コード例 #1
0
def get_repository_file_contents(app,
                                 file_path,
                                 repository_id,
                                 is_admin=False):
    """Return the display-safe contents of a repository file for display in a browser."""
    safe_str = ''
    if not is_path_browsable(app, file_path, repository_id, is_admin):
        log.warning(
            'Request tries to access a file outside of the repository location. File path: %s',
            file_path)
        return 'Invalid file path'
    # Symlink targets are checked by is_path_browsable
    if os.path.islink(file_path):
        safe_str = 'link to: ' + basic_util.to_html_string(
            os.readlink(file_path))
        return safe_str
    elif checkers.is_gzip(file_path):
        return '<br/>gzip compressed file<br/>'
    elif checkers.is_bz2(file_path):
        return '<br/>bz2 compressed file<br/>'
    elif checkers.check_zip(file_path):
        return '<br/>zip compressed file<br/>'
    elif checkers.check_binary(file_path):
        return '<br/>Binary file<br/>'
    else:
        for i, line in enumerate(open(file_path)):
            safe_str = '%s%s' % (safe_str, basic_util.to_html_string(line))
            # Stop reading after string is larger than MAX_CONTENT_SIZE.
            if len(safe_str) > MAX_CONTENT_SIZE:
                large_str = \
                    '<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
                    util.nice_size( MAX_CONTENT_SIZE )
                safe_str = '%s%s' % (safe_str, large_str)
                break

        if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
            # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
            # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
            join_by_str = \
                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
                util.nice_size( basic_util.MAX_DISPLAY_SIZE )
            safe_str = util.shrink_string_by_size(safe_str,
                                                  basic_util.MAX_DISPLAY_SIZE,
                                                  join_by=join_by_str,
                                                  left_larger=True,
                                                  beginning_on_size_error=True)
        return safe_str
コード例 #2
0
ファイル: upload.py プロジェクト: BinglanLi/galaxy
 def upload( self, trans, **kwd ):
     message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     commit_message = escape( kwd.get( 'commit_message', 'Uploaded'  ) )
     category_ids = util.listify( kwd.get( 'category_id', '' ) )
     categories = suc.get_categories( trans.app )
     repository_id = kwd.get( 'repository_id', '' )
     repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
     repo_dir = repository.repo_path( trans.app )
     repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
     uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
     remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
     uploaded_file = None
     upload_point = commit_util.get_upload_point( repository, **kwd )
     tip = repository.tip( trans.app )
     file_data = kwd.get( 'file_data', '' )
     url = kwd.get( 'url', '' )
     # Part of the upload process is sending email notification to those that have registered to
     # receive them.  One scenario occurs when the first change set is produced for the repository.
     # See the suc.handle_email_alerts() method for the definition of the scenarios.
     new_repo_alert = repository.is_new( trans.app )
     uploaded_directory = None
     if kwd.get( 'upload_button', False ):
         if file_data == '' and url == '':
             message = 'No files were entered on the upload form.'
             status = 'error'
             uploaded_file = None
         elif url and url.startswith( 'hg' ):
             # Use mercurial clone to fetch repository, contents will then be copied over.
             uploaded_directory = tempfile.mkdtemp()
             repo_url = 'http%s' % url[ len( 'hg' ): ]
             repo_url = repo_url.encode( 'ascii', 'replace' )
             try:
                 commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
             except Exception, e:
                 message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string( str( e ) )
                 status = 'error'
                 basic_util.remove_dir( uploaded_directory )
                 uploaded_directory = 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( util.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
コード例 #3
0
ファイル: upload.py プロジェクト: mb12985/Galaxy
 def upload( self, trans, **kwd ):
     message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     commit_message = escape( kwd.get( 'commit_message', 'Uploaded'  ) )
     repository_id = kwd.get( 'repository_id', '' )
     repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
     repo_dir = repository.repo_path( trans.app )
     repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
     uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
     remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
     uploaded_file = None
     upload_point = commit_util.get_upload_point( repository, **kwd )
     tip = repository.tip( trans.app )
     file_data = kwd.get( 'file_data', '' )
     url = kwd.get( 'url', '' )
     # Part of the upload process is sending email notification to those that have registered to
     # receive them.  One scenario occurs when the first change set is produced for the repository.
     # See the suc.handle_email_alerts() method for the definition of the scenarios.
     new_repo_alert = repository.is_new( trans.app )
     uploaded_directory = None
     if kwd.get( 'upload_button', False ):
         if file_data == '' and url == '':
             message = 'No files were entered on the upload form.'
             status = 'error'
             uploaded_file = None
         elif url and url.startswith( 'hg' ):
             # Use mercurial clone to fetch repository, contents will then be copied over.
             uploaded_directory = tempfile.mkdtemp()
             repo_url = 'http%s' % url[ len( 'hg' ): ]
             repo_url = repo_url.encode( 'ascii', 'replace' )
             try:
                 commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
             except Exception, e:
                 message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string( str( e ) )
                 status = 'error'
                 basic_util.remove_dir( uploaded_directory )
                 uploaded_directory = 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( util.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
コード例 #4
0
def build_readme_files_dict( app, repository, changeset_revision, metadata, tool_path=None ):
    """
    Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata.  Since the
    received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
    file contents may not be available on disk.  This method is used by both Galaxy and the Tool Shed.
    """
    if app.name == 'galaxy':
        can_use_disk_files = True
    else:
        repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
        latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
        can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
    readme_files_dict = {}
    if metadata:
        if 'readme_files' in metadata:
            for relative_path_to_readme_file in metadata[ 'readme_files' ]:
                readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
                if can_use_disk_files:
                    if tool_path:
                        full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) )
                    else:
                        full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
                    text = None
                    try:
                        f = open( full_path_to_readme_file, 'r' )
                        text = unicodify( f.read() )
                        f.close()
                    except Exception, e:
                        log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) )
                        text = None
                    if text:
                        text_of_reasonable_length = basic_util.size_string( text )
                        if text_of_reasonable_length.find( '.. image:: ' ) >= 0:
                            # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
                            lock = threading.Lock()
                            lock.acquire( True )
                            try:
                                text_of_reasonable_length = suc.set_image_paths( app,
                                                                                 app.security.encode_id( repository.id ),
                                                                                 text_of_reasonable_length )
                            except Exception, e:
                                log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) )
                            finally:
                                lock.release()
                        if readme_file_name.endswith( '.rst' ):
                            text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ),
                                                                  input_encoding='utf-8',
                                                                  output_encoding='utf-8',
                                                                  default_filters=[ 'decode.utf8' ],
                                                                  encoding_errors='replace' )
                            text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ),
                                                                                          host_url=web.url_for( '/', qualified=True ) )
                            text_of_reasonable_length = unicodify( text_of_reasonable_length )
                        else:
                            text_of_reasonable_length = basic_util.to_html_string( text_of_reasonable_length )
                        readme_files_dict[ readme_file_name ] = text_of_reasonable_length
コード例 #5
0
def build_readme_files_dict( app, repository, changeset_revision, metadata, tool_path=None ):
    """
    Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata.  Since the
    received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
    file contents may not be available on disk.  This method is used by both Galaxy and the Tool Shed.
    """
    if app.name == 'galaxy':
        can_use_disk_files = True
    else:
        repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
        latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
        can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
    readme_files_dict = {}
    if metadata:
        if 'readme_files' in metadata:
            for relative_path_to_readme_file in metadata[ 'readme_files' ]:
                readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
                if can_use_disk_files:
                    if tool_path:
                        full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) )
                    else:
                        full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
                    text = None
                    try:
                        f = open( full_path_to_readme_file, 'r' )
                        text = unicodify( f.read() )
                        f.close()
                    except Exception, e:
                        log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) )
                        text = None
                    if text:
                        text_of_reasonable_length = basic_util.size_string( text )
                        if text_of_reasonable_length.find( '.. image:: ' ) >= 0:
                            # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
                            lock = threading.Lock()
                            lock.acquire( True )
                            try:
                                text_of_reasonable_length = suc.set_image_paths( app,
                                                                                 app.security.encode_id( repository.id ),
                                                                                 text_of_reasonable_length )
                            except Exception, e:
                                log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) )
                            finally:
                                lock.release()
                        if readme_file_name.endswith( '.rst' ):
                            text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ),
                                                                  input_encoding='utf-8',
                                                                  output_encoding='utf-8',
                                                                  default_filters=[ 'decode.utf8' ],
                                                                  encoding_errors='replace' )
                            text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ),
                                                                                          host_url=web.url_for( '/', qualified=True ) )
                            text_of_reasonable_length = unicodify( text_of_reasonable_length )
                        else:
                            text_of_reasonable_length = basic_util.to_html_string( text_of_reasonable_length )
                        readme_files_dict[ readme_file_name ] = text_of_reasonable_length
コード例 #6
0
def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
    """Return the display-safe contents of a repository file for display in a browser."""
    safe_str = ''
    if not is_path_browsable(app, file_path, repository_id, is_admin):
        log.warning('Request tries to access a file outside of the repository location. File path: %s', file_path)
        return 'Invalid file path'
    # Symlink targets are checked by is_path_browsable
    if os.path.islink(file_path):
        safe_str = 'link to: ' + basic_util.to_html_string(os.readlink(file_path))
        return safe_str
    elif checkers.is_gzip(file_path):
        return '<br/>gzip compressed file<br/>'
    elif checkers.is_bz2(file_path):
        return '<br/>bz2 compressed file<br/>'
    elif checkers.is_zip(file_path):
        return '<br/>zip compressed file<br/>'
    elif checkers.check_binary(file_path):
        return '<br/>Binary file<br/>'
    else:
        for i, line in enumerate(open(file_path)):
            safe_str = '%s%s' % (safe_str, basic_util.to_html_string(line))
            # Stop reading after string is larger than MAX_CONTENT_SIZE.
            if len(safe_str) > MAX_CONTENT_SIZE:
                large_str = \
                    '<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
                    util.nice_size(MAX_CONTENT_SIZE)
                safe_str = '%s%s' % (safe_str, large_str)
                break

        if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
            # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
            # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
            join_by_str = \
                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
                util.nice_size(basic_util.MAX_DISPLAY_SIZE)
            safe_str = util.shrink_string_by_size(safe_str,
                                                  basic_util.MAX_DISPLAY_SIZE,
                                                  join_by=join_by_str,
                                                  left_larger=True,
                                                  beginning_on_size_error=True)
        return safe_str
コード例 #7
0
def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_path=None):
    """
    Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata.  Since the
    received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
    file contents may not be available on disk.  This method is used by both Galaxy and the Tool Shed.
    """
    if app.name == 'galaxy':
        can_use_disk_files = True
    else:
        latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(app, repository)
        can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
    readme_files_dict = {}
    if metadata:
        if 'readme_files' in metadata:
            for relative_path_to_readme_file in metadata['readme_files']:
                readme_file_name = os.path.split(relative_path_to_readme_file)[1]
                if can_use_disk_files:
                    if tool_path:
                        full_path_to_readme_file = os.path.abspath(os.path.join(tool_path, relative_path_to_readme_file))
                    else:
                        full_path_to_readme_file = os.path.abspath(relative_path_to_readme_file)
                    text = None
                    try:
                        with open(full_path_to_readme_file, encoding='utf-8') as f:
                            text = f.read()
                    except Exception:
                        log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
                        text = None
                    if text:
                        text_of_reasonable_length = basic_util.size_string(text)
                        if text_of_reasonable_length.find('.. image:: ') >= 0:
                            # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
                            try:
                                text_of_reasonable_length = suc.set_image_paths(app,
                                                                                text_of_reasonable_length,
                                                                                encoded_repository_id=app.security.encode_id(repository.id))
                            except Exception:
                                log.exception("Exception in build_readme_files_dict, so images may not be properly displayed")
                        if readme_file_name.endswith('.rst'):
                            text_of_reasonable_length = Template(rst_to_html(text_of_reasonable_length),
                                                                 input_encoding='utf-8',
                                                                 default_filters=['decode.utf8'],
                                                                 encoding_errors='replace')
                            text_of_reasonable_length = text_of_reasonable_length.render(static_path=web.url_for('/static'),
                                                                                         host_url=web.url_for('/', qualified=True))
                            text_of_reasonable_length = unicodify(text_of_reasonable_length)
                        else:
                            text_of_reasonable_length = basic_util.to_html_string(text_of_reasonable_length)
                        readme_files_dict[readme_file_name] = text_of_reasonable_length
                else:
                    # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest.
                    repo = repository.hg_repo
                    ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
                    if ctx:
                        fctx = hg_util.get_file_context_from_ctx(ctx, readme_file_name)
                        if fctx and fctx not in ['DELETED']:
                            try:
                                text = unicodify(fctx.data())
                                readme_files_dict[readme_file_name] = basic_util.size_string(text)
                            except Exception:
                                log.exception("Error reading README file '%s' from repository manifest", relative_path_to_readme_file)
    return readme_files_dict
コード例 #8
0
ファイル: upload.py プロジェクト: ImmPortDB/immport-galaxy
 def upload(self, trans, **kwd):
     message = escape(kwd.get('message', ''))
     status = kwd.get('status', 'done')
     commit_message = escape(kwd.get('commit_message', 'Uploaded'))
     repository_id = kwd.get('repository_id', '')
     repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
     repo_dir = repository.repo_path(trans.app)
     repo = hg_util.get_repo_for_repository(trans.app, repository=None, repo_path=repo_dir, create=False)
     uncompress_file = util.string_as_bool(kwd.get('uncompress_file', 'true'))
     remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
     uploaded_file = None
     upload_point = commit_util.get_upload_point(repository, **kwd)
     tip = repository.tip(trans.app)
     file_data = kwd.get('file_data', '')
     url = kwd.get('url', '')
     # Part of the upload process is sending email notification to those that have registered to
     # receive them.  One scenario occurs when the first change set is produced for the repository.
     # See the suc.handle_email_alerts() method for the definition of the scenarios.
     new_repo_alert = repository.is_new(trans.app)
     uploaded_directory = None
     if kwd.get('upload_button', False):
         if file_data == '' and url == '':
             message = 'No files were entered on the upload form.'
             status = 'error'
             uploaded_file = None
         elif url and url.startswith('hg'):
             # Use mercurial clone to fetch repository, contents will then be copied over.
             uploaded_directory = tempfile.mkdtemp()
             repo_url = 'http%s' % url[len('hg'):]
             repo_url = repo_url.encode('ascii', 'replace')
             try:
                 commands.clone(hg_util.get_configured_ui(), repo_url, uploaded_directory)
             except Exception as e:
                 message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string(str(e))
                 status = 'error'
                 basic_util.remove_dir(uploaded_directory)
                 uploaded_directory = None
         elif url:
             valid_url = True
             try:
                 stream = requests.get(url, stream=True)
             except Exception as 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')
                 for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
                     if chunk:
                         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 = os.path.split(file_data.filename)[-1]
             isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
         if uploaded_file or uploaded_directory:
             rdah = attribute_handlers.RepositoryDependencyAttributeHandler(trans.app, unpopulate=False)
             tdah = attribute_handlers.ToolDependencyAttributeHandler(trans.app, unpopulate=False)
             stdtm = ShedToolDataTableManager(trans.app)
             ok = True
             isgzip = False
             isbz2 = False
             if uploaded_file:
                 if uncompress_file:
                     isgzip = checkers.is_gzip(uploaded_file_name)
                     if not isgzip:
                         isbz2 = checkers.is_bz2(uploaded_file_name)
                 if isempty:
                     tar = None
                     istar = False
                 else:
                     # Determine what we have - a single file or an archive
                     try:
                         if (isgzip or isbz2) and uncompress_file:
                             # Open for reading with transparent compression.
                             tar = tarfile.open(uploaded_file_name, 'r:*')
                         else:
                             tar = tarfile.open(uploaded_file_name)
                         istar = True
                     except tarfile.ReadError as e:
                         tar = None
                         istar = False
             else:
                 # Uploaded directory
                 istar = False
             if istar:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     repository_content_util.upload_tar(
                         trans,
                         rdah,
                         tdah,
                         repository,
                         tar,
                         uploaded_file,
                         upload_point,
                         remove_repo_files_not_in_tar,
                         commit_message,
                         new_repo_alert
                     )
             elif uploaded_directory:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_directory(trans,
                                           rdah,
                                           tdah,
                                           repository,
                                           uploaded_directory,
                                           upload_point,
                                           remove_repo_files_not_in_tar,
                                           commit_message,
                                           new_repo_alert)
             else:
                 if (isgzip or isbz2) and uncompress_file:
                     uploaded_file_filename = commit_util.uncompress(repository,
                                                                     uploaded_file_name,
                                                                     uploaded_file_filename,
                                                                     isgzip=isgzip,
                                                                     isbz2=isbz2)
                 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and \
                         uploaded_file_filename != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
                     ok = False
                     message = 'Repositories of type <b>Repository suite definition</b> can only contain a single file named '
                     message += '<b>repository_dependencies.xml</b>.'
                 elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and \
                         uploaded_file_filename != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
                     ok = False
                     message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named '
                     message += '<b>tool_dependencies.xml</b>.'
                 if ok:
                     if upload_point is not None:
                         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 some version of the uploaded file to the load_point within the repository hierarchy.
                     if uploaded_file_filename in [rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME]:
                         # Inspect the contents of the file to see if toolshed or changeset_revision attributes
                         # are missing and if so, set them appropriately.
                         altered, root_elem, error_message = rdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
                             ok = False
                             message = error_message
                             status = 'error'
                         elif altered:
                             tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                             shutil.move(tmp_filename, full_path)
                         else:
                             shutil.move(uploaded_file_name, full_path)
                     elif uploaded_file_filename in [rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME]:
                         # Inspect the contents of the file to see if changeset_revision values are
                         # missing and if so, set them appropriately.
                         altered, root_elem, error_message = tdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
                             ok = False
                             message = error_message
                             status = 'error'
                         if ok:
                             if altered:
                                 tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                                 shutil.move(tmp_filename, full_path)
                             else:
                                 shutil.move(uploaded_file_name, full_path)
                     else:
                         shutil.move(uploaded_file_name, full_path)
                     if ok:
                         # See if any admin users have chosen to receive email alerts when a repository is updated.
                         # If so, check every uploaded file to ensure content is appropriate.
                         check_contents = commit_util.check_file_contents_for_email_alerts(trans.app)
                         if check_contents and os.path.isfile(full_path):
                             content_alert_str = commit_util.check_file_content_for_html_and_images(full_path)
                         else:
                             content_alert_str = ''
                         hg_util.add_changeset(repo.ui, repo, full_path)
                         # Convert from unicode to prevent "TypeError: array item must be char"
                         full_path = full_path.encode('ascii', 'replace')
                         hg_util.commit_changeset(repo.ui,
                                                  repo,
                                                  full_path_to_changeset=full_path,
                                                  username=trans.user.username,
                                                  message=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.
                             error, error_message = stdtm.handle_sample_tool_data_table_conf_file(full_path, persist=False)
                             if error:
                                 message = '%s<br/>%s' % (message, error_message)
                         # See if the content of the change set was valid.
                         admin_only = len(repository.downloadable_revisions) != 1
                         suc.handle_email_alerts(trans.app,
                                                 trans.request.host,
                                                 repository,
                                                 content_alert_str=content_alert_str,
                                                 new_repo_alert=new_repo_alert,
                                                 admin_only=admin_only)
             if ok:
                 # Update the repository files for browsing.
                 hg_util.update_repository(repo)
                 # Get the new repository tip.
                 if tip == repository.tip(trans.app):
                     message = 'No changes to repository.  '
                     status = 'warning'
                 else:
                     if (isgzip or isbz2) and uncompress_file:
                         uncompress_str = ' uncompressed and '
                     else:
                         uncompress_str = ' '
                     if uploaded_directory:
                         source_type = "repository"
                         source = url
                     else:
                         source_type = "file"
                         source = uploaded_file_filename
                     message = "The %s <b>%s</b> has been successfully%suploaded to the repository.  " % \
                         (source_type, escape(source), uncompress_str)
                     if istar and (undesirable_dirs_removed or undesirable_files_removed):
                         items_removed = undesirable_dirs_removed + undesirable_files_removed
                         message += "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) " % items_removed
                         message += "were removed from the archive.  "
                     if istar and remove_repo_files_not_in_tar and files_to_remove:
                         if upload_point is not None:
                             message += "  %d files were removed from the repository relative to the selected upload point '%s'.  " % \
                                 (len(files_to_remove), upload_point)
                         else:
                             message += "  %d files were removed from the repository root.  " % len(files_to_remove)
                     rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
                                                                                 user=trans.user,
                                                                                 repository=repository)
                     status, error_message = \
                         rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
                                                                    content_alert_str=content_alert_str,
                                                                    **kwd)
                     if error_message:
                         message = error_message
                     kwd['message'] = message
                 if repository.metadata_revisions:
                     # A repository's metadata revisions are order descending by update_time, so the zeroth revision
                     # will be the tip just after an upload.
                     metadata_dict = repository.metadata_revisions[0].metadata
                 else:
                     metadata_dict = {}
                 dd = dependency_display.DependencyDisplayer(trans.app)
                 if str(repository.type) not in [rt_util.REPOSITORY_SUITE_DEFINITION,
                                                 rt_util.TOOL_DEPENDENCY_DEFINITION]:
                     change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
                                                                                                          repository)
                     if change_repository_type_message:
                         message += change_repository_type_message
                         status = 'warning'
                     else:
                         # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies
                         # weren't loaded due to a requirement tag mismatch or some other problem.  Tool dependency
                         # definitions can define orphan tool dependencies (no relationship to any tools contained in the
                         # repository), so warning messages are important because orphans are always valid.  The repository
                         # owner must be warned in case they did not intend to define an orphan dependency, but simply
                         # provided incorrect information (tool shed, name owner, changeset_revision) for the definition.
                         orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata_dict)
                         if orphan_message:
                             message += orphan_message
                             status = 'warning'
                 # Handle messaging for invalid tool dependencies.
                 invalid_tool_dependencies_message = dd.generate_message_for_invalid_tool_dependencies(metadata_dict)
                 if invalid_tool_dependencies_message:
                     message += invalid_tool_dependencies_message
                     status = 'error'
                 # Handle messaging for invalid repository dependencies.
                 invalid_repository_dependencies_message = \
                     dd.generate_message_for_invalid_repository_dependencies(metadata_dict,
                                                                             error_from_tuple=True)
                 if invalid_repository_dependencies_message:
                     message += invalid_repository_dependencies_message
                     status = 'error'
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                 stdtm.reset_tool_data_tables()
                 if uploaded_directory:
                     basic_util.remove_dir(uploaded_directory)
                 trans.response.send_redirect(web.url_for(controller='repository',
                                                          action='browse_repository',
                                                          id=repository_id,
                                                          commit_message='Deleted selected files',
                                                          message=message,
                                                          status=status))
             else:
                 if uploaded_directory:
                     basic_util.remove_dir(uploaded_directory)
                 status = 'error'
             # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
             stdtm.reset_tool_data_tables()
     return trans.fill_template('/webapps/tool_shed/repository/upload.mako',
                                repository=repository,
                                changeset_revision=tip,
                                url=url,
                                commit_message=commit_message,
                                uncompress_file=uncompress_file,
                                remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
                                message=message,
                                status=status)
コード例 #9
0
 def upload(self, trans, **kwd):
     message = escape(kwd.get('message', ''))
     status = kwd.get('status', 'done')
     commit_message = escape(kwd.get('commit_message', 'Uploaded'))
     repository_id = kwd.get('repository_id', '')
     repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
     repo_dir = repository.repo_path(trans.app)
     repo = hg_util.get_repo_for_repository(trans.app, repository=None, repo_path=repo_dir, create=False)
     uncompress_file = util.string_as_bool(kwd.get('uncompress_file', 'true'))
     remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
     uploaded_file = None
     upload_point = commit_util.get_upload_point(repository, **kwd)
     tip = repository.tip(trans.app)
     file_data = kwd.get('file_data', '')
     url = kwd.get('url', '')
     # Part of the upload process is sending email notification to those that have registered to
     # receive them.  One scenario occurs when the first change set is produced for the repository.
     # See the suc.handle_email_alerts() method for the definition of the scenarios.
     new_repo_alert = repository.is_new(trans.app)
     uploaded_directory = None
     if kwd.get('upload_button', False):
         if file_data == '' and url == '':
             message = 'No files were entered on the upload form.'
             status = 'error'
             uploaded_file = None
         elif url and url.startswith('hg'):
             # Use mercurial clone to fetch repository, contents will then be copied over.
             uploaded_directory = tempfile.mkdtemp()
             repo_url = 'http%s' % url[len('hg'):]
             repo_url = repo_url.encode('ascii', 'replace')
             try:
                 commands.clone(hg_util.get_configured_ui(), repo_url, uploaded_directory)
             except Exception as e:
                 message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string(str(e))
                 status = 'error'
                 basic_util.remove_dir(uploaded_directory)
                 uploaded_directory = None
         elif url:
             valid_url = True
             try:
                 stream = requests.get(url, stream=True)
             except Exception as 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')
                 for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
                     if chunk:
                         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 = os.path.split(file_data.filename)[-1]
             isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
         if uploaded_file or uploaded_directory:
             rdah = attribute_handlers.RepositoryDependencyAttributeHandler(trans.app, unpopulate=False)
             tdah = attribute_handlers.ToolDependencyAttributeHandler(trans.app, unpopulate=False)
             tdtm = data_table_manager.ToolDataTableManager(trans.app)
             ok = True
             isgzip = False
             isbz2 = False
             if uploaded_file:
                 if uncompress_file:
                     isgzip = checkers.is_gzip(uploaded_file_name)
                     if not isgzip:
                         isbz2 = checkers.is_bz2(uploaded_file_name)
                 if isempty:
                     tar = None
                     istar = False
                 else:
                     # Determine what we have - a single file or an archive
                     try:
                         if (isgzip or isbz2) and uncompress_file:
                             # Open for reading with transparent compression.
                             tar = tarfile.open(uploaded_file_name, 'r:*')
                         else:
                             tar = tarfile.open(uploaded_file_name)
                         istar = True
                     except tarfile.ReadError as e:
                         tar = None
                         istar = False
             else:
                 # Uploaded directory
                 istar = False
             if istar:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     repository_content_util.upload_tar(
                         trans,
                         rdah,
                         tdah,
                         repository,
                         tar,
                         uploaded_file,
                         upload_point,
                         remove_repo_files_not_in_tar,
                         commit_message,
                         new_repo_alert
                     )
             elif uploaded_directory:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_directory(trans,
                                           rdah,
                                           tdah,
                                           repository,
                                           uploaded_directory,
                                           upload_point,
                                           remove_repo_files_not_in_tar,
                                           commit_message,
                                           new_repo_alert)
             else:
                 if (isgzip or isbz2) and uncompress_file:
                     uploaded_file_filename = commit_util.uncompress(repository,
                                                                     uploaded_file_name,
                                                                     uploaded_file_filename,
                                                                     isgzip=isgzip,
                                                                     isbz2=isbz2)
                 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and \
                         uploaded_file_filename != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
                     ok = False
                     message = 'Repositories of type <b>Repository suite definition</b> can only contain a single file named '
                     message += '<b>repository_dependencies.xml</b>.'
                 elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and \
                         uploaded_file_filename != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
                     ok = False
                     message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named '
                     message += '<b>tool_dependencies.xml</b>.'
                 if ok:
                     if upload_point is not None:
                         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 some version of the uploaded file to the load_point within the repository hierarchy.
                     if uploaded_file_filename in [rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME]:
                         # Inspect the contents of the file to see if toolshed or changeset_revision attributes
                         # are missing and if so, set them appropriately.
                         altered, root_elem, error_message = rdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
                             ok = False
                             message = error_message
                             status = 'error'
                         elif altered:
                             tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                             shutil.move(tmp_filename, full_path)
                         else:
                             shutil.move(uploaded_file_name, full_path)
                     elif uploaded_file_filename in [rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME]:
                         # Inspect the contents of the file to see if changeset_revision values are
                         # missing and if so, set them appropriately.
                         altered, root_elem, error_message = tdah.handle_tag_attributes(uploaded_file_name)
                         if error_message:
                             ok = False
                             message = error_message
                             status = 'error'
                         if ok:
                             if altered:
                                 tmp_filename = xml_util.create_and_write_tmp_file(root_elem)
                                 shutil.move(tmp_filename, full_path)
                             else:
                                 shutil.move(uploaded_file_name, full_path)
                     else:
                         shutil.move(uploaded_file_name, full_path)
                     if ok:
                         # See if any admin users have chosen to receive email alerts when a repository is updated.
                         # If so, check every uploaded file to ensure content is appropriate.
                         check_contents = commit_util.check_file_contents_for_email_alerts(trans.app)
                         if check_contents and os.path.isfile(full_path):
                             content_alert_str = commit_util.check_file_content_for_html_and_images(full_path)
                         else:
                             content_alert_str = ''
                         hg_util.add_changeset(repo.ui, repo, full_path)
                         # Convert from unicode to prevent "TypeError: array item must be char"
                         full_path = full_path.encode('ascii', 'replace')
                         hg_util.commit_changeset(repo.ui,
                                                  repo,
                                                  full_path_to_changeset=full_path,
                                                  username=trans.user.username,
                                                  message=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.
                             error, error_message = tdtm.handle_sample_tool_data_table_conf_file(full_path, persist=False)
                             if error:
                                 message = '%s<br/>%s' % (message, error_message)
                         # See if the content of the change set was valid.
                         admin_only = len(repository.downloadable_revisions) != 1
                         suc.handle_email_alerts(trans.app,
                                                 trans.request.host,
                                                 repository,
                                                 content_alert_str=content_alert_str,
                                                 new_repo_alert=new_repo_alert,
                                                 admin_only=admin_only)
             if ok:
                 # Update the repository files for browsing.
                 hg_util.update_repository(repo)
                 # Get the new repository tip.
                 if tip == repository.tip(trans.app):
                     message = 'No changes to repository.  '
                     status = 'warning'
                 else:
                     if (isgzip or isbz2) and uncompress_file:
                         uncompress_str = ' uncompressed and '
                     else:
                         uncompress_str = ' '
                     if uploaded_directory:
                         source_type = "repository"
                         source = url
                     else:
                         source_type = "file"
                         source = uploaded_file_filename
                     message = "The %s <b>%s</b> has been successfully%suploaded to the repository.  " % \
                         (source_type, escape(source), uncompress_str)
                     if istar and (undesirable_dirs_removed or undesirable_files_removed):
                         items_removed = undesirable_dirs_removed + undesirable_files_removed
                         message += "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) " % items_removed
                         message += "were removed from the archive.  "
                     if istar and remove_repo_files_not_in_tar and files_to_remove:
                         if upload_point is not None:
                             message += "  %d files were removed from the repository relative to the selected upload point '%s'.  " % \
                                 (len(files_to_remove), upload_point)
                         else:
                             message += "  %d files were removed from the repository root.  " % len(files_to_remove)
                     rmm = repository_metadata_manager.RepositoryMetadataManager(app=trans.app,
                                                                                 user=trans.user,
                                                                                 repository=repository)
                     status, error_message = \
                         rmm.set_repository_metadata_due_to_new_tip(trans.request.host,
                                                                    content_alert_str=content_alert_str,
                                                                    **kwd)
                     if error_message:
                         message = error_message
                     kwd['message'] = message
                 if repository.metadata_revisions:
                     # A repository's metadata revisions are order descending by update_time, so the zeroth revision
                     # will be the tip just after an upload.
                     metadata_dict = repository.metadata_revisions[0].metadata
                 else:
                     metadata_dict = {}
                 dd = dependency_display.DependencyDisplayer(trans.app)
                 if str(repository.type) not in [rt_util.REPOSITORY_SUITE_DEFINITION,
                                                 rt_util.TOOL_DEPENDENCY_DEFINITION]:
                     change_repository_type_message = rt_util.generate_message_for_repository_type_change(trans.app,
                                                                                                          repository)
                     if change_repository_type_message:
                         message += change_repository_type_message
                         status = 'warning'
                     else:
                         # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies
                         # weren't loaded due to a requirement tag mismatch or some other problem.  Tool dependency
                         # definitions can define orphan tool dependencies (no relationship to any tools contained in the
                         # repository), so warning messages are important because orphans are always valid.  The repository
                         # owner must be warned in case they did not intend to define an orphan dependency, but simply
                         # provided incorrect information (tool shed, name owner, changeset_revision) for the definition.
                         orphan_message = dd.generate_message_for_orphan_tool_dependencies(repository, metadata_dict)
                         if orphan_message:
                             message += orphan_message
                             status = 'warning'
                 # Handle messaging for invalid tool dependencies.
                 invalid_tool_dependencies_message = dd.generate_message_for_invalid_tool_dependencies(metadata_dict)
                 if invalid_tool_dependencies_message:
                     message += invalid_tool_dependencies_message
                     status = 'error'
                 # Handle messaging for invalid repository dependencies.
                 invalid_repository_dependencies_message = \
                     dd.generate_message_for_invalid_repository_dependencies(metadata_dict,
                                                                             error_from_tuple=True)
                 if invalid_repository_dependencies_message:
                     message += invalid_repository_dependencies_message
                     status = 'error'
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                 tdtm.reset_tool_data_tables()
                 if uploaded_directory:
                     basic_util.remove_dir(uploaded_directory)
                 trans.response.send_redirect(web.url_for(controller='repository',
                                                          action='browse_repository',
                                                          id=repository_id,
                                                          commit_message='Deleted selected files',
                                                          message=message,
                                                          status=status))
             else:
                 if uploaded_directory:
                     basic_util.remove_dir(uploaded_directory)
                 status = 'error'
             # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
             tdtm.reset_tool_data_tables()
     return trans.fill_template('/webapps/tool_shed/repository/upload.mako',
                                repository=repository,
                                changeset_revision=tip,
                                url=url,
                                commit_message=commit_message,
                                uncompress_file=uncompress_file,
                                remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
                                message=message,
                                status=status)
コード例 #10
0
def render_body(context,**pageargs):
    context.caller_stack._push_frame()
    try:
        __M_locals = __M_dict_builtin(pageargs=pageargs)
        _import_ns = {}
        _mako_get_namespace(context, '__anon_0x112a2f8d0')._populate(_import_ns, [u'render_msg'])
        _mako_get_namespace(context, '__anon_0x112a2fed0')._populate(_import_ns, [u'common_misc_javascripts'])
        _mako_get_namespace(context, '__anon_0x112a2fa90')._populate(_import_ns, [u'*'])
        status = _import_ns.get('status', context.get('status', UNDEFINED))
        render_msg = _import_ns.get('render_msg', context.get('render_msg', UNDEFINED))
        repository = _import_ns.get('repository', context.get('repository', UNDEFINED))
        h = _import_ns.get('h', context.get('h', UNDEFINED))
        render_galaxy_repository_actions = _import_ns.get('render_galaxy_repository_actions', context.get('render_galaxy_repository_actions', UNDEFINED))
        uninstalled_tool_dependencies_select_field = _import_ns.get('uninstalled_tool_dependencies_select_field', context.get('uninstalled_tool_dependencies_select_field', UNDEFINED))
        message = _import_ns.get('message', context.get('message', UNDEFINED))
        trans = _import_ns.get('trans', context.get('trans', UNDEFINED))
        installed_tool_dependencies_select_field = _import_ns.get('installed_tool_dependencies_select_field', context.get('installed_tool_dependencies_select_field', UNDEFINED))
        __M_writer = context.writer()
        # SOURCE LINE 1
        __M_writer(u'\n')
        # SOURCE LINE 2
        __M_writer(u'\n')
        # SOURCE LINE 3
        __M_writer(u'\n')
        # SOURCE LINE 4
        __M_writer(u'\n\n')
        # SOURCE LINE 9
        __M_writer(u'\n\n')
        # SOURCE LINE 14
        __M_writer(u'\n\n')
        # SOURCE LINE 16
        __M_writer(unicode(render_galaxy_repository_actions( repository )))
        __M_writer(u'\n\n')
        # SOURCE LINE 18
        if message:
            # SOURCE LINE 19
            __M_writer(u'    ')
            __M_writer(unicode(render_msg( message, status )))
            __M_writer(u'\n')
            pass
        # SOURCE LINE 21
        __M_writer(u'\n<div class="toolForm">\n    <div class="toolFormTitle">Tool shed repository \'')
        # SOURCE LINE 23
        __M_writer(filters.html_escape(unicode(repository.name)))
        __M_writer(u"' tool dependencies</div>\n        ")
        # SOURCE LINE 24

        can_install = False
        can_uninstall = False
                
        
        __M_locals_builtin_stored = __M_locals_builtin()
        __M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['can_install','can_uninstall'] if __M_key in __M_locals_builtin_stored]))
        # SOURCE LINE 27
        __M_writer(u'\n        <br/><br/>\n        <table class="grid">\n            <tr><th  bgcolor="#D8D8D8">Name</th><th  bgcolor="#D8D8D8">Version</th><th  bgcolor="#D8D8D8">Type</th><th bgcolor="#D8D8D8">Status</th><th bgcolor="#D8D8D8">Error</th></tr>\n')
        # SOURCE LINE 31
        for tool_dependency in repository.tool_dependencies:
            # SOURCE LINE 32
            __M_writer(u'                ')

            if tool_dependency.error_message:
                from tool_shed.util.basic_util import to_html_string
                error_message = to_html_string( tool_dependency.error_message )
            else:
                error_message = ''
            if not can_install:
                if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
                                               trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
                    can_install = True
            if not can_uninstall:
                if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
                                                   trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
                    can_uninstall = True
                            
            
            __M_locals_builtin_stored = __M_locals_builtin()
            __M_locals.update(__M_dict_builtin([(__M_key, __M_locals_builtin_stored[__M_key]) for __M_key in ['can_install','error_message','can_uninstall','to_html_string'] if __M_key in __M_locals_builtin_stored]))
            # SOURCE LINE 46
            __M_writer(u'\n                <tr>\n                    <td>\n')
            # SOURCE LINE 49
            if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
                # SOURCE LINE 50
                __M_writer(u'                            <a target="galaxy_main" href="')
                __M_writer(unicode(h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )))
                __M_writer(u'">\n                                ')
                # SOURCE LINE 51
                __M_writer(filters.html_escape(unicode(tool_dependency.name)))
                __M_writer(u'\n                            </a>\n')
                # SOURCE LINE 53
            else:
                # SOURCE LINE 54
                __M_writer(u'                            ')
                __M_writer(filters.html_escape(unicode(tool_dependency.name)))
                __M_writer(u'\n')
                pass
            # SOURCE LINE 56
            __M_writer(u'                    </td>\n                    <td>')
            # SOURCE LINE 57
            __M_writer(filters.html_escape(unicode(tool_dependency.version)))
            __M_writer(u'</td>\n                    <td>')
            # SOURCE LINE 58
            __M_writer(filters.html_escape(unicode(tool_dependency.type)))
            __M_writer(u'</td>\n                    <td>')
            # SOURCE LINE 59
            __M_writer(filters.html_escape(unicode(tool_dependency.status)))
            __M_writer(u'</td>\n                    <td>')
            # SOURCE LINE 60
            __M_writer(filters.html_escape(unicode(error_message)))
            __M_writer(u'</td>\n                </tr>\n')
            pass
        # SOURCE LINE 63
        __M_writer(u'        </table>\n')
        # SOURCE LINE 64
        if can_install:
            # SOURCE LINE 65
            __M_writer(u'            <br/>\n            <form name="install_tool_dependencies" id="install_tool_dependencies" action="')
            # SOURCE LINE 66
            __M_writer(unicode(h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install', repository_id=trans.security.encode_id( repository.id ) )))
            __M_writer(u'" method="post" >\n                <div class="form-row">\n                    Check each tool dependency that you want to install and click <b>Install</b>.\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    <input type="checkbox" id="checkAllUninstalled" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllUninstalledToolDependencyIdFields(1);"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b>\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    ')
            # SOURCE LINE 76
            __M_writer(unicode(uninstalled_tool_dependencies_select_field.get_html()))
            __M_writer(u'\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    <input type="submit" name="install_button" value="Install"/></td>\n                </div>\n            </form>\n            <br/>\n')
            pass
        # SOURCE LINE 85
        if can_uninstall:
            # SOURCE LINE 86
            __M_writer(u'            <br/>\n            <form name="uninstall_tool_dependencies" id="uninstall_tool_dependencies" action="')
            # SOURCE LINE 87
            __M_writer(unicode(h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='uninstall', repository_id=trans.security.encode_id( repository.id ) )))
            __M_writer(u'" method="post" >\n                <div class="form-row">\n                    Check each tool dependency that you want to uninstall and click <b>Uninstall</b>.\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    <input type="checkbox" id="checkAllInstalled" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllInstalledToolDependencyIdFields(1);"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b>\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    ')
            # SOURCE LINE 97
            __M_writer(unicode(installed_tool_dependencies_select_field.get_html()))
            __M_writer(u'\n                </div>\n                <div style="clear: both"></div>\n                <div class="form-row">\n                    <input type="submit" name="uninstall_button" value="Uninstall"/></td>\n                </div>\n            </form>\n            <br/>\n')
            pass
        # SOURCE LINE 106
        __M_writer(u'    </div>\n</div>\n')
        return ''
    finally:
        context.caller_stack._pop_frame()