported workflow except the name is hard-coded, so there's + no real way to differentiate versions of exported workflows. If this changes at some future + time, this method should be enhanced accordingly. + """ + if 'workflows' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + if repository_metadata.metadata: + # The repository has metadata, so update the workflows value - no new record is needed. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table + # record is not needed. + return False +def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied + to the received datatypes_config. + """ + # Parse datatypes_config. + tree = ElementTree.parse( datatypes_config ) + root = tree.getroot() + ElementInclude.include( root ) + repository_datatype_code_files = [] + datatype_files = root.find( 'datatype_files' ) + if datatype_files: + for elem in datatype_files.findall( 'datatype_file' ): + name = elem.get( 'name', None ) + repository_datatype_code_files.append( name ) + metadata_dict[ 'datatype_files' ] = repository_datatype_code_files + datatypes = [] + registration = root.find( 'registration' ) + if registration: + for elem in registration.findall( 'datatype' ): + extension = elem.get( 'extension', None ) + dtype = elem.get( 'type', None ) + mimetype = elem.get( 'mimetype', None ) + datatypes.append( dict( extension=extension, + dtype=dtype, + mimetype=mimetype ) ) + metadata_dict[ 'datatypes' ] = datatypes + return metadata_dict def set_repository_metadata( trans, id, changeset_revision, **kwd ): """Set repository metadata""" message = '' @@ -322,28 +350,34 @@ repo = hg.repository( get_configured_ui(), repo_dir ) invalid_files = [] sample_files = [] + datatypes_config = None ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} if changeset_revision == repository.tip: - # Find all special .sample files first. + # Find datatypes_conf.xml if it exists. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + # Find all special .sample files. for root, dirs, files in os.walk( repo_dir ): if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + # Find all tool configs and exported workflows. for root, dirs, files in os.walk( repo_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) for name in files: # Find all tool configs. - if name.endswith( '.xml' ): + if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): try: full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) @@ -373,11 +407,13 @@ # Find all special .sample files first. for filename in ctx: if filename.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, filename ) ) ) + sample_files.append( os.path.abspath( filename ) ) # Get all tool config file names from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml for filename in ctx: - # Find all tool configs - should not have to update metadata for workflows for now. + # Find all tool configs - we do not have to update metadata for workflows or datatypes in anything + # but repository tips (handled above) since at the time this code was written, no workflows or + # dataytpes_conf.xml files exist in tool shed repositories, so they can only be added in future tips. if filename.endswith( '.xml' ): fctx = ctx[ filename ] # Write the contents of the old tool config to a temporary file. @@ -532,25 +568,41 @@ # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) repo.ui.pushbuffer() + files_to_remove_from_disk = [] + files_to_commit = [] commands.status( repo.ui, repo, all=True ) status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) - # status_and_file_names looks something like: - # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] - # The codes used to show the status of files are: - # M = modified - # A = added - # R = removed - # C = clean - # ! = deleted, but still tracked - # ? = not tracked - # I = ignored - files_to_remove_from_disk = [] - files_to_commit = [] - for status_and_file_name in status_and_file_names: - if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): - files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): - files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) + if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]: + # status_and_file_names looks something like: + # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] + # The codes used to show the status of files are: + # M = modified + # A = added + # R = removed + # C = clean + # ! = deleted, but still tracked + # ? = not tracked + # I = ignored + for status_and_file_name in status_and_file_names: + if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): + files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) + elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): + files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) + # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. + cmd = 'hg status' + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stdout = open( tmp_name, 'wb' ) + os.chdir( repo_dir ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=tmp_stdout.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stdout.close() + if returncode == 0: + for i, line in enumerate( open( tmp_name ) ): + if line.startswith( '?' ) or line.startswith( 'I' ): + files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) ) + elif line.startswith( 'M' ) or line.startswith( 'A' ) or line.startswith( 'R' ): + files_to_commit.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) ) for full_path in files_to_remove_from_disk: # We'll remove all files that are not tracked or ignored. if os.path.isdir( full_path ):

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1007,17 +1007,19 @@ if repository_path.startswith( './' ): repository_path = repository_path.replace( './', '', 1 ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) + tmp_fd, tmp_fname = tempfile.mkstemp() if os.path.exists( hgweb_config ): # Make a backup of the hgweb.config file since we're going to be changing it. self.__make_hgweb_config_copy( trans, hgweb_config ) - tmp_fname = tempfile.NamedTemporaryFile() + new_hgweb_config = open( tmp_fname, 'wb' ) for i, line in enumerate( open( hgweb_config ) ): - tmp_fname.write( line ) + new_hgweb_config.write( line ) else: - tmp_fname.write( '[paths]\n' ) - tmp_fname.write( "%s\n" % entry ) - tmp_fname.flush() - shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) ) + new_hgweb_config = open( tmp_fname, 'wb' ) + new_hgweb_config.write( '[paths]\n' ) + new_hgweb_config.write( "%s\n" % entry ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): # Change an entry in the hgweb.config file for a repository. This only happens when # the owner changes the name of the repository. An entry looks something like: @@ -1028,14 +1030,15 @@ repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) - tmp_fname = tempfile.NamedTemporaryFile() + tmp_fd, tmp_fname = tempfile.mkstemp() + new_hgweb_config = open( tmp_fname, 'wb' ) for i, line in enumerate( open( hgweb_config ) ): if line.startswith( old_lhs ): - tmp_fname.write( new_entry ) + new_hgweb_config.write( new_entry ) else: - tmp_fname.write( line ) - tmp_fname.flush() - shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) ) + new_hgweb_config.write( line ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path.

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,4 +1,4 @@ -import sys, os, shutil, logging, tarfile, tempfile +import sys, os, shutil, logging, tarfile, tempfile, urllib from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes.checkers import * @@ -11,9 +11,6 @@ SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" CHUNK_SIZE = 2**20 # 1Mb

-class UploadError( Exception ): - pass - class UploadController( BaseUIController ): @web.expose @web.require_login( 'upload', use_panels=True, webapp='community' ) @@ -32,20 +29,40 @@ remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = self.__get_upload_point( repository, **kwd ) - # Get the current repository tip. tip = repository.tip + file_data = params.get( 'file_data', '' ) + url = params.get( 'url', '' ) if params.get( 'upload_button', False ): current_working_dir = os.getcwd() - file_data = params.get( 'file_data', '' ) - if file_data == '': + if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error uploading file via http: %s' % str( e ) + status = 'error' + uploaded_file = None + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 elif file_data not in ( '', None ): uploaded_file = file_data.file uploaded_file_name = uploaded_file.name uploaded_file_filename = file_data.filename - isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file: isgzip = False isbz2 = False @@ -84,30 +101,32 @@ full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) ) else: full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) - # Move the uploaded file to the load_point within the repository hierarchy. - shutil.move( uploaded_file_name, full_path ) - commands.add( repo.ui, repo, full_path ) - try: - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) - except Exception, e: - # I never have a problem with commands.commit on a Mac, but in the test/production - # tool shed environment, it occasionally throws a "TypeError: array item must be char" - # exception. If this happens, we'll try the following. - repo.dirstate.write() - repo.commit( user=trans.user.username, text=commit_message ) - if full_path.endswith( 'tool_data_table_conf.xml.sample' ): - # Handle the special case where a tool_data_table_conf.xml.sample - # file is being uploaded by parsing the file and adding new entries - # to the in-memory trans.app.tool_data_tables dictionary as well as - # appending them to the shed's tool_data_table_conf.xml file on disk. - error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path ) - if error: - message = '%s<br/>%s' % ( message, error_message ) - if full_path.endswith( '.loc.sample' ): - # Handle the special case where a xxx.loc.sample file is - # being uploaded by copying it to ~/tool-data/xxx.loc. - copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + ok, message = self.__check_file_content( uploaded_file_name ) + if ok: + # Move the uploaded file to the load_point within the repository hierarchy. + shutil.move( uploaded_file_name, full_path ) + commands.add( repo.ui, repo, full_path ) + try: + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + except Exception, e: + # I never have a problem with commands.commit on a Mac, but in the test/production + # tool shed environment, it occasionally throws a "TypeError: array item must be char" + # exception. If this happens, we'll try the following. + repo.dirstate.write() + repo.commit( user=trans.user.username, text=commit_message ) + if full_path.endswith( 'tool_data_table_conf.xml.sample' ): + # Handle the special case where a tool_data_table_conf.xml.sample + # file is being uploaded by parsing the file and adding new entries + # to the in-memory trans.app.tool_data_tables dictionary as well as + # appending them to the shed's tool_data_table_conf.xml file on disk. + error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path ) + if error: + message = '%s<br/>%s' % ( message, error_message ) + if full_path.endswith( '.loc.sample' ): + # Handle the special case where a xxx.loc.sample file is + # being uploaded by copying it to ~/tool-data/xxx.loc. + copy_sample_loc_file( trans, full_path ) + handle_email_alerts( trans, repository ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -146,6 +165,7 @@ selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, + url=url, commit_message=commit_message, uncompress_file=uncompress_file, remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, @@ -172,6 +192,14 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() + for filename_in_archive in filenames_in_archive: + if os.path.isfile( filename_in_archive ): + ok, message = self.__check_file_content( filename_in_archive ) + if not ok: + # Refresh the repository files for browsing. + current_working_dir = os.getcwd() + update_for_browsing( trans, repository, current_working_dir ) + return False, message, [] if remove_repo_files_not_in_tar and not repository.is_new: # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. @@ -314,4 +342,14 @@ message = "Uploaded archives cannot contain hgrc files." return False, message return True, '' - + def __check_file_content( self, file_path ): + message = '' + ok = True + if check_html( file_path ): + message = 'Files containing HTML content cannot be uploaded to a Galaxy tool shed.' + ok = False + elif check_image( file_path ): + # For now we won't allow images to be uploaded. + message = 'Files containing images cannot be uploaded to a Galaxy tool shed.' + ok = False + return ok, message

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def>

-<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"><% from galaxy.webapps.community.controllers.common import encode, decode %> %if metadata or can_set_metadata: <p/> @@ -195,6 +195,45 @@ </div><div style="clear: both"></div> %endif + %if 'datatypes' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Data types</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% datatypes_dicts = metadata[ 'datatypes' ] %> + <table class="grid"> + <tr> + <td><b>extension</b></td> + <td><b>dtype</b></td> + <td><b>mimetype</b></td> + </tr> + %for datatypes_dict in datatypes_dicts: + <% + extension = datatypes_dict[ 'extension' ] + dtype = datatypes_dict[ 'dtype' ] + mimetype = datatypes_dict[ 'mimetype' ] + %> + <tr> + <td>${extension}</td> + <td>${dtype}</td> + <td> + %if mimetype: + ${mimetype} + %else: + &nbsp; + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %endif %if can_set_metadata: <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post">

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -184,7 +184,7 @@ </form></div></div> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )} +${render_repository_items( repository_metadata_id, metadata, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div>

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -104,4 +104,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata, webapp=webapp )}

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -73,7 +73,16 @@ </div><div style="clear: both"></div></div> - + <div class="form-row"> + <label>Url:</label> + <div class="form-row-input"> + <input name="url" type="textfield" value="${url}" size="40"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Enter a URL to upload your files via http. + </div> + <div style="clear: both"></div> + </div><div class="form-row"><% if uncompress_file:

diff -r 128f167ce12bd5723c5a8124d1d7ea692daf240f -r f640c7bd6ffc4904996859e06157a5f67671f978 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -186,7 +186,7 @@ %endif </div></div> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} %if repository.categories: <p/><div class="toolForm">

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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