4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1ecb6aaebaf4/ Changeset: 1ecb6aaebaf4 Branch: compressed_upload User: BjoernGruening Date: 2015-01-12 21:36:20+00:00 Summary: Add CompressedArchive as datatype and do not uncomress it during upload. Affected #: 3 files diff -r b5c7266dbb69f81864d96247ff11be42246e94de -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -140,6 +140,8 @@ <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/><datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/><datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/><datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/><datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/> diff -r b5c7266dbb69f81864d96247ff11be42246e94de -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -106,6 +106,30 @@ Binary.register_unsniffable_binary_ext("ab1") +class CompressedArchive( Binary ): + """ + Class describing an compressed binary file + This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py. + """ + file_ext = "compressed_archive" + compressed = True + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = "Compressed binary file" + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "Compressed binary file (%s)" % ( data.nice_size( dataset.get_size() ) ) + +Binary.register_unsniffable_binary_ext("compressed_archive") + class GenericAsn1Binary( Binary ): """Class for generic ASN.1 binary format""" diff -r b5c7266dbb69f81864d96247ff11be42246e94de -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -120,171 +120,176 @@ data_type = type_info[0] ext = type_info[1] if not data_type: - # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress - is_gzipped, is_valid = check_gzip( dataset.path ) - if is_gzipped and not is_valid: - file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) - return - elif is_gzipped and is_valid: - if link_data_only == 'copy_files': - # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) - while 1: - try: - chunk = gzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing gzipped data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - gzipped_file.close() - # Replace the gzipped file with the decompressed file if it's safe to do so - if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: - dataset.path = uncompressed - else: - shutil.move( uncompressed, dataset.path ) - os.chmod(dataset.path, 0644) - dataset.name = dataset.name.rstrip( '.gz' ) - data_type = 'gzip' - if not data_type and bz2 is not None: - # See if we have a bz2 file, much like gzip - is_bzipped, is_valid = check_bz2( dataset.path ) - if is_bzipped and not is_valid: + root_datatype = registry.get_datatype_by_extension( dataset.file_type ) + if getattr( root_datatype, 'compressed', False ): + data_type = 'compressed archive' + ext = dataset.file_type + else: + # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress + is_gzipped, is_valid = check_gzip( dataset.path ) + if is_gzipped and not is_valid: file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return - elif is_bzipped and is_valid: + elif is_gzipped and is_valid: if link_data_only == 'copy_files': - # We need to uncompress the temp_name file + # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) while 1: try: - chunk = bzipped_file.read( CHUNK_SIZE ) + chunk = gzipped_file.read( CHUNK_SIZE ) except IOError: os.close( fd ) os.remove( uncompressed ) - file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + file_err( 'Problem decompressing gzipped data', dataset, json_file ) return if not chunk: break os.write( fd, chunk ) os.close( fd ) - bzipped_file.close() - # Replace the bzipped file with the decompressed file if it's safe to do so + gzipped_file.close() + # Replace the gzipped file with the decompressed file if it's safe to do so if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) os.chmod(dataset.path, 0644) - dataset.name = dataset.name.rstrip( '.bz2' ) - data_type = 'bz2' - if not data_type: - # See if we have a zip archive - is_zipped = check_zip( dataset.path ) - if is_zipped: - if link_data_only == 'copy_files': - CHUNK_SIZE = 2**20 # 1Mb - uncompressed = None - uncompressed_name = None - unzipped = False - z = zipfile.ZipFile( dataset.path ) - for name in z.namelist(): - if name.endswith('/'): - continue - if unzipped: - stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' - break - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - if sys.version_info[:2] >= ( 2, 6 ): - zipped_file = z.open( name ) - while 1: + dataset.name = dataset.name.rstrip( '.gz' ) + data_type = 'gzip' + if not data_type and bz2 is not None: + # See if we have a bz2 file, much like gzip + is_bzipped, is_valid = check_bz2( dataset.path ) + if is_bzipped and not is_valid: + file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) + return + elif is_bzipped and is_valid: + if link_data_only == 'copy_files': + # We need to uncompress the temp_name file + CHUNK_SIZE = 2**20 # 1Mb + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) + while 1: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + # Replace the bzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) + dataset.name = dataset.name.rstrip( '.bz2' ) + data_type = 'bz2' + if not data_type: + # See if we have a zip archive + is_zipped = check_zip( dataset.path ) + if is_zipped: + if link_data_only == 'copy_files': + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None + unzipped = False + z = zipfile.ZipFile( dataset.path ) + for name in z.namelist(): + if name.endswith('/'): + continue + if unzipped: + stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' + break + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + if sys.version_info[:2] >= ( 2, 6 ): + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + else: + # python < 2.5 doesn't have a way to read members in chunks(!) try: - chunk = zipped_file.read( CHUNK_SIZE ) + outfile = open( uncompressed, 'wb' ) + outfile.write( z.read( name ) ) + outfile.close() + uncompressed_name = name + unzipped = True except IOError: os.close( fd ) os.remove( uncompressed ) file_err( 'Problem decompressing zipped data', dataset, json_file ) return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - zipped_file.close() - uncompressed_name = name - unzipped = True + z.close() + # Replace the zipped file with the decompressed file if it's safe to do so + if uncompressed is not None: + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) + dataset.name = uncompressed_name + data_type = 'zip' + if not data_type: + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): + # We have a binary dataset, but it is not Bam, Sff or Pdf + data_type = 'binary' + #binary_ok = False + parts = dataset.name.split( "." ) + if len( parts ) > 1: + ext = parts[-1].strip().lower() + if not Binary.is_ext_unsniffable(ext): + file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) + return + elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: + err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) + file_err( err_msg, dataset, json_file ) + return + if not data_type: + # We must have a text file + if check_html( dataset.path ): + file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) + return + if data_type != 'binary': + if link_data_only == 'copy_files': + if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: + in_place = False + # Convert universal line endings to Posix line endings, but allow the user to turn it off, + # so that is becomes possible to upload gzip, bz2 or zip files with binary data without + # corrupting the content of those files. + if dataset.to_posix_lines: + tmpdir = output_adjacent_tmpdir( output_path ) + tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id + if dataset.space_to_tab: + line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) else: - # python < 2.5 doesn't have a way to read members in chunks(!) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - uncompressed_name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return - z.close() - # Replace the zipped file with the decompressed file if it's safe to do so - if uncompressed is not None: - if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: - dataset.path = uncompressed - else: - shutil.move( uncompressed, dataset.path ) - os.chmod(dataset.path, 0644) - dataset.name = uncompressed_name - data_type = 'zip' - if not data_type: - # TODO refactor this logic. check_binary isn't guaranteed to be - # correct since it only looks at whether the first 100 chars are - # printable or not. If someone specifies a known unsniffable - # binary datatype and check_binary fails, the file gets mangled. - if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): - # We have a binary dataset, but it is not Bam, Sff or Pdf - data_type = 'binary' - #binary_ok = False - parts = dataset.name.split( "." ) - if len( parts ) > 1: - ext = parts[-1].strip().lower() - if not Binary.is_ext_unsniffable(ext): - file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) - return - elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: - err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) - file_err( err_msg, dataset, json_file ) - return - if not data_type: - # We must have a text file - if check_html( dataset.path ): - file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) - return - if data_type != 'binary': - if link_data_only == 'copy_files': - if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: - in_place = False - # Convert universal line endings to Posix line endings, but allow the user to turn it off, - # so that is becomes possible to upload gzip, bz2 or zip files with binary data without - # corrupting the content of those files. - if dataset.to_posix_lines: - tmpdir = output_adjacent_tmpdir( output_path ) - tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id - if dataset.space_to_tab: - line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) - else: - line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) - if dataset.file_type == 'auto': - ext = sniff.guess_ext( dataset.path, registry.sniff_order ) - else: - ext = dataset.file_type - data_type = ext + line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) + if dataset.file_type == 'auto': + ext = sniff.guess_ext( dataset.path, registry.sniff_order ) + else: + ext = dataset.file_type + data_type = ext # Save job info for the framework if ext == 'auto' and dataset.ext: ext = dataset.ext https://bitbucket.org/galaxy/galaxy-central/commits/4a8a610a97e1/ Changeset: 4a8a610a97e1 Branch: compressed_upload User: BjoernGruening Date: 2015-01-16 22:30:05+00:00 Summary: merge Affected #: 110 files diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,16 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02 -9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 -6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 -3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 -425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 -9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 -9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 -81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 -2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 +9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 +8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 +b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 +dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 +19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 +cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 +7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 +0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 +f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -5834b1066462dd219f67c1c3cbd77c78e7cf3a6c latest_2014.10.06 +9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee latest_2015.01.13 diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/galaxy.workflow_editor.canvas.js --- a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js +++ b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js @@ -1089,7 +1089,11 @@ if ( this.active_node != node ) { this.check_changes_in_active_form(); this.clear_active_node(); - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } node.make_active(); this.active_node = node; } @@ -1099,7 +1103,11 @@ if ( this.active_node == node && (!parent.__NEWTOOLFORM__ || force)) { // Reactive with new form_html this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped) - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } } }, layout : function () { @@ -1305,13 +1313,6 @@ return node; } -function update_node( data ) { - var node = workflow.active_node; - if (node) { - node.update_field_data(data, true); - } -} - var ext_to_type = null; var type_to_type = null; diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -76,6 +76,20 @@ } }, + /** Highlights errors + */ + _errors: function(options) { + if (options && options.errors) { + var error_messages = this.tree.matchResponse(options.errors); + for (var input_id in this.element_list) { + var input = this.element_list[input_id]; + if (error_messages[input_id]) { + this.highlight(input_id, error_messages[input_id], true); + } + } + } + }, + /** Main tool form build function. This function is called once a new model is available. */ _buildForm: function() { @@ -111,16 +125,11 @@ this.tree.finalize(); // show errors - if (!this.workflow && options.errors) { - var error_messages = this.tree.matchResponse(options.errors); - for (var input_id in error_messages) { - this.highlight(input_id, error_messages[input_id], true); - } - } + this._errors(options); // add refresh listener this.on('refresh', function() { - // by using/reseting the deferred ajax queue the number of redundant calls is reduced + // by using/resetting the deferred ajax queue the number of redundant calls is reduced self.deferred.reset(); self.deferred.execute(function(){self._updateModel()}); }); @@ -131,6 +140,9 @@ this.element_list[i].reset(); } }); + + // refresh + this.trigger('refresh'); }, /** Renders the UI elements required for the form @@ -145,7 +157,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : 'Requirements', + title : (!this.workflow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -170,7 +182,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : 'Versions', + title : (!this.workflow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -200,7 +212,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : 'Options', + title : (!this.workflow && 'Options') || null, tooltip : 'View available options' }); @@ -276,6 +288,11 @@ buttons : this.buttons }); + // remove padding + if (this.options.workflow) { + this.portlet.$content.css('padding', '0px'); + } + // append message this.portlet.append(this.message.$el, true); diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -7,13 +7,254 @@ // create form view var View = ToolFormBase.extend({ initialize: function(options) { + // link with node representation in workflow module + this.node = workflow.active_node; + + if (!this.node) { + console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.'); + return; + } + + // initialize parameters this.workflow = true; - ToolFormBase.prototype.initialize.call(this, options); + this.options = options; + + // declare fields as optional + Utils.deepeach(options.inputs, function(item) { + if (item.type) { + item.optional = (['data', 'data_hidden', 'hidden', 'drill_down']).indexOf(item.type) == -1; + } + }); + + // declare conditional fields as not optional + Utils.deepeach(options.inputs, function(item) { + if (item.type) { + if (item.type == 'conditional') { + item.test_param.optional = false; + } + } + }); + + // load extension + var self = this; + Utils.get({ + url : galaxy_config.root + 'api/datatypes', + cache : true, + success : function(datatypes) { + self.datatypes = datatypes; + self._makeSections(options.inputs); + ToolFormBase.prototype.initialize.call(self, options); + } + }); + }, + + /** Builds all sub sections + */ + _makeSections: function(inputs){ + // for annotation + inputs[Utils.uuid()] = { + label : 'Edit Step Attributes', + type : 'section', + expand : this.node.annotation, + inputs : [{ + label : 'Annotation / Notes', + name : 'annotation', + type : 'text', + area : true, + help : 'Add an annotation or notes to this step; annotations are available when a workflow is viewed.', + value : this.node.annotation + }] + } + + // for actions + this.post_job_actions = this.node.post_job_actions; + for (var i in this.node.output_terminals) { + inputs[Utils.uuid()] = this._makeSection(i); + } + }, + + /** Builds sub section with step actions/annotation + */ + _makeSection: function(output_id){ + // format datatypes + var extensions = []; + for (key in this.datatypes) { + extensions.push({ + 0 : this.datatypes[key], + 1 : this.datatypes[key] + }); + } + + // sort extensions + extensions.sort(function(a, b) { + return a.label > b.label ? 1 : a.label < b.label ? -1 : 0; + }); + + // add additional options + extensions.unshift({ + 0 : 'Sequences', + 1 : 'Sequences' + }); + extensions.unshift({ + 0 : 'Roadmaps', + 1 : 'Roadmaps' + }); + extensions.unshift({ + 0 : 'Leave unchanged', + 1 : 'None' + }); + + // create custom sub section + var input_config = { + label : 'Edit Step Action: \'' + output_id + '\'', + type : 'section', + inputs : [{ + action : 'RenameDatasetAction', + argument : 'newname', + label : 'Rename dataset', + type : 'text', + value : '', + ignore : '', + help : 'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.' + },{ + action : 'ChangeDatatypeAction', + argument : 'newtype', + label : 'Change datatype', + type : 'select', + ignore : 'None', + options : extensions, + help : 'This action will change the datatype of the output to the indicated value.' + },{ + action : 'TagDatasetAction', + argument : 'tags', + label : 'Tags', + type : 'text', + value : '', + ignore : '', + help : 'This action will set tags for the dataset.' + },{ + label : 'Assign columns', + type : 'section', + inputs : [{ + action : 'ColumnSetAction', + argument : 'chromCol', + label : 'Chrom column', + type : 'text', + value : '', + ignore : '' + },{ + action : 'ColumnSetAction', + argument : 'startCol', + label : 'Start column', + type : 'text', + value : '', + ignore : '' + },{ + action : 'ColumnSetAction', + argument : 'endCol', + label : 'End column', + type : 'text', + value : '', + ignore : '' + },{ + action : 'ColumnSetAction', + argument : 'strandCol', + label : 'Strand column', + type : 'text', + value : '', + ignore : '' + },{ + action : 'ColumnSetAction', + argument : 'nameCol', + label : 'Name column', + type : 'text', + value : '', + ignore : '' + }], + help : 'This action will set column assignments in the output dataset. Blank fields are ignored.' + },{ + action : 'EmailAction', + label : 'Email notification', + type : 'boolean', + value : 'false', + ignore : 'false', + help : 'This action will send an email notifying you when the job is done.', + payload : { + 'host' : window.location.host + } + },{ + action : 'DeleteIntermediatesAction', + label : 'Delete non-outputs', + type : 'boolean', + value : 'false', + ignore : 'false', + help : 'All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect.' + }] + }; + + // visit input nodes and enrich by name/value pairs from server data + var self = this; + function visit (head, head_list) { + head_list = head_list || []; + head_list.push(head); + for (var i in head.inputs) { + var input = head.inputs[i]; + if (input.action) { + // construct identifier as expected by backend + input.name = 'pja__' + output_id + '__' + input.action; + if (input.argument) { + input.name += '__' + input.argument; + } + + // modify names of payload arguments + if (input.payload) { + for (var p_id in input.payload) { + var p = input.payload[p_id]; + input.payload[input.name + '__' + p_id] = p; + delete p; + } + } + + // access/verify existence of value + var d = self.post_job_actions[input.action + output_id]; + if (d) { + // mark as expanded + for (var j in head_list) { + head_list[j].expand = true; + } + + // update input field value + if (input.argument) { + input.value = d.action_arguments && d.action_arguments[input.argument] || input.value; + } else { + input.value = 'true'; + } + } + } + // continue with sub section + if (input.inputs) { + visit(input, head_list.slice(0)); + } + } + } + visit(input_config); + + // return final configuration + return input_config; }, /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { + Galaxy.modal.show({ + title : 'Coming soon...', + body : 'This feature has not been implemented yet.', + buttons : { + 'Close' : function() { + Galaxy.modal.hide(); + } + } + }); }, /** Request a new model for an already created tool form and updates the form inputs @@ -38,15 +279,19 @@ type : 'GET', url : model_url, data : current_state, - success : function(node) { - parent.update_node(node); - + success : function(data) { + // update node in workflow module + self.node.update_field_data(data); + + // highlight errors + self._errors(data && data.tool_model); + // process completed self.deferred.done(process_id); // log success console.debug('tools-form::_refreshForm() - States refreshed.'); - console.debug(node); + console.debug(data); }, error : function(response) { // process completed diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -12,6 +12,7 @@ // link field this.field = options.field; + this.defaultvalue = options.defaultvalue; // set element this.setElement(this._template(options)); @@ -25,8 +26,13 @@ // add field element this.$field.prepend(this.field.$el); - // start with enabled optional fields + // decide wether to expand or collapse optional fields this.field.skip = false; + var v = this.field.value && this.field.value(); + this.field.skip = Boolean(options.optional && + ((this.field.validate && !this.field.validate()) || !v || + (v == this.defaultvalue) || (Number(v) == Number(this.defaultvalue)) || + (JSON.stringify(v) == JSON.stringify(this.defaultvalue)))); // refresh view this._refresh(); @@ -45,9 +51,11 @@ /** Set error text */ error: function(text) { - this.$error_text.html(text); - this.$error.fadeIn(); - this.$el.addClass('ui-error'); + if (!this.field.skip) { + this.$error_text.html(text); + this.$error.fadeIn(); + this.$el.addClass('ui-error'); + } }, /** Reset this view @@ -63,11 +71,13 @@ if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); - this.app.trigger('refresh'); } else { + this.reset(); this.$field.hide(); this.$title_optional.html('Enable'); + this.field.value && this.field.value(this.defaultvalue); } + this.app.trigger('refresh'); }, /** Main Template @@ -82,7 +92,7 @@ // is optional if (options.optional) { - tmp += 'Optional: ' + options.label + + tmp += options.label + '<span> [<span class="ui-table-form-title-optional"/>]</span>'; } else { tmp += options.label; diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -1,8 +1,8 @@ /** This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _createField() function. */ -define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], - function(Utils, Table, Ui, Repeat, SelectContent, InputElement) { +define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], + function(Utils, Table, Ui, Portlet, Repeat, SelectContent, InputElement) { // create form view var View = Backbone.View.extend({ @@ -36,13 +36,13 @@ // load settings elements into table for (var i in this.inputs) { - this._add(this.inputs[i]); + this.add(this.inputs[i]); } }, /** Add a new input element */ - _add: function(input) { + add: function(input) { // link this var self = this; @@ -66,6 +66,10 @@ case 'repeat': this._addRepeat(input_def); break; + // customized section + case 'section': + this._addSection(input_def); + break; // default single element row default: this._addRow(input_def); @@ -103,8 +107,7 @@ // check if non-hidden elements exist var nonhidden = false; for (var j in case_def.inputs) { - var type = case_def.inputs[j].type; - if (type && type !== 'hidden') { + if (!case_def.inputs[j].hidden) { nonhidden = true; break; } @@ -229,9 +232,9 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.title, - help : input_def.help, - field : repeat + label : input_def.title, + help : input_def.help, + field : repeat }); // displays as grouped subsection @@ -244,6 +247,63 @@ this.table.append(input_def.id); }, + /** Add a customized section + */ + _addSection: function(input_def) { + // link this + var self = this; + + // create sub section + var sub_section = new View(self.app, { + inputs : input_def.inputs, + cls : 'ui-table-plain' + }); + + // delete button + var button_visible = new Ui.ButtonIcon({ + icon : 'fa-eye-slash', + tooltip : 'Show/hide section', + cls : 'ui-button-icon-plain' + }); + + // create portlet for sub section + var portlet = new Portlet.View({ + title : input_def.label, + cls : 'ui-portlet-section', + operations : { + button_visible: button_visible + } + }); + portlet.append(sub_section.$el); + + // add event handler visibility button + var visible = false; + portlet.$content.hide(); + portlet.$header.css('cursor', 'pointer'); + portlet.$header.on('click', function() { + if (visible) { + visible = false; + portlet.$content.hide(); + button_visible.setIcon('fa-eye-slash'); + } else { + visible = true; + portlet.$content.fadeIn('fast'); + button_visible.setIcon('fa-eye'); + } + }); + + // show sub section if requested + if (input_def.expand) { + portlet.$header.trigger('click'); + } + + // create table row + this.table.add(portlet.$el); + + // append row to table + this.table.append(input_def.id); + }, + /** Add a single input field element */ _addRow: function(input_def) { @@ -258,10 +318,11 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.label, - optional : input_def.optional, - help : input_def.help, - field : field + label : input_def.label, + defaultvalue : input_def.defaultvalue, + optional : input_def.optional, + help : input_def.help, + field : field }); // add to element list @@ -273,6 +334,11 @@ // append to table this.table.append(id); + // hide row if neccessary + if (input_def.hidden) { + this.table.get(id).hide(); + } + // return created field return field; }, @@ -316,7 +382,7 @@ field = this._fieldHidden(input_def); break; - // hidden field + // hidden data field case 'hidden_data': field = this._fieldHidden(input_def); break; @@ -465,9 +531,9 @@ _fieldText : function(input_def) { var self = this; return new Ui.Input({ - id : 'field-' + input_def.id, - area : input_def.area, - onchange: function() { + id : 'field-' + input_def.id, + area : input_def.area, + onchange : function() { self.app.trigger('refresh'); } }); @@ -476,11 +542,15 @@ /** Slider field */ _fieldSlider: function(input_def) { + var self = this; return new Ui.Slider.View({ - id : 'field-' + input_def.id, - precise : input_def.type == 'float', - min : input_def.min, - max : input_def.max + id : 'field-' + input_def.id, + precise : input_def.type == 'float', + min : input_def.min, + max : input_def.max, + onchange : function() { + self.app.trigger('refresh'); + } }); }, @@ -488,18 +558,22 @@ */ _fieldHidden : function(input_def) { return new Ui.Hidden({ - id : 'field-' + input_def.id, - info : input_def.info + id : 'field-' + input_def.id, + info : input_def.info }); }, /** Boolean field */ _fieldBoolean : function(input_def) { + var self = this; return new Ui.RadioButton.View({ - id : 'field-' + input_def.id, - data : [ { label : 'Yes', value : 'true' }, - { label : 'No', value : 'false' }] + id : 'field-' + input_def.id, + data : [ { label : 'Yes', value : 'true' }, + { label : 'No', value : 'false' }], + onchange : function() { + self.app.trigger('refresh'); + } }); } }); diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -4,7 +4,7 @@ // tool form templates return { help: function(content) { - return '<div class="toolHelp">' + + return '<div class="toolHelp" style="overflow: auto;">' + '<div class="toolHelpBody">' + content + '</div>' + diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -108,22 +108,37 @@ convert(job_input_id, head[input.id + '-section-' + selectedCase]); } break; + // handle custom sub sections + case 'section': + convert('', node); + break; default: // get field var field = self.app.field_list[input.id]; - - // get and patch field value - var value = field.value(); - if (patch[input.type]) { - value = patch[input.type](value); - } - - // handle default value - if (!field.skip) { - if (field.validate && !field.validate(value)) { - value = null; + if (field && field.value) { + // get and patch field value + var value = field.value(); + if (patch[input.type]) { + value = patch[input.type](value); } - add (job_input_id, input.id, value); + + // handle simple value + if (!field.skip ) { + if (field.validate && !field.validate()) { + value = null; + } + if (input.ignore === undefined || (value !== null && input.ignore != value)) { + // add value to submission + add (job_input_id, input.id, value); + + // add payload to submission + if (input.payload) { + for (var p_id in input.payload) { + add (p_id, input.id, input.payload[p_id]); + } + } + } + } } } } diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -193,6 +193,12 @@ this.disabled = false; }, + // change icon + setIcon: function(icon_cls) { + this.$('i').removeClass(this.options.icon).addClass(icon_cls); + this.options.icon = icon_cls; + }, + // template _template: function(options) { // width diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/mvc/ui/ui-portlet.js --- a/client/galaxy/scripts/mvc/ui/ui-portlet.js +++ b/client/galaxy/scripts/mvc/ui/ui-portlet.js @@ -25,6 +25,7 @@ $content : null, $buttons : null, $operations : null, + $header : null, // initialize initialize : function(options) { @@ -35,22 +36,16 @@ this.setElement(this._template(this.options)); // link content - this.$content = this.$el.find('#content'); + this.$content = this.$el.find('.content'); // link title - this.$title = this.$el.find('#portlet-title-text'); + this.$title = this.$el.find('.portlet-title-text'); - // set content format - var $portlet_content = this.$el.find('#portlet-content'); - if (!this.options.scrollable) { - if (this.options.title) { - $portlet_content.addClass('no-scroll'); - } else { - $portlet_content.addClass('no-scroll-no-title'); - } - } else { - $portlet_content.addClass('scroll'); - } + // link header + this.$header = this.$el.find('.portlet-header'); + + // link portlet content (wraps 'content') + var $portlet_content = this.$el.find('.portlet-content'); // set content padding if (this.options.nopadding) { @@ -59,7 +54,7 @@ } // append buttons - this.$buttons = $(this.el).find('#buttons'); + this.$buttons = $(this.el).find('.buttons'); if (this.options.buttons) { // link functions var self = this; @@ -72,7 +67,7 @@ } // append operations - this.$operations = $(this.el).find('#operations'); + this.$operations = $(this.el).find('.operations'); if (this.options.operations) { // link functions var self = this; @@ -161,27 +156,27 @@ var tmpl = '<div id="' + options.id + '" class="' + options.cls + '">'; if (options.title) { - tmpl += '<div id="portlet-header" class="portlet-header">' + - '<div id="operations" style="float: ' + options.operations_flt + ';"></div>' + + tmpl += '<div class="portlet-header">' + + '<div class="operations" style="float: ' + options.operations_flt + ';"></div>' + '<div class="portlet-title">'; if (options.icon) tmpl += '<i class="icon fa ' + options.icon + '"> </i>'; - tmpl += '<span id="portlet-title-text" class="portlet-title-text">' + options.title + '</span>' + + tmpl += '<span class="portlet-title-text">' + options.title + '</span>' + '</div>' + '</div>'; } - tmpl += '<div id="portlet-content" class="portlet-content">'; + tmpl += '<div class="portlet-content">'; if (options.placement == 'top') { - tmpl += '<div id="buttons" class="buttons"></div>'; + tmpl += '<div class="buttons"></div>'; } - tmpl += '<div id="content" class="content"></div>'; + tmpl += '<div class="content"></div>'; if (options.placement == 'bottom') { - tmpl += '<div id="buttons" class="buttons"></div>'; + tmpl += '<div class="buttons"></div>'; } tmpl += '</div>' + diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -6,6 +6,18 @@ // dependencies define(["libs/underscore"], function(_) { +/** Traverse through json +*/ +function deepeach(dict, callback) { + for (var i in dict) { + var d = dict[i]; + if (d && typeof(d) == "object") { + callback(d); + deepeach(d, callback); + } + } +} + /** * Sanitize/escape a string * @param{String} content - Content to be sanitized @@ -248,7 +260,8 @@ request: request, sanitize: sanitize, textify: textify, - validate: validate + validate: validate, + deepeach: deepeach }; }); diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 client/galaxy/scripts/viz/trackster.js --- a/client/galaxy/scripts/viz/trackster.js +++ b/client/galaxy/scripts/viz/trackster.js @@ -12,7 +12,6 @@ [ // load js libraries 'utils/utils', - 'mvc/ui/icon-button', 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.mousewheel', @@ -32,9 +31,8 @@ }); // trackster viewer -define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], - function(_, base, tracks, visualization) { - +define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ], + function(_, base, tracks, visualization, mod_icon_btn) { /** * User interface controls for trackster */ diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -140,6 +140,7 @@ <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/><datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/><datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/> + <datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="True"/><datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/><datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/><datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/> diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -354,10 +354,6 @@ # If no message specified the warning box will not be shown. #registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. -# When users opt to reset passwords, new ones are created, this option -# specifies the length of these passwords. -#reset_password_length = 15 - # -- Account activation diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -1,6 +1,6 @@ -// Underscore.js 1.4.4 +// Underscore.js 1.7.0 // http://underscorejs.org -// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. +// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o){var u=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),f=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),h=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),p=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),d=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),v=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),m=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:h,Button:l,ButtonIcon:c,ButtonMenu:s,Icon:f,Image:u,Input:v,Label:a,Message:p,Modal:o,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:d,Select:t,Hidden:m,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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u=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),f=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),h=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),p=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),d=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),v=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),m=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<label>"+e.info+"</label>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:h,Button:l,ButtonIcon:c,ButtonMenu:s,Icon:f,Image:u,Input:v,Label:a,Message:p,Modal:o,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:d,Select:t,Hidden:m,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata 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"'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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Charts are saved upon creation.')); + $main.append(Utils.wrap()); $main.append(Utils.wrap(this.types.$el)); // add tab @@ -189,7 +191,9 @@ _refreshTitle: function() { var title = this.chart.get('title'); this.portlet.title(title); - this.title.value(title); + if (this.title.value() != title) { + this.title.value(title); + } }, // refresh group diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -254,7 +254,9 @@ if (key_text === undefined) { key_text = ''; } - this.group_key.value(key_text); + if (key_text != this.group_key.value()) { + this.group_key.value(key_text); + } } }); diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -99,7 +99,6 @@ this.portlet = new Portlet.View({ icon : 'fa-bar-chart-o', title: 'Viewport', - scrollable: false, operations: { edit_button: new Ui.ButtonIcon({ icon : 'fa-edit', diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -30,6 +30,14 @@ // use full screen for viewer this._fullscreen(this.$el, 100); + // prevent window scrolling + var initial_overflow = $('body').css('overflow'); + this.$el.on('mouseover', function() { + $('body').css('overflow', 'hidden'); + }).on('mouseout', function() { + $('body').css('overflow', initial_overflow); + }); + // create container element this._createContainer('div'); diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -34,7 +34,7 @@ amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 -bioblend = 0.4.2 +bioblend = 0.5.2 boto = 2.27.0 decorator = 3.1.2 docutils = 0.7 @@ -63,6 +63,7 @@ requests = 2.2.1 Routes = 1.12.3 simplejson = 2.1.1 +six = 1.9.0 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 SVGFig = 1.1.6 diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -161,7 +161,6 @@ self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u] - self.reset_password_length = int( kwargs.get('reset_password_length', '15') ) self.mailing_join_addr = kwargs.get('mailing_join_addr', 'galaxy-announce-join@bx.psu.edu') self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/dataset_collections/registry.py --- a/lib/galaxy/dataset_collections/registry.py +++ b/lib/galaxy/dataset_collections/registry.py @@ -1,6 +1,6 @@ from .types import list from .types import paired - +from galaxy import model PLUGIN_CLASSES = [list.ListDatasetCollectionType, paired.PairedDatasetCollectionType] @@ -12,3 +12,13 @@ def get( self, plugin_type ): return self.__plugins[ plugin_type ] + + def prototype( self, plugin_type ): + plugin_type_object = self.get( plugin_type ) + if not hasattr( plugin_type_object, 'prototype_elements' ): + raise Exception( "Cannot pre-determine structure for collection of type %s" % plugin_type ) + + dataset_collection = model.DatasetCollection() + elements = [ e for e in plugin_type_object.prototype_elements() ] + dataset_collection.elements = elements + return dataset_collection diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/dataset_collections/types/paired.py --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -1,6 +1,6 @@ from ..types import BaseDatasetCollectionType -from galaxy.model import DatasetCollectionElement +from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation FORWARD_IDENTIFIER = "forward" REVERSE_IDENTIFIER = "reverse" @@ -32,3 +32,15 @@ ) yield left_association yield right_association + + def prototype_elements( self ): + left_association = DatasetCollectionElement( + element=HistoryDatasetAssociation(), + element_identifier=FORWARD_IDENTIFIER, + ) + right_association = DatasetCollectionElement( + element=HistoryDatasetAssociation(), + element_identifier=REVERSE_IDENTIFIER, + ) + yield left_association + yield right_association diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -20,6 +20,7 @@ import galaxy.model from galaxy.util import listify +from galaxy.util.object_wrapper import sanitize_lists_to_string from galaxy.util import stringify_dictionary_keys from galaxy.util import string_as_bool from galaxy.util import in_directory @@ -232,6 +233,9 @@ def to_string( self, value ): return str( value ) + def to_safe_string( self, value ): + return sanitize_lists_to_string( self.to_string( value ) ) + def make_copy( self, value, target_context = None, source_context = None ): return copy.deepcopy( value ) @@ -480,6 +484,10 @@ def to_string( self, value ): return json.dumps( value ) + def to_safe_string( self, value ): + # We do not sanitize json dicts + return json.safe_dumps( value ) + class PythonObjectParameter( MetadataParameter ): @@ -510,6 +518,10 @@ return str( self.spec.no_value ) return value.file_name + def to_safe_string( self, value ): + # We do not sanitize file names + return self.to_string( value ) + def get_html_field( self, value=None, context=None, other_values=None, **kwd ): context = context or {} other_values = other_values or {} diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -17,7 +17,7 @@ from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.sniff import get_test_fname, get_headers from galaxy.datatypes.metadata import MetadataElement - +from galaxy.datatypes.util.image_util import check_image_type try: eggs.require( "bx-python" ) @@ -814,3 +814,34 @@ except: return False + +class RNADotPlotMatrix( data.Data ): + file_ext = "rna_eps" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = 'RNA Dot Plot format (Postscript derivative)' + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff(self, filename): + """Determine if the file is in RNA dot plot format.""" + if check_image_type( filename, ['EPS'] ): + seq = False + coor = False + pairs = False + with open( filename ) as handle: + for line in handle: + line = line.strip() + if line: + if line.startswith('/sequence'): + seq = True + elif line.startswith('/coor'): + coor = True + elif line.startswith('/pairs'): + pairs = True + if seq and coor and pairs: + return True + return False \ No newline at end of file diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/datatypes/util/image_util.py --- a/lib/galaxy/datatypes/util/image_util.py +++ b/lib/galaxy/datatypes/util/image_util.py @@ -71,6 +71,4 @@ return 'pbm' if format == 'PGM': return 'pgm' - if format == 'EPS': - return 'eps' return None diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1202,6 +1202,11 @@ out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + + # TODO: eliminate overlap with tools/evaluation.py + out_collections = dict( [ ( obj.name, obj.dataset_collection_instance ) for obj in job.output_dataset_collection_instances ] ) + out_collections.update( [ ( obj.name, obj.dataset_collection ) for obj in job.output_dataset_collections ] ) + input_ext = 'data' for _, data in inp_data.items(): # For loop odd, but sort simulating behavior in galaxy.tools.actions @@ -1218,6 +1223,12 @@ 'children': self.tool.collect_child_datasets(out_data, self.working_directory), 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext) } + self.tool.collect_dynamic_collections( + out_collections, + job_working_directory=self.working_directory, + inp_data=inp_data, + job=job, + ) param_dict.update({'__collected_datasets__': collected_datasets}) # Certain tools require tasks to be completed after job execution # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ). diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -216,7 +216,7 @@ job_tool = job_wrapper.tool for (joda, dataset) in self._walk_dataset_outputs( job ): if joda and job_tool: - hda_tool_output = job_tool.outputs.get( joda.name, None ) + hda_tool_output = job_tool.find_output_def( joda.name ) if hda_tool_output and hda_tool_output.from_work_dir: # Copy from working dir to HDA. # TODO: move instead of copy to save time? diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/managers/collections.py --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -28,6 +28,7 @@ Abstraction for interfacing with dataset collections instance - ideally abstarcts out model and plugin details. """ + ELEMENTS_UNINITIALIZED = object() def __init__( self, app ): self.type_registry = DatasetCollectionTypesRegistry( app ) @@ -72,7 +73,11 @@ for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]: dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) for output_dataset in implicit_collection_info.get( "outputs" ): - output_dataset.hidden_beneath_collection_instance = dataset_collection_instance + if isinstance( output_dataset, model.HistoryDatasetCollectionAssociation ): + dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) + else: + # dataset collection, don't need to do anything... + pass trans.sa_session.add( output_dataset ) dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ] @@ -92,6 +97,18 @@ return self.__persist( dataset_collection_instance ) + def create_dataset_collection( + self, + trans, + collection_type, + elements=None, + ): + return self.__create_dataset_collection( + trans=trans, + collection_type=collection_type, + elements=elements, + ) + def __create_dataset_collection( self, trans, @@ -113,9 +130,24 @@ elements = self.__load_elements( trans, element_identifiers ) # else if elements is set, it better be an ordered dict! + if elements is not self.ELEMENTS_UNINITIALIZED: + type_plugin = collection_type_description.rank_type_plugin() + dataset_collection = builder.build_collection( type_plugin, elements ) + else: + dataset_collection = model.DatasetCollection( populated=False ) + dataset_collection.collection_type = collection_type + return dataset_collection + + def set_collection_elements( self, dataset_collection, dataset_instances ): + if dataset_collection.populated: + raise Exception("Cannot reset elements of an already populated dataset collection.") + + collection_type = dataset_collection.collection_type + collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type ) type_plugin = collection_type_description.rank_type_plugin() - dataset_collection = builder.build_collection( type_plugin, elements ) - dataset_collection.collection_type = collection_type + builder.set_collection_elements( dataset_collection, type_plugin, dataset_instances ) + dataset_collection.mark_as_populated() + return dataset_collection def delete( self, trans, instance_type, id ): diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/managers/collections_util.py --- a/lib/galaxy/managers/collections_util.py +++ b/lib/galaxy/managers/collections_util.py @@ -77,7 +77,9 @@ # TODO: Work in progress - this end-point is not right yet... dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) if view == "element": - dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements ) + collection = dataset_colleciton_instance.collection + dict_value[ 'elements' ] = map( dictify_element, collection.elements ) + dict_value[ 'populated' ] = collection.populated security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this. return dict_value @@ -87,7 +89,9 @@ object_detials = element.element_object.to_dict() if element.child_collection: # Recursively yield elements for each nested collection... - object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements ) + child_collection = element.child_collection + object_detials[ "elements" ] = map( dictify_element, child_collection.elements ) + object_detials[ "populated" ] = child_collection.populated dictified[ "object" ] = object_detials return dictified diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -18,6 +18,7 @@ import socket import time import numbers +from datetime import datetime, timedelta from uuid import UUID, uuid4 from string import Template from itertools import ifilter @@ -31,7 +32,7 @@ import galaxy.model.orm.now from galaxy.security import get_permitted_actions from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail -from galaxy.util import ready_name_for_url +from galaxy.util import ready_name_for_url, unique_id from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.util.directory_hash import directory_hash_id @@ -261,6 +262,14 @@ environment = User.user_template_environment( user ) return Template( in_string ).safe_substitute( environment ) +class PasswordResetToken( object ): + def __init__( self, user, token=None): + if token: + self.token = token + else: + self.token = unique_id() + self.user = user + self.expiration_time = datetime.now() + timedelta(hours=24) class BaseJobMetric( object ): @@ -320,6 +329,7 @@ self.input_datasets = [] self.output_datasets = [] self.input_dataset_collections = [] + self.output_dataset_collection_instances = [] self.output_dataset_collections = [] self.input_library_datasets = [] self.output_library_datasets = [] @@ -463,8 +473,10 @@ self.output_datasets.append( JobToOutputDatasetAssociation( name, dataset ) ) def add_input_dataset_collection( self, name, dataset ): self.input_dataset_collections.append( JobToInputDatasetCollectionAssociation( name, dataset ) ) - def add_output_dataset_collection( self, name, dataset ): - self.output_dataset_collections.append( JobToOutputDatasetCollectionAssociation( name, dataset ) ) + def add_output_dataset_collection( self, name, dataset_collection_instance ): + self.output_dataset_collection_instances.append( JobToOutputDatasetCollectionAssociation( name, dataset_collection_instance ) ) + def add_implicit_output_dataset_collection( self, name, dataset_collection ): + self.output_dataset_collections.append( JobToImplicitOutputDatasetCollectionAssociation( name, dataset_collection ) ) def add_input_library_dataset( self, name, dataset ): self.input_library_datasets.append( JobToInputLibraryDatasetAssociation( name, dataset ) ) def add_output_library_dataset( self, name, dataset ): @@ -725,7 +737,18 @@ self.dataset = dataset +# Many jobs may map to one HistoryDatasetCollection using these for a given +# tool output (if mapping over an input collection). class JobToOutputDatasetCollectionAssociation( object ): + def __init__( self, name, dataset_collection_instance ): + self.name = name + self.dataset_collection_instance = dataset_collection_instance + + +# A DatasetCollection will be mapped to at most one job per tool output +# using these. (You can think of many of these models as going into the +# creation of a JobToOutputDatasetCollectionAssociation.) +class JobToImplicitOutputDatasetCollectionAssociation( object ): def __init__( self, name, dataset_collection ): self.name = name self.dataset_collection = dataset_collection @@ -2653,14 +2676,37 @@ """ dict_collection_visible_keys = ( 'id', 'collection_type' ) dict_element_visible_keys = ( 'id', 'collection_type' ) + populated_states = Bunch( + NEW='new', # New dataset collection, unpopulated elements + OK='ok', # Collection elements populated (HDAs may or may not have errors) + FAILED='failed', # some problem populating state, won't be populated + ) def __init__( self, id=None, collection_type=None, + populated=True, ): self.id = id self.collection_type = collection_type + if not populated: + self.populated_state = DatasetCollection.populated_states.NEW + + @property + def populated( self ): + return self.populated_state == DatasetCollection.populated_states.OK + + @property + def waiting_for_elements( self ): + return self.populated_state == DatasetCollection.populated_states.NEW + + def mark_as_populated( self ): + self.populated_state = DatasetCollection.populated_states.OK + + def handle_population_failed( self, message ): + self.populated_state = DatasetCollection.populated_states.FAILED + self.populated_state_message = message @property def dataset_instances( self ): diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -68,6 +68,11 @@ Column( "provider", TrimmedString( 255 ) ), ) +model.PasswordResetToken.table = Table("password_reset_token", metadata, + Column( "token", String( 32 ), primary_key=True, unique=True, index=True ), + Column( "expiration_time", DateTime ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) ) + model.History.table = Table( "history", metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -443,6 +448,12 @@ Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ), Column( "name", Unicode(255) ) ) +model.JobToImplicitOutputDatasetCollectionAssociation.table = Table( "job_to_implicit_output_dataset_collection", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "dataset_collection_id", Integer, ForeignKey( "dataset_collection.id" ), index=True ), + Column( "name", Unicode(255) ) ) + model.JobToOutputDatasetCollectionAssociation.table = Table( "job_to_output_dataset_collection", metadata, Column( "id", Integer, primary_key=True ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), @@ -610,6 +621,8 @@ model.DatasetCollection.table = Table( "dataset_collection", metadata, Column( "id", Integer, primary_key=True ), Column( "collection_type", Unicode(255), nullable=False ), + Column( "populated_state", TrimmedString( 64 ), default='ok', nullable=False ), + Column( "populated_state_message", TEXT ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), ) @@ -1564,6 +1577,10 @@ api_keys=relation( model.APIKeys, backref="user", order_by=desc( model.APIKeys.table.c.create_time ) ), ) ) +mapper( model.PasswordResetToken, model.PasswordResetToken.table, + properties=dict( user=relation( model.User, backref="reset_tokens") ) ) + + # Set up proxy so that this syntax is possible: # <user_obj>.preferences[pref_name] = pref_value model.User.preferences = association_proxy('_preferences', 'value', creator=model.UserPreference) @@ -1800,8 +1817,13 @@ mapper( model.JobToOutputDatasetCollectionAssociation, model.JobToOutputDatasetCollectionAssociation.table, properties=dict( + job=relation( model.Job ), dataset_collection_instance=relation( + model.HistoryDatasetCollectionAssociation, lazy=False, backref="output_dataset_collection_instances" ) ) ) + +mapper( model.JobToImplicitOutputDatasetCollectionAssociation, + model.JobToImplicitOutputDatasetCollectionAssociation.table, properties=dict( job=relation( model.Job ), dataset_collection=relation( - model.HistoryDatasetCollectionAssociation, lazy=False ) ) ) + model.DatasetCollection, backref="output_dataset_collections" ) ) ) mapper( model.JobToInputLibraryDatasetAssociation, model.JobToInputLibraryDatasetAssociation.table, properties=dict( @@ -1886,6 +1908,8 @@ parameters=relation( model.JobParameter, lazy=False ), input_datasets=relation( model.JobToInputDatasetAssociation ), output_datasets=relation( model.JobToOutputDatasetAssociation ), + output_dataset_collection_instances=relation( model.JobToOutputDatasetCollectionAssociation ), + output_dataset_collections=relation( model.JobToImplicitOutputDatasetCollectionAssociation ), post_job_actions=relation( model.PostJobActionAssociation, lazy=False ), input_library_datasets=relation( model.JobToInputLibraryDatasetAssociation ), output_library_datasets=relation( model.JobToOutputLibraryDatasetAssociation ), diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/model/migrate/versions/0126_password_reset.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0126_password_reset.py @@ -0,0 +1,43 @@ +""" +Migration script for the password reset table +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + +PasswordResetToken_table = Table("password_reset_token", metadata, + Column( "token", String( 32 ), primary_key=True, unique=True, index=True ), + Column( "expiration_time", DateTime ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )) + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + PasswordResetToken_table.create() + except Exception as e: + print str(e) + log.exception("Creating %s table failed: %s" % (PasswordResetToken_table.name, str( e ) ) ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + PasswordResetToken_table.drop() + except Exception as e: + print str(e) + log.exception("Dropping %s table failed: %s" % (PasswordResetToken_table.name, str( e ) ) ) diff -r 1ecb6aaebaf4247a7c71b77cb9a74f63dc937cff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py @@ -0,0 +1,85 @@ +""" +Migration script updating collections tables for output collections. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + +JobToImplicitOutputDatasetCollectionAssociation_table = Table( + "job_to_implicit_output_dataset_collection", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "dataset_collection_id", Integer, ForeignKey( "dataset_collection.id" ), index=True ), + Column( "name", Unicode(255) ) +) + + +TABLES = [ + JobToImplicitOutputDatasetCollectionAssociation_table, +] + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + for table in TABLES: + __create(table) + + try: + dataset_collection_table = Table( "dataset_collection", metadata, autoload=True ) + # need server_default because column in non-null + populated_state_column = Column( 'populated_state', TrimmedString( 64 ), default='ok', server_default="ok", nullable=False ) + populated_state_column.create( dataset_collection_table ) + + populated_message_column = Column( 'populated_state_message', TEXT, nullable=True ) + populated_message_column.create( dataset_collection_table ) + except Exception as e: + print str(e) + log.exception( "Creating dataset collection populated column failed." ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + + for table in TABLES: + __drop(table) + + try: + dataset_collection_table = Table( "dataset_collection", metadata, autoload=True ) + populated_state_column = dataset_collection_table.c.populated_state + populated_state_column.drop() + populated_message_column = dataset_collection_table.c.populated_state_message + populated_message_column.drop() + except Exception as e: + print str(e) + log.exception( "Dropping dataset collection populated_state/ column failed." ) + + +def __create(table): + try: + table.create() + except Exception as e: + print str(e) + log.exception("Creating %s table failed: %s" % (table.name, str( e ) ) ) + + +def __drop(table): + try: + table.drop() + except Exception as e: + print str(e) + log.exception("Dropping %s table failed: %s" % (table.name, str( e ) ) ) This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/4366bbe56e0a/ Changeset: 4366bbe56e0a Branch: compressed_upload User: BjoernGruening Date: 2015-01-16 22:38:41+00:00 Summary: add back RNADotPlotMatrix sniffing Affected #: 1 file diff -r 4a8a610a97e1762b8ae78280566a23c11676bce9 -r 4366bbe56e0a6c53f621cdf2ff049d65d5c7502a config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -307,6 +307,7 @@ <sniffer type="galaxy.datatypes.text:Arff"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/> + <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/> https://bitbucket.org/galaxy/galaxy-central/commits/9ef517d8e767/ Changeset: 9ef517d8e767 User: jmchilton Date: 2015-01-23 19:13:25+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/compressed_upload (pull request #630) Add CompressedArchive as datatype and do not uncomress it during upload. Affected #: 3 files diff -r a6855d0b02d70cd35ae312f48bd704590805ca15 -r 9ef517d8e767037e1633f6063c6edb3023f86499 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -141,6 +141,8 @@ <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/><datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/><datatype extension="rna_eps" type="galaxy.datatypes.sequence:RNADotPlotMatrix" mimetype="image/eps" display_in_upload="True"/> + <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/><datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/><datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/> diff -r a6855d0b02d70cd35ae312f48bd704590805ca15 -r 9ef517d8e767037e1633f6063c6edb3023f86499 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -106,6 +106,30 @@ Binary.register_unsniffable_binary_ext("ab1") +class CompressedArchive( Binary ): + """ + Class describing an compressed binary file + This class can be sublass'ed to implement archive filetypes that will not be unpacked by upload.py. + """ + file_ext = "compressed_archive" + compressed = True + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = "Compressed binary file" + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "Compressed binary file (%s)" % ( data.nice_size( dataset.get_size() ) ) + +Binary.register_unsniffable_binary_ext("compressed_archive") + class GenericAsn1Binary( Binary ): """Class for generic ASN.1 binary format""" diff -r a6855d0b02d70cd35ae312f48bd704590805ca15 -r 9ef517d8e767037e1633f6063c6edb3023f86499 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -120,171 +120,176 @@ data_type = type_info[0] ext = type_info[1] if not data_type: - # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress - is_gzipped, is_valid = check_gzip( dataset.path ) - if is_gzipped and not is_valid: - file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) - return - elif is_gzipped and is_valid: - if link_data_only == 'copy_files': - # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) - while 1: - try: - chunk = gzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing gzipped data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - gzipped_file.close() - # Replace the gzipped file with the decompressed file if it's safe to do so - if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: - dataset.path = uncompressed - else: - shutil.move( uncompressed, dataset.path ) - os.chmod(dataset.path, 0644) - dataset.name = dataset.name.rstrip( '.gz' ) - data_type = 'gzip' - if not data_type and bz2 is not None: - # See if we have a bz2 file, much like gzip - is_bzipped, is_valid = check_bz2( dataset.path ) - if is_bzipped and not is_valid: + root_datatype = registry.get_datatype_by_extension( dataset.file_type ) + if getattr( root_datatype, 'compressed', False ): + data_type = 'compressed archive' + ext = dataset.file_type + else: + # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress + is_gzipped, is_valid = check_gzip( dataset.path ) + if is_gzipped and not is_valid: file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return - elif is_bzipped and is_valid: + elif is_gzipped and is_valid: if link_data_only == 'copy_files': - # We need to uncompress the temp_name file + # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) while 1: try: - chunk = bzipped_file.read( CHUNK_SIZE ) + chunk = gzipped_file.read( CHUNK_SIZE ) except IOError: os.close( fd ) os.remove( uncompressed ) - file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + file_err( 'Problem decompressing gzipped data', dataset, json_file ) return if not chunk: break os.write( fd, chunk ) os.close( fd ) - bzipped_file.close() - # Replace the bzipped file with the decompressed file if it's safe to do so + gzipped_file.close() + # Replace the gzipped file with the decompressed file if it's safe to do so if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) os.chmod(dataset.path, 0644) - dataset.name = dataset.name.rstrip( '.bz2' ) - data_type = 'bz2' - if not data_type: - # See if we have a zip archive - is_zipped = check_zip( dataset.path ) - if is_zipped: - if link_data_only == 'copy_files': - CHUNK_SIZE = 2**20 # 1Mb - uncompressed = None - uncompressed_name = None - unzipped = False - z = zipfile.ZipFile( dataset.path ) - for name in z.namelist(): - if name.endswith('/'): - continue - if unzipped: - stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' - break - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) - if sys.version_info[:2] >= ( 2, 6 ): - zipped_file = z.open( name ) - while 1: + dataset.name = dataset.name.rstrip( '.gz' ) + data_type = 'gzip' + if not data_type and bz2 is not None: + # See if we have a bz2 file, much like gzip + is_bzipped, is_valid = check_bz2( dataset.path ) + if is_bzipped and not is_valid: + file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) + return + elif is_bzipped and is_valid: + if link_data_only == 'copy_files': + # We need to uncompress the temp_name file + CHUNK_SIZE = 2**20 # 1Mb + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) + while 1: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + # Replace the bzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) + dataset.name = dataset.name.rstrip( '.bz2' ) + data_type = 'bz2' + if not data_type: + # See if we have a zip archive + is_zipped = check_zip( dataset.path ) + if is_zipped: + if link_data_only == 'copy_files': + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None + unzipped = False + z = zipfile.ZipFile( dataset.path ) + for name in z.namelist(): + if name.endswith('/'): + continue + if unzipped: + stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' + break + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + if sys.version_info[:2] >= ( 2, 6 ): + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + else: + # python < 2.5 doesn't have a way to read members in chunks(!) try: - chunk = zipped_file.read( CHUNK_SIZE ) + outfile = open( uncompressed, 'wb' ) + outfile.write( z.read( name ) ) + outfile.close() + uncompressed_name = name + unzipped = True except IOError: os.close( fd ) os.remove( uncompressed ) file_err( 'Problem decompressing zipped data', dataset, json_file ) return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - zipped_file.close() - uncompressed_name = name - unzipped = True + z.close() + # Replace the zipped file with the decompressed file if it's safe to do so + if uncompressed is not None: + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) + dataset.name = uncompressed_name + data_type = 'zip' + if not data_type: + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): + # We have a binary dataset, but it is not Bam, Sff or Pdf + data_type = 'binary' + #binary_ok = False + parts = dataset.name.split( "." ) + if len( parts ) > 1: + ext = parts[-1].strip().lower() + if not Binary.is_ext_unsniffable(ext): + file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) + return + elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: + err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) + file_err( err_msg, dataset, json_file ) + return + if not data_type: + # We must have a text file + if check_html( dataset.path ): + file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) + return + if data_type != 'binary': + if link_data_only == 'copy_files': + if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: + in_place = False + # Convert universal line endings to Posix line endings, but allow the user to turn it off, + # so that is becomes possible to upload gzip, bz2 or zip files with binary data without + # corrupting the content of those files. + if dataset.to_posix_lines: + tmpdir = output_adjacent_tmpdir( output_path ) + tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id + if dataset.space_to_tab: + line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) else: - # python < 2.5 doesn't have a way to read members in chunks(!) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - uncompressed_name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return - z.close() - # Replace the zipped file with the decompressed file if it's safe to do so - if uncompressed is not None: - if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: - dataset.path = uncompressed - else: - shutil.move( uncompressed, dataset.path ) - os.chmod(dataset.path, 0644) - dataset.name = uncompressed_name - data_type = 'zip' - if not data_type: - # TODO refactor this logic. check_binary isn't guaranteed to be - # correct since it only looks at whether the first 100 chars are - # printable or not. If someone specifies a known unsniffable - # binary datatype and check_binary fails, the file gets mangled. - if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): - # We have a binary dataset, but it is not Bam, Sff or Pdf - data_type = 'binary' - #binary_ok = False - parts = dataset.name.split( "." ) - if len( parts ) > 1: - ext = parts[-1].strip().lower() - if not Binary.is_ext_unsniffable(ext): - file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) - return - elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext: - err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) - file_err( err_msg, dataset, json_file ) - return - if not data_type: - # We must have a text file - if check_html( dataset.path ): - file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) - return - if data_type != 'binary': - if link_data_only == 'copy_files': - if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: - in_place = False - # Convert universal line endings to Posix line endings, but allow the user to turn it off, - # so that is becomes possible to upload gzip, bz2 or zip files with binary data without - # corrupting the content of those files. - if dataset.to_posix_lines: - tmpdir = output_adjacent_tmpdir( output_path ) - tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id - if dataset.space_to_tab: - line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) - else: - line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) - if dataset.file_type == 'auto': - ext = sniff.guess_ext( dataset.path, registry.sniff_order ) - else: - ext = dataset.file_type - data_type = ext + line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix ) + if dataset.file_type == 'auto': + ext = sniff.guess_ext( dataset.path, registry.sniff_order ) + else: + ext = dataset.file_type + data_type = ext # Save job info for the framework if ext == 'auto' and dataset.ext: ext = dataset.ext Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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