view data_manager/data_manager_rsync.py @ 1:861c071a6cd5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f

+
−#!/usr/bin/env python
+
−# Dan Blankenberg
+
−from __future__ import print_function
+
−
+
−import datetime
+
−import logging
+
−import optparse
+
−import os
+
−import shutil
+
−import subprocess
+
−import tempfile
+
−from json import (
+
−    dumps,
+
−    loads
+
−)
+
−from os.path import basename
+
−from xml.etree.ElementTree import tostring
+
−try:
+
−    # For Python 3.0 and later
+
−    from urllib.request import urlopen
+
−except ImportError:
+
−    # Fall back to Python 2 imports
+
−    from urllib2 import urlopen
+
−
+
−_log_name = __name__
+
−if _log_name == '__builtin__':
+
−    _log_name = 'toolshed.installed.g2.rsync.data.manager'
+
−log = logging.getLogger( _log_name )
+
−
+
−# Get the Data from the Galaxy Project rsync server
+
−RSYNC_CMD = 'rsync'
+
−RSYNC_SERVER = "rsync://datacache.g2.bx.psu.edu/"
+
−LOCATION_DIR = "location"
+
−INDEX_DIR = "indexes"
+
−
+
−# Pull the Tool Data Table files from github
+
−# FIXME: These files should be accessible from the rsync server directly.
+
−TOOL_DATA_TABLE_CONF_XML_URLS = {'main': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml",
+
−                                 'test': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml" }
+
−
+
−# Replace data table source entries with local temporary location
+
−GALAXY_DATA_CANONICAL_PATH = "/galaxy/data/"
+
−TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE = '<file path="%slocation/' % ( GALAXY_DATA_CANONICAL_PATH )
+
−TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET = '<file path="%s/'
+
−
+
−# Some basic Caching, so we don't have to reload and download everything every time
+
−CACHE_TIME = datetime.timedelta( minutes=10 )
+
−TOOL_DATA_TABLES_LOADED_BY_URL = {}
+
−
+
−# Entries will not be selected by default
+
−DEFAULT_SELECTED = False
+
−
+
−# Exclude data managers without 'path' column or that are in the manual exclude list
+
−PATH_COLUMN_NAMES = ['path']
+
−EXCLUDE_DATA_TABLES = []
+
−# TODO: Make additional handler actions available for tables that can't fit into the the basic
+
−# "take the value of path" as a dir and copy contents.
+
−# e.g. mafs. Although this maf table is goofy and doesn't have path defined in <table> def,
+
−# but it does exit in the .loc.
+
−
+
−
+
−# --- These methods are called by/within the Galaxy Application
+
−def exec_before_job( app, inp_data, out_data, param_dict, tool=None, **kwd ):
+
−    # Look for any data tables that haven't been defined for this data manager before and dynamically add them to Galaxy
+
−    param_dict = dict( **param_dict )
+
−    param_dict['data_table_entries'] = param_dict.get( 'data_table_entries', [] )
+
−    if not isinstance( param_dict['data_table_entries'], list ):
+
−        param_dict['data_table_entries'] = [param_dict['data_table_entries']]
+
−    param_dict['data_table_entries'] = ",".join( param_dict['data_table_entries'] )
+
−    if tool:
+
−        tool_shed_repository = tool.tool_shed_repository
+
−    else:
+
−        tool_shed_repository = None
+
−    tdtm = None
+
−    data_manager = app.data_managers.get_manager( tool.data_manager_id, None )
+
−    data_table_entries = get_data_table_entries( param_dict )
+
−    data_tables = load_data_tables_from_url( data_table_class=app.tool_data_tables.__class__ ).get( 'data_tables' )
+
−    for data_table_name, entries in data_table_entries.items():
+
−        # get data table managed by this data Manager
+
−        has_data_table = app.tool_data_tables.get_tables().get( data_table_name )
+
−        if has_data_table:
+
−            has_data_table = bool( has_data_table.get_filename_for_source( data_manager, None ) )
+
−        if not has_data_table:
+
−            if tdtm is None:
+
−                from tool_shed.tools import data_table_manager
+
−                tdtm = data_table_manager.ToolDataTableManager( app )
+
−                target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir( tool_shed_repository )
+
−            # Dynamically add this data table
+
−            log.debug( "Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name )
+
−            data_table = data_tables[data_table_name]
+
−            repo_info = tdtm.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None )
+
−            if repo_info is not None:
+
−                repo_info = tostring( repo_info )
+
−            tmp_file = tempfile.NamedTemporaryFile()
+
−            tmp_file.write( get_new_xml_definition( app, data_table, data_manager, repo_info, target_dir ) )
+
−            tmp_file.flush()
+
−            app.tool_data_tables.add_new_entries_from_config_file( tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True )
+
−            tmp_file.close()
+
−
+
−
+
−def galaxy_code_get_available_data_tables( trans ):
+
−    # list of data tables
+
−    found_tables = get_available_tables( trans )
+
−    rval = [ ( x, x, DEFAULT_SELECTED ) for x in found_tables]
+
−    return rval
+
−
+
−
+
−def galaxy_code_get_available_data_tables_entries( trans, dbkey, data_table_names ):
+
−    # available entries, optionally filtered by dbkey and table names
+
−    if dbkey in [ None, '', '?' ]:
+
−        dbkey = None
+
−    if data_table_names in [ None, '', '?' ]:
+
−        data_table_names = None
+
−    found_tables = get_available_tables_for_dbkey( trans, dbkey, data_table_names )
+
−    dbkey_text = '(%s) ' % ( dbkey ) if dbkey else ''
+
−    rval = [( "%s%s" % ( dbkey_text, x[0] ), dumps( dict( name=x[0].split( ': ' )[0], entry=x[1] ) ).encode( 'base64' ).rstrip(), DEFAULT_SELECTED ) for x in found_tables.items()]
+
−    return rval
+
−
+
−# --- End Galaxy called Methods ---
+
−
+
−
+
−def rsync_urljoin( base, url ):
+
−    # urlparse.urljoin doesn't work correctly for our use-case
+
−    # probably because it doesn't recognize the rsync scheme
+
−    base = base.rstrip( '/' )
+
−    url = url.lstrip( '/' )
+
−    return "%s/%s" % ( base, url )
+
−
+
−
+
−def rsync_list_dir( server, dir=None, skip_names=[] ):
+
−    # drwxr-xr-x          50 2014/05/16 20:58:11 .
+
−    if dir:
+
−        dir = rsync_urljoin( server, dir )
+
−    else:
+
−        dir = server
+
−    rsync_response = tempfile.NamedTemporaryFile()
+
−    rsync_stderr = tempfile.NamedTemporaryFile()
+
−    rsync_cmd = [ RSYNC_CMD, '--list-only', dir ]
+
−    return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
+
−    rsync_response.flush()
+
−    rsync_response.seek(0)
+
−    rsync_stderr.flush()
+
−    rsync_stderr.seek(0)
+
−    if return_code:
+
−        msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
+
−        rsync_response.close()
+
−        rsync_stderr.close()
+
−        raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (  rsync_cmd, return_code, msg ) )
+
−    rsync_stderr.close()
+
−    rval = {}
+
−    for line in rsync_response:
+
−        perms, line = line.split( None, 1 )
+
−        line = line.strip()
+
−        size, line = line.split( None, 1 )
+
−        line = line.strip()
+
−        date, line = line.split( None, 1 )
+
−        line = line.strip()
+
−        time, line = line.split( None, 1 )
+
−        name = line.strip()
+
−        if name in skip_names:
+
−            continue
+
−        size = line.strip()
+
−        rval[ name ] = dict( name=name, permissions=perms, bytes=size, date=date, time=time )
+
−    rsync_response.close()
+
−    return rval
+
−
+
−
+
−def rsync_sync_to_dir( source, target ):
+
−    rsync_response = tempfile.NamedTemporaryFile()
+
−    rsync_stderr = tempfile.NamedTemporaryFile()
+
−    rsync_cmd = [ RSYNC_CMD, '-avzP', source, target ]
+
−    return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
+
−    rsync_response.flush()
+
−    rsync_response.seek(0)
+
−    rsync_stderr.flush()
+
−    rsync_stderr.seek(0)
+
−    if return_code:
+
−        msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
+
−        rsync_response.close()
+
−        rsync_stderr.close()
+
−        raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % (  rsync_cmd, return_code, msg ) )
+
−    rsync_response.close()
+
−    rsync_stderr.close()
+
−    return return_code
+
−
+
−
+
−def data_table_needs_refresh( cached_data_table, url ):
+
−    if cached_data_table is None:
+
−        return True, {}
+
−    if datetime.datetime.now() - cached_data_table.get( 'time_loaded' ) > CACHE_TIME:
+
−        data_table_text = urlopen( url ).read()
+
−        if cached_data_table.get( 'data_table_text', None ) != data_table_text:
+
−            return True, {'data_table_text': data_table_text}
+
−        loc_file_attrs = rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
+
−        if cached_data_table.get( 'loc_file_attrs', None ) != loc_file_attrs:
+
−            return True, {'loc_file_attrs': loc_file_attrs}
+
−    return False, {}
+
−
+
−
+
−def load_data_tables_from_url( url=None, site='main', data_table_class=None  ):
+
−    if not url:
+
−        url = TOOL_DATA_TABLE_CONF_XML_URLS.get( site, None )
+
−    assert url, ValueError( 'You must provide either a URL or a site=name.' )
+
−
+
−    cached_data_table = TOOL_DATA_TABLES_LOADED_BY_URL.get( url, None )
+
−    refresh, attribs = data_table_needs_refresh( cached_data_table, url )
+
−    if refresh:
+
−        data_table_text = attribs.get( 'data_table_text' )or urlopen( url ).read()
+
−        loc_file_attrs = attribs.get( 'loc_file_attrs' ) or rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
+
−
+
−        tmp_dir = tempfile.mkdtemp( prefix='rsync_g2_' )
+
−        tmp_loc_dir = os.path.join( tmp_dir, 'location' )
+
−        os.mkdir( tmp_loc_dir )
+
−        rsync_sync_to_dir( rsync_urljoin( RSYNC_SERVER, LOCATION_DIR ), os.path.abspath( tmp_loc_dir ) )
+
−
+
−        new_data_table_text = data_table_text.replace( TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE, TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET % ( tmp_loc_dir ) )
+
−        data_table_fh = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix='rysnc_data_manager_data_table_conf_' )
+
−        data_table_fh.write( new_data_table_text )
+
−        data_table_fh.flush()
+
−        tmp_data_dir = os.path.join( tmp_dir, 'tool-data' )
+
−        os.mkdir( tmp_data_dir )
+
−        data_tables = data_table_class( tmp_data_dir, config_filename=data_table_fh.name )
+
−        for name, data_table in list(data_tables.data_tables.items()):
+
−            if name in EXCLUDE_DATA_TABLES or not data_table_has_path_column( data_table ):
+
−                log.debug( 'Removing data table "%s" because it is excluded by name or does not have a defined "path" column.', name )
+
−                del data_tables.data_tables[name]
+
−        cached_data_table = { 'data_tables': data_tables, 'tmp_dir': tmp_dir, 'data_table_text': data_table_text, 'tmp_loc_dir': tmp_loc_dir, 'loc_file_attrs': loc_file_attrs, 'time_loaded': datetime.datetime.now() }
+
−        TOOL_DATA_TABLES_LOADED_BY_URL[ url ] = cached_data_table
+
−        # delete the files
+
−        data_table_fh.close()
+
−        cleanup_before_exit( tmp_dir )
+
−    return cached_data_table
+
−
+
−
+
−def data_table_has_path_column( data_table ):
+
−    col_names = data_table.get_column_name_list()
+
−    for name in PATH_COLUMN_NAMES:
+
−        if name in col_names:
+
−            return True
+
−    return False
+
−
+
−
+
−def get_available_tables( trans ):
+
−    # list of data tables
+
−    data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
+
−    return list(data_tables.get( 'data_tables' ).get_tables().keys())
+
−
+
−
+
−def get_new_xml_definition( app, data_table, data_manager, repo_info=None, location_file_dir=None ):
+
−    sub_dict = { 'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': '' }
+
−    sub_dict.update( data_manager.get_tool_shed_repository_info_dict() )
+
−    if data_table.comment_char:
+
−        sub_dict['comment_char'] = 'comment_char="%s"' % ( data_table.comment_char )
+
−    for i, name in enumerate( data_table.get_column_name_list() ):
+
−        if name is not None:
+
−            sub_dict['columns'] = "%s\n%s" % ( sub_dict['columns'], '<column name="%s" index="%s" />' % ( name, i ) )
+
−    location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path
+
−    for filename in data_table.filenames.keys():
+
−        sub_dict['file_path'] = basename( filename )
+
−        sub_dict['file_path'] = os.path.join( location_file_dir, sub_dict['file_path'] )  # os.path.abspath?
+
−        if not os.path.exists( sub_dict['file_path'] ):
+
−            # Create empty file
+
−            open( sub_dict['file_path'], 'wb+' ).close()
+
−        break
+
−    sub_dict[ 'repo_info' ] = repo_info or ''
+
−    return """
+
−            <tables><table name="%(table_name)s" %(comment_char)s>
+
−                %(columns)s
+
−                <file path="%(file_path)s" />
+
−                %(repo_info)s
+
−            </table></tables>
+
−           """ % sub_dict
+
−
+
−
+
−def get_available_tables_for_dbkey( trans, dbkey, data_table_names ):
+
−    data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
+
−    rval = {}
+
−    for name, data_table in data_tables.get( 'data_tables' ).get_tables().items():
+
−        if ( not data_table_names or name in data_table_names ):
+
−            # TODO: check that columns are similiar
+
−            if not dbkey:
+
−                entry_getter = data_table.get_named_fields_list()
+
−            else:
+
−                entry_getter = data_table.get_entries( 'dbkey', dbkey, None, default=[] )
+
−            for entry in entry_getter:
+
−                name = "%s: %s" % ( data_table.name, dumps( entry ) )
+
−                rval[name] = entry
+
−    return rval
+
−
+
−
+
−def split_path_all( path ):
+
−    rval = []
+
−    path = path.rstrip( '/' )
+
−    while True:
+
−        head, tail = os.path.split( path )
+
−        if tail:
+
−            rval.append( tail )
+
−            path = head
+
−        elif head:
+
−            rval.append( head )
+
−            break
+
−        else:
+
−            break
+
−    rval.reverse()
+
−    return rval
+
−
+
−
+
−def get_data_for_path( path, data_root_dir ):
+
−    # We list dir with a /, but copy data without
+
−    # listing with / gives a . entry when its a dir
+
−    # cloning without the / will copy that whole directory into the target,
+
−    # instead of just that target's contents
+
−    if path.startswith( GALAXY_DATA_CANONICAL_PATH ):
+
−        path = path[ len( GALAXY_DATA_CANONICAL_PATH ):]
+
−    make_path = path
+
−    rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), path )
+
−    if rsync_source.endswith( '/' ):
+
−        rsync_source = rsync_source[:-1]
+
−    try:
+
−        dir_list = rsync_list_dir( rsync_source + "/" )
+
−    except Exception:
+
−        dir_list = None
+
−    while not dir_list or '.' not in dir_list:
+
−        head, tail = os.path.split( make_path )
+
−        if not head:
+
−            head = tail
+
−        make_path = head
+
−        rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), head )  # if we error here, likely due to a connection issue
+
−        if rsync_source.endswith( '/' ):
+
−            rsync_source = rsync_source[:-1]
+
−        dir_list = rsync_list_dir( rsync_source + "/" )
+
−    split_path = split_path_all( make_path )
+
−    target_path = data_root_dir
+
−    for p in split_path[:-1]:
+
−        target_path = os.path.join( target_path, p )
+
−        if not os.path.exists( target_path ):
+
−            os.mkdir( target_path )
+
−    rsync_sync_to_dir( rsync_source, target_path )
+
−    return path
+
−
+
−
+
−def get_data_and_munge_path( data_table_name, data_table_entry, data_root_dir ):
+
−    path_cols = []
+
−    for key, value in data_table_entry.items():
+
−        if key in PATH_COLUMN_NAMES:
+
−            path_cols.append( ( key, value ) )
+
−    if path_cols:
+
−        for col_name, value in path_cols:
+
−            if value.startswith( GALAXY_DATA_CANONICAL_PATH ):
+
−                data_table_entry[col_name] = get_data_for_path( value, data_root_dir )
+
−            else:
+
−                print('unable to determine location of rsync data for', data_table_name, data_table_entry)
+
−    return data_table_entry
+
−
+
−
+
−def fulfill_data_table_entries( data_table_entries, data_manager_dict, data_root_dir ):
+
−    for data_table_name, entries in data_table_entries.items():
+
−        for entry in entries:
+
−            entry = get_data_and_munge_path( data_table_name, entry, data_root_dir )
+
−            _add_data_table_entry( data_manager_dict, data_table_name, entry )
+
−    return data_manager_dict
+
−
+
−
+
−def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+
−    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+
−    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
+
−    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+
−    return data_manager_dict
+
−
+
−
+
−def cleanup_before_exit( tmp_dir ):
+
−    if tmp_dir and os.path.exists( tmp_dir ):
+
−        shutil.rmtree( tmp_dir )
+
−
+
−
+
−def get_data_table_entries( params ):
+
−    rval = {}
+
−    data_table_entries = params.get( 'data_table_entries', None )
+
−    if data_table_entries:
+
−        for entry_text in data_table_entries.split( ',' ):
+
−            entry_text = entry_text.strip().decode( 'base64' )
+
−            entry_dict = loads( entry_text )
+
−            data_table_name = entry_dict['name']
+
−            data_table_entry = entry_dict['entry']
+
−            rval[ data_table_name ] = rval.get( data_table_name, [] )
+
−            rval[ data_table_name ].append( data_table_entry )
+
−    return rval
+
−
+
−
+
−def main():
+
−    parser = optparse.OptionParser()
+
−    (options, args) = parser.parse_args()
+
−
+
−    filename = args[0]
+
−
+
−    params = loads( open( filename ).read() )
+
−    target_directory = params[ 'output_data' ][0]['extra_files_path']
+
−    os.mkdir( target_directory )
+
−    data_manager_dict = {}
+
−
+
−    data_table_entries = get_data_table_entries( params['param_dict'] )
+
−
+
−    # Populate the data Tables
+
−    data_manager_dict = fulfill_data_table_entries( data_table_entries, data_manager_dict, target_directory )
+
−
+
−    # save info to json file
+
−    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
−
+
−
+
−if __name__ == "__main__":
+
−    main()