1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/689aa9c246fe/ changeset: 689aa9c246fe user: dan date: 2011-11-18 19:48:06 summary: Update GenomeSpace import from file browser tool to use new versioned API. affected #: 2 files
diff -r 43219da282f61f1a3ee2f2578a247f673116ac7b -r 689aa9c246fed392b4eccbf6642d4871a7cf612f tools/data_source/genomespace_file_browser.py --- a/tools/data_source/genomespace_file_browser.py +++ b/tools/data_source/genomespace_file_browser.py @@ -8,32 +8,16 @@ pkg_resources.require( "simplejson" ) import simplejson
+GENOMESPACE_API_VERSION_STRING = "v1.0" +GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.propertie..." + CHUNK_SIZE = 2**20 #1mb
DEFAULT_GALAXY_EXT = "data"
#genomespace format identifier is the URL -GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = { 'http://www.genomespace.org/datamanager/dataformat/res/0.0.0': 'res', - 'http://www.genomespace.org/datamanager/dataformat/cbs/0.0.0': 'CBS', - 'http://www.genomespace.org/datamanager/dataformat/lowercasetxt/0.0.0': 'lowercasetxt', - 'http://www.genomespace.org/datamanager/dataformat/gff/0.0.0': 'GFF', - 'http://www.genomespace.org/datamanager/dataformat/reversedtxt/0.0.0': 'reversedtxt', - 'http://www.genomespace.org/datamanager/dataformat/gxp/0.0.0': 'gxp', - 'http://www.genomespace.org/datamanager/dataformat/unknown/0.0.0': 'unknown', - 'http://www.genomespace.org/datamanager/dataformat/gtf/0.0.0': 'GTF', - 'http://www.genomespace.org/datamanager/dataformat/cn/0.0.0': 'cn', - 'http://www.genomespace.org/datamanager/dataformat/gct/0.0.0': 'gct', - 'http://www.genomespace.org/datamanager/dataformat/nowhitespace/0.0.0': 'nowhitespace', - 'http://www.genomespace.org/datamanager/dataformat/gistic/0.0.0': 'GISTIC', - 'http://www.genomespace.org/datamanager/dataformat/rifles/0.0.0': 'rifles', - 'http://www.genomespace.org/datamanager/dataformat/bed/0.0.0': 'bed', - 'http://www.genomespace.org/datamanager/dataformat/txt/0.0.0': 'txt', - 'http://www.genomespace.org/datamanager/dataformat/uppercasetxt/0.0.0': 'uppercasetxt', - 'http://www.genomespace.org/datamanager/dataformat/xcn/0.0.0': 'xcn', - 'http://www.genomespace.org/datamanager/dataformat/gmt/0.0.0': 'gmt', - 'http://www.genomespace.org/datamanager/dataformat/genomicatab/0.0.0': 'genomicatab', - 'http://www.genomespace.org/datamanager/dataformat/lifes/0.0.0': 'lifes' } - +GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = {} #TODO: fix this so it is not a global variable +#TODO: we should use a better way to set up this mapping GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles', 'lifes': 'lifes', 'cn': 'cn', @@ -48,29 +32,13 @@ 'reversedtxt': 'reversedtxt', 'nowhitespace': 'nowhitespace', 'unknown': 'unknown', - 'txt': 'txt', 'uppercasetxt': - 'uppercasetxt', + 'txt': 'txt', + 'uppercasetxt': 'uppercasetxt', 'GISTIC': 'gistic', 'GFF': 'gff', 'gmt': 'gmt', 'gct': 'gct'}
-''' -https://dmdev.genomespace.org:8444/datamanager/dataformat/list -from galaxy import eggs -import pkg_resources -pkg_resources.require( "simplejson" ) -import simplejson -formats = simplejson.loads( '[{"name":"GISTIC","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gistic/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gff/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gct/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/lifes/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gtf/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/rifles/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/cbs/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/unknown/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/reversedtxt/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/res/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/cn/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gmt/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/bed/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gxp/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/uppercasetxt/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/lowercasetxt/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/genomicatab/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/nowhitespace/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/xcn/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/txt/0.0.0","fileExtension":"txt"}]' ) -formats = [{"name":"GISTIC","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gistic/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gff/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gct/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/lifes/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gtf/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/rifles/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/cbs/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/unknown/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/reversedtxt/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/res/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/cn/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gmt/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/bed/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/gxp/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/uppercasetxt/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/lowercasetxt/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/genomicatab/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/nowhitespace/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/xcn/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http://www.genomespace.org/datamanager/dataformat/txt/0.0.0","fileExtension":"txt"}] -GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT = {} -for format in formats: - GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT[ format[ 'url' ] ] = format['name'] - -print GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT -#do manual change to galaxy exts -''' -
def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ): source_method = getattr( source_stream, source_method ) @@ -101,7 +69,28 @@ ext = DEFAULT_GALAXY_EXT return ext
-def download_from_genomespace_file_browser( json_parameter_file ): +def get_genomespace_site_urls(): + genomespace_sites = {} + for line in urllib2.urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ): + line = line.rstrip() + if not line or line.startswith( "#" ): + continue + server, line = line.split( '.', 1 ) + if server not in genomespace_sites: + genomespace_sites[server] = {} + line = line.split( "=", 1 ) + genomespace_sites[server][line[0]] = line[1] + return genomespace_sites + +def set_genomespace_format_identifiers( url_opener, dm_site ): + gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) ) + gs_request.get_method = lambda: 'GET' + opened_gs_request = url_opener.open( gs_request ) + genomespace_formats = simplejson.loads( opened_gs_request.read() ) + for format in genomespace_formats: + GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name'] + +def download_from_genomespace_file_browser( json_parameter_file, genomespace_site ): json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() ) datasource_params = json_params.get( 'param_dict' ) username = datasource_params.get( "gs-username", None ) @@ -111,6 +100,10 @@ dataset_id = json_params['output_data'][0]['dataset_id'] hda_id = json_params['output_data'][0]['hda_id'] url_opener = get_cookie_opener( username, token ) + #load and set genomespace format ids to galaxy exts + genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ] + set_genomespace_format_identifiers( url_opener, genomespace_site_dict['dmServer'] ) + file_url_prefix = "fileUrl" file_type_prefix = "fileFormat" metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' ) @@ -149,6 +142,7 @@ #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file' ) + parser.add_option( '-s', '--genomespace_site', dest='genomespace_site', action='store', type="string", default=None, help='genomespace_site' ) (options, args) = parser.parse_args()
- download_from_genomespace_file_browser( options.json_parameter_file ) + download_from_genomespace_file_browser( options.json_parameter_file, options.genomespace_site )
diff -r 43219da282f61f1a3ee2f2578a247f673116ac7b -r 689aa9c246fed392b4eccbf6642d4871a7cf612f tools/data_source/genomespace_file_browser_dev.xml --- a/tools/data_source/genomespace_file_browser_dev.xml +++ b/tools/data_source/genomespace_file_browser_dev.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><tool name="GenomeSpace import" id="genomespace_file_browser_dev" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1"> - <description>from file browser</description> - <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}"</command> + <description>from file browser (development)</description> + <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "dev"</command><inputs action="https://dmdev.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"><display>go to GenomeSpace Data Manager </display><param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&runtool_btn=Execute" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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