- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2894: Fix setting the peek when a line is already un...
by Greg Von Kuster 28 Oct '09

28 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ea29f33390d3 changeset: 2894:ea29f33390d3 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Oct 20 10:39:30 2009 -0400 description: Fix setting the peek when a line is already unicode (when does this happen?) 1 file(s) affected in this change: lib/galaxy/datatypes/data.py diffs (15 lines): diff -r 55d479c8d592 -r ea29f33390d3 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Oct 19 12:05:19 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Oct 20 10:39:30 2009 -0400 @@ -136,7 +136,10 @@ line = line.strip() if not line: continue - out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) + if type( line ) is unicode: + out.append( '<tr><td>%s</td></tr>' % escape( line ) ) + else: + out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc:

1 0

[hg] galaxy 2895: Show encoded URL, while still allowing unencod...
by Greg Von Kuster 28 Oct '09

28 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/61684a4d6b9e changeset: 2895:61684a4d6b9e user: Kanwei Li <kanwei(a)gmail.com> date: Tue Oct 20 15:34:47 2009 -0400 description: Show encoded URL, while still allowing unencoded ids for backward compatibility. Revert to "display" displaying whole file. 6 file(s) affected in this change: lib/galaxy/web/buildapp.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py templates/dataset/large_file.mako templates/root/history_common.mako test/base/twilltestcase.py diffs (213 lines): diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/buildapp.py Tue Oct 20 15:34:47 2009 -0400 @@ -77,7 +77,7 @@ webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) - webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) + webapp.add_route( '/datasets/:encoded_id/:action/:filename', controller='dataset', action='index', encoded_id=None, filename=None) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Oct 20 15:34:47 2009 -0400 @@ -199,8 +199,14 @@ return 'This link may not be followed from within Galaxy.' @web.expose - def display(self, trans, dataset_id=None, filename=None, show_all=False, **kwd): + def display(self, trans, encoded_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" + + # DEPRECATION: We still support unencoded ids for backward compatibility + try: + dataset_id = int( encoded_id ) + except ValueError: + dataset_id = trans.security.decode_id( encoded_id ) data = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) @@ -208,30 +214,47 @@ if trans.app.security_agent.can_access_dataset( roles, data.dataset ): if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - if filename is None or filename.lower() == "index": - file_path = data.file_name - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - - else: + + if filename and filename != "index": file_path = os.path.join( data.extra_files_path, filename ) - mime, encoding = mimetypes.guess_type( file_path ) - if mime is None: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) - trans.response.set_content_type( mime ) + if os.path.exists( file_path ): + mime, encoding = mimetypes.guess_type( file_path ) + if not mime: + try: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) + except: + mime = "txt" - if os.path.exists( file_path ): - max_peek_size = 1000000 # 1 MB - if show_all or os.stat( file_path ).st_size < max_peek_size: + trans.response.set_content_type( mime ) return open( file_path ) else: + return "Could not find '%s' on the extra files path." % filename + + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + trans.response.set_content_type(mime) + trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) + + if to_ext: # Saving the file + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) + if to_ext[0] != ".": + to_ext = "." + to_ext + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = data.name + fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext) + return open( data.file_name ) + + if os.path.exists( data.file_name ): + max_peek_size = 1000000 # 1 MB + if preview and os.stat( data.file_name ).st_size > max_peek_size: trans.response.set_content_type( "text/html" ) - return trans.fill_template( "/dataset/large_file.mako", - truncated_data = open( file_path ).read(max_peek_size), + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( data.file_name ).read(max_peek_size), data = data ) + else: + return open( data.file_name ) else: - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % ( filename ) ) + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) else: return trans.show_error_message( "You are not allowed to access this dataset" ) diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue Oct 20 15:34:47 2009 -0400 @@ -139,49 +139,13 @@ @web.expose def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): """ - Returns data directly into the browser. - Sets the mime-type according to the extension + Backward compatibility. """ - if hid is not None: - try: - hid = int( hid ) - except: - return "hid '%s' is invalid" %str( hid ) - history = trans.get_history() - for dataset in history.datasets: - if dataset.hid == hid: - data = dataset - break - else: - raise Exception( "No dataset with hid '%d'" % hid ) + if tofile: + to_ext = toext else: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) - except: - return "Dataset id '%s' is invalid" %str( id ) - if data: - user, roles = trans.get_user_and_roles() - if trans.app.security_agent.can_access_dataset( roles, data.dataset ): - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - if tofile: - fStat = os.stat(data.file_name) - trans.response.headers['Content-Length'] = int(fStat.st_size) - if toext[0:1] != ".": - toext = "." + toext - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) - trans.log_event( "Display dataset id: %s" % str(id) ) - try: - return open( data.file_name ) - except: - return "This dataset contains no content" - else: - return "You are not allowed to access this dataset" - else: - return "No dataset with id '%s'" % str( id ) + to_ext = None + return trans.webapp.controllers['dataset'].display( trans, encoded_id=id, to_ext=to_ext ) @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"): diff -r ea29f33390d3 -r 61684a4d6b9e templates/dataset/large_file.mako --- a/templates/dataset/large_file.mako Tue Oct 20 10:39:30 2009 -0400 +++ b/templates/dataset/large_file.mako Tue Oct 20 15:34:47 2009 -0400 @@ -2,8 +2,8 @@ <div class="warningmessagelarge"> This dataset is large and only the first megabyte is shown below.<br /> - <a href="${h.url_for( controller='dataset', action='display', dataset_id=data.id, show_all=True )}">Show all</a> | - <a href="${h.url_for( controller='root', action='display', id=data.id, tofile='yes', toext=data.ext )}">Save</a> + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), filename='' )}">Show all</a> | + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">Save</a> </div> <pre> diff -r ea29f33390d3 -r 61684a4d6b9e templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Oct 20 10:39:30 2009 -0400 +++ b/templates/root/history_common.mako Tue Oct 20 15:34:47 2009 -0400 @@ -33,7 +33,7 @@ <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> %endif %else: - <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"></a> + <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), preview=True, filename='' )}" target="galaxy_main"></a> %if user_owns_dataset: <a class="icon-button edit" title="edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> %endif @@ -87,7 +87,7 @@ <div class="info">${_('Info: ')}${data.display_info()}</div> <div> %if data.has_data: - <a href="${h.url_for( controller='root', action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">save</a> %if user_owns_dataset: | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> %endif diff -r ea29f33390d3 -r 61684a4d6b9e test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Oct 20 10:39:30 2009 -0400 +++ b/test/base/twilltestcase.py Tue Oct 20 15:34:47 2009 -0400 @@ -419,9 +419,9 @@ self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, hda_id ) ) if check_str: self.check_page_for_string( check_str ) - def display_history_item( self, id, check_str='' ): + def display_history_item( self, hda_id, check_str='' ): """Displays a history item - simulates eye icon click""" - self.visit_url( '%s/datasets/%s/display/index' % ( self.url, id ) ) + self.visit_url( '%s/datasets/%s/display/' % ( self.url, self.security.encode_id( hda_id ) ) ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -554,7 +554,7 @@ def verify_composite_datatype_file_content( self, file_name, hda_id ): local_name = self.get_filename( file_name ) temp_name = self.get_filename( 'temp_%s' % file_name ) - self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, hda_id, file_name ) ) + self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, self.security.encode_id( hda_id ), file_name ) ) data = self.last_page() file( temp_name, 'wb' ).write( data ) try:

1 0

Re: [galaxy-dev] Error in my functional test
by Vipin TS 26 Oct '09

26 Oct '09

Hi Nate, I tried to run the tool with a small input file. Then that case also the test fails and returns the same error message. FAIL: mGenePredict ( mgenepredict ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 114, in test_tool self.do_it() File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 54, in do_it self.verify_dataset_correctness( file ) File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 323, in verify_dataset_correctness if wait: self.wait() #wait for job to finish File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 617, in wait self.assertNotEqual(count, maxiter) AssertionError: 20 == 20 Also I can find that the job is not finished even though I got the fail message. I confirmed the same, when I run the test again it produces an error message stating that the Galaxy port is already in use. I hope my assumption is true, if not please let me know. Many thanks, Vipin T S

2 3

Error in my functional test
by Vipin Thankam Sreedharan 23 Oct '09

23 Oct '09

Hi all, I wrote a functional test for my tool. Here is the test code. <tests> <test> <param name="source" value="history" /> <param name="fasta_input" value="tair9_chr4_10000.fas" ftype="fasta" /> <param name="source" value="pretrained" /> <param name="organism" value="arabidopsis" /> <output name="output" file="tair9_chr4_output.gff3" /> </test> </tests> While running the test I am getting an error message like the following. ERROR: test module functional in /home/galaxy/galaxy-2.1.2009/test ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/suite.py", line 46, in run self.setUp() File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/suite.py", line 200, in setUp try_run(self.module, names) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/util.py", line 200, in try_run return func() File "/home/galaxy/galaxy-2.1.2009/test/functional/__init__.py", line 88, in setup server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1257, in serve threadpool_options=threadpool_options) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1107, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1087, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.5/SocketServer.py", line 330, in __init__ self.server_bind() File "/usr/lib/python2.5/BaseHTTPServer.py", line 101, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind error: (98, 'Address already in use') ************************************************************ It will be great if you can give me a suggestion. Thanks in advance, Vipin T S

4 6

[hg] galaxy 2892: Fixed a form definition editing bug
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2f249afc66ea changeset: 2892:2f249afc66ea user: rc date: Mon Oct 19 09:53:04 2009 -0400 description: Fixed a form definition editing bug 3 file(s) affected in this change: lib/galaxy/web/controllers/forms.py templates/admin/forms/manage_forms.mako templates/admin/forms/show_form_read_only.mako diffs (69 lines): diff -r 38bbf36f70e8 -r 2f249afc66ea lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Sun Oct 18 18:19:12 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon Oct 19 09:53:04 2009 -0400 @@ -313,10 +313,10 @@ ctr=0 sb_options = [] while True: - option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) - ctr = ctr+1 - if option: + if kwd.has_key( 'field_'+str(index)+'_option_'+str(ctr) ): + option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None ) sb_options.append(util.restore_text(option)) + ctr = ctr+1 else: return sb_options def __get_saved_form(self, fd): @@ -342,8 +342,8 @@ layout = [] index = 0 while True: - grid_name = util.restore_text( params.get( 'grid_layout%i' % index, '' ) ) - if grid_name: + if kwd.has_key( 'grid_layout%i' % index ): + grid_name = util.restore_text( params.get( 'grid_layout%i' % index, '' ) ) layout.append( grid_name ) index = index + 1 else: @@ -355,7 +355,7 @@ # get the user entered fields index = 0 while True: - if params.get( 'field_name_%i' % index, False ): + if kwd.has_key( 'field_name_%i' % index ): fields.append( self.__get_field( index, **kwd ) ) index = index + 1 else: diff -r 38bbf36f70e8 -r 2f249afc66ea templates/admin/forms/manage_forms.mako --- a/templates/admin/forms/manage_forms.mako Sun Oct 18 18:19:12 2009 -0400 +++ b/templates/admin/forms/manage_forms.mako Mon Oct 19 09:53:04 2009 -0400 @@ -23,7 +23,7 @@ </div> %else: <div popupmenu="form-${form.id}-popup"> - <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit form definition</a> + <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a> <a class="action-button" confirm="Click OK to delete the form ${form.name}." href="${h.url_for( action='delete', form_id=form.id )}">Delete</a> </div> %endif diff -r 38bbf36f70e8 -r 2f249afc66ea templates/admin/forms/show_form_read_only.mako --- a/templates/admin/forms/show_form_read_only.mako Sun Oct 18 18:19:12 2009 -0400 +++ b/templates/admin/forms/show_form_read_only.mako Mon Oct 19 09:53:04 2009 -0400 @@ -63,14 +63,14 @@ <div class="toolForm"> %if form.desc: - <div class="toolFormTitle">${form.name} - <i>${form.desc}</i> + <div class="toolFormTitle">${form.name} - <i> ${form.desc}</i> (${form.type}) <a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="form-${form.id}-popup"> <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a> </div> </div> %else: - <div class="toolFormTitle">${form.name} + <div class="toolFormTitle">${form.name} (${form.type}) <a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="form-${form.id}-popup"> <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a>

1 0

[hg] galaxy 2893: removed bogus unit tests from new gg/gff
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/55d479c8d592 changeset: 2893:55d479c8d592 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Mon Oct 19 12:05:19 2009 -0400 description: removed bogus unit tests from new gg/gff 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (55 lines): diff -r 2f249afc66ea -r 55d479c8d592 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Oct 19 09:53:04 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Oct 19 12:05:19 2009 -0400 @@ -28,26 +28,6 @@ gal_Log = logging.getLogger(__name__) verbose = False - - -""" -Want to make some wig tracks from each analysis -Best n -log10(p). Make top hit the window. - - -from ucsc wig docs -ll options are placed in a single line separated by spaces: - - track type=wiggle_0 name=track_label description=center_label \ - visibility=display_mode color=r,g,b altColor=r,g,b \ - priority=priority autoScale=on|off \ - gridDefault=on|off maxHeightPixels=max:default:min \ - graphType=bar|points viewLimits=lower:upper \ - yLineMark=real-value yLineOnOff=on|off \ - windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16 - -The track type with version is REQUIRED, and it currently must be wiggle_0: -""" class GenomeGraphs(Interval): @@ -131,7 +111,7 @@ else: # We've spanned a chromosome break - if i > 10: + if i > 10: # span 10 features break except: seqid, start, stop = ( '', '', '' ) @@ -189,15 +169,6 @@ Determines whether the file is in gff format GFF lines have nine required fields that must be tab-separated. - - For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format3 - - >>> fname = get_test_fname( 'gff_version_3.gff' ) - >>> Gff().sniff( fname ) - False - >>> fname = get_test_fname( 'test.gff' ) - >>> Gff().sniff( fname ) - True """ f = open(filename,'r') headers = f.readline().split

1 0

[hg] galaxy 2891: Remove Genome Graphs and replace with topTable...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/38bbf36f70e8 changeset: 2891:38bbf36f70e8 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Sun Oct 18 18:19:12 2009 -0400 description: Remove Genome Graphs and replace with topTable (eg 1000 best p values) as a ucsc compatible gff 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (321 lines): diff -r 16a0c13c94cc -r 38bbf36f70e8 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Fri Oct 16 15:54:43 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Sun Oct 18 18:19:12 2009 -0400 @@ -16,126 +16,222 @@ import data from galaxy import util from cgi import escape -import urllib +import urllib, binascii from galaxy.web import url_for from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.data import Text from galaxy.datatypes.tabular import Tabular from galaxy.datatypes.images import Html +from galaxy.datatypes.interval import Interval +from galaxy.util.hash_util import * gal_Log = logging.getLogger(__name__) verbose = False -class GenomeGraphs( Tabular ): - """Tab delimited data containing a marker id and any number of numeric values""" + +""" +Want to make some wig tracks from each analysis +Best n -log10(p). Make top hit the window. + + +from ucsc wig docs +ll options are placed in a single line separated by spaces: + + track type=wiggle_0 name=track_label description=center_label \ + visibility=display_mode color=r,g,b altColor=r,g,b \ + priority=priority autoScale=on|off \ + gridDefault=on|off maxHeightPixels=max:default:min \ + graphType=bar|points viewLimits=lower:upper \ + yLineMark=real-value yLineOnOff=on|off \ + windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16 + +The track type with version is REQUIRED, and it currently must be wiggle_0: +""" + +class GenomeGraphs(Interval): + + """gg version viewable at ucsc of Gff format""" + file_ext = "gg" + column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] """Add metadata elements""" - MetadataElement( name="markerCol", default=1, desc="Marker ID column", param=metadata.ColumnParameter ) - MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) - MetadataElement( name="column_types", default=[], desc="Column types", readonly=True, visible=False ) - file_ext = 'gg' + MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="column_types", default=['str','str','str','int','int','int','str','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) + MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) + MetadataElement( name="startCol", default=4, desc="Start column", param=metadata.ColumnParameter ) + MetadataElement( name="endCol", default=5, desc="End column", param=metadata.ColumnParameter ) + MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) + ###do we need to repeat these? they are the same as should be inherited from interval type + + def __init__(self, **kwd): + """Initialize datatype, by adding GBrowse display app""" + Interval.__init__(self, **kwd) + self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) - def __init__(self, **kwd): - """Initialize gg datatype, by adding UCSC display apps""" - Tabular.__init__(self, **kwd) - self.add_display_app ( 'ucsc', 'Genome Graph', 'as_ucsc_display_file', 'ucsc_links' ) - - def set_peek( self, dataset ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name ) - dataset.blurb = util.commaify( str( data.get_line_count( dataset.file_name ) ) ) + " rows" - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' + def as_ucsc_display_file( self, dataset, **kwd ): + return open( dataset.file_name ) - def get_mime(self): - """Returns the mime type of the datatype""" - return 'application/vnd.msexcel' + def set_meta( self, dataset, overwrite = True, **kwd ): + i = 0 + for i, line in enumerate( file ( dataset.file_name ) ): + line = line.rstrip('\r\n') + if line and not line.startswith( '#' ): + elems = line.split( '\t' ) + if len(elems) == 9: + try: + int( elems[3] ) + int( elems[4] ) + break + except: + pass + Interval.set_meta( self, dataset, overwrite = overwrite, skip = i ) + + def make_html_table( self, dataset, skipchars=[] ): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">'] + comments = [] + try: + # Generate column header + out.append( '<tr>' ) + for i, name in enumerate( self.column_names ): + out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( '</table>' ) + out = "".join( out ) + except Exception, exc: + out = "Can't create peek %s" % exc + return out def get_estimated_display_viewport( self, dataset ): - """Return a chrom, start, stop tuple for viewing a file.""" - raise notImplemented - - def as_ucsc_display_file( self, dataset, **kwd ): - """Returns file""" - return file(dataset.file_name,'r') - + """ + Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 + formats. This function should correctly handle both... + """ + if True or (dataset.has_data() and dataset.state == dataset.states.OK): + try: + seqid = '' + start = 2147483647 # Maximum value of a signed 32 bit integer ( 2**31 - 1 ) + stop = 0 + for i, line in enumerate( file( dataset.file_name ) ): + if i == 0: # track stuff there + continue + line = line.rstrip( '\r\n' ) + if not line: + continue + if not line.startswith( '#' ): + elems = line.split( '\t' ) + if not seqid: + # We can only set the viewport for a single chromosome + seqid = elems[0] + if seqid == elems[0]: + # Make sure we have not spanned chromosomes + start = min( start, int( elems[3] ) ) + stop = max( stop, int( elems[4] ) ) + else: + # We've spanned a chromosome + break + if i > 10: + break + except: + seqid, start, stop = ( '', '', '' ) + return ( seqid, str( start ), str( stop ) ) + else: + return ( '', '', '' ) + + def gbrowse_links( self, dataset, type, app, base_url ): + ret_val = [] + if dataset.has_data: + viewport_tuple = self.get_estimated_display_viewport( dataset ) + seqid = viewport_tuple[0] + start = viewport_tuple[1] + stop = viewport_tuple[2] + if seqid and start and stop: + for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): + if site_name in app.config.gbrowse_display_sites: + link = "%s?start=%s&stop=%s&ref=%s&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey ) + ret_val.append( ( site_name, link ) ) + return ret_val + def ucsc_links( self, dataset, type, app, base_url ): - """ from the ever-helpful angie hinrichs angie(a)soe.ucsc.edu - a genome graphs call looks like this - http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGe… - &hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess - &hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals= - &hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index - &hgGenome_doSubmitUpload=submit - Galaxy gives this for an interval file - http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.cu… - http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc - """ ret_val = [] - ggtail = '&hgGenome_doSubmitUpload=submit' - if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! - ret_val = [] - ggtail = '&hgGenome_doSubmitUpload=submit' - if not dataset.dbkey: - dataset.dbkey = 'hg18' # punt! - if dataset.has_data: - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): + if dataset.has_data: + viewport_tuple = self.get_estimated_display_viewport(dataset) + if viewport_tuple: + chrom = viewport_tuple[0] + start = viewport_tuple[1] + stop = viewport_tuple[2] + if start == '' or int(start) < 1: + start='1' + if stop == '' or int(stop) <= start: + stop = '%d' % (int(start) + 10000) + for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: - site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) - sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] - sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) - sl.append("&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess") - sl.append("&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=") - s = urllib.quote_plus( ''.join(sl) ) - link = "%s%s%s" % (s, display_url, ggtail ) + # HACK: UCSC doesn't support https, so force http even + # if our URL scheme is https. Making this work + # requires additional hackery in your upstream proxy. + # If UCSC ever supports https, remove this hack. + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) + else: + gal_Log.debug('@@@ gg ucsc_links - no viewport_tuple') return ret_val - def validate( self, dataset ): - """Validate a gg file - all numeric after header row""" - errors = list() - infile = open(dataset.file_name, "r") - for i,row in enumerate(infile): #drop header - badvals = [] - if i > 0: - ll = row.strip().split('\t') - for j,x in enumerate(ll): - try: - x = float(x) - except: - badval.append('col%d:%s' % (j+1,x)) - if len(badvals) > 0: - errors.append('row %d, %s' % (' '.join(badvals))) - return errors + def sniff( self, filename ): + """ + Determines whether the file is in gff format - def repair_methods( self, dataset ): - """Return options for removing errors along with a description""" - return [("lines","Remove erroneous lines")] + GFF lines have nine required fields that must be tab-separated. + + For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format3 + + >>> fname = get_test_fname( 'gff_version_3.gff' ) + >>> Gff().sniff( fname ) + False + >>> fname = get_test_fname( 'test.gff' ) + >>> Gff().sniff( fname ) + True + """ + f = open(filename,'r') + headers = f.readline().split + if headers[0].lower() == 'track': + headers = f.readline.split() + #headers = get_headers( filename, '\t' ) + try: + if len(headers) < 2: + return False + for hdr in headers: + if hdr and hdr[0].startswith( '##gff-version' ) and hdr[0].find( '2' ) < 0: + return False + if hdr and hdr[0] and not hdr[0].startswith( '#' ): + if len(hdr) != 9: + return False + try: + int( hdr[3] ) + int( hdr[4] ) + except: + return False + if hdr[5] != '.': + try: + score = int(hdr[5]) + except: + return False + if (score < 0 or score > 1000): + return False + if hdr[6] not in data.valid_strand: + return False + return True + except: + return False + - def sniff(self,filename): - """ - """ - infile = open(dataset.file_name, "r") - header= infile.next() # header - badvals = [] - for i,row in enumerate(infile[:10]): # sample first 10 rows - ll = row.strip().split('\t') - for j,x in enumerate(ll[1:]): # ignore first identifier col - try: - x = float(x) - except: - badval.append('col%d:%s' % (j+1,x)) - if len(badvals) > 0: - return False - else: - return True class rgTabList(Tabular): """ for sampleid and for featureid lists of exclusions or inclusions in the clean tool

1 0

[hg] galaxy 2888: moved the rgGRR svg scripts to static/scripts/...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e945dcdfd578 changeset: 2888:e945dcdfd578 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Thu Oct 15 19:01:07 2009 -0400 description: moved the rgGRR svg scripts to static/scripts/tools/rgenetics and decreased chattiness in genetics.py 8 file(s) affected in this change: lib/galaxy/datatypes/genetics.py scripts/check_eggs.py static/scripts/checkbox_and_radiobutton.js static/scripts/helper_functions.js static/scripts/timer.js static/scripts/tools/rgenetics/checkbox_and_radiobutton.js static/scripts/tools/rgenetics/helper_functions.js static/scripts/tools/rgenetics/timer.js diffs (1353 lines): diff -r cbe28b41fb9d -r e945dcdfd578 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Thu Oct 15 10:48:38 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Oct 15 19:01:07 2009 -0400 @@ -25,6 +25,7 @@ from galaxy.datatypes.images import Html gal_Log = logging.getLogger(__name__) +verbose = False class GenomeGraphs( Tabular ): """Tab delimited data containing a marker id and any number of numeric values""" @@ -247,7 +248,8 @@ head,rest = os.path.split(old) newpath = os.path.join(head,newbase) newpath = '%s%s' % (newpath,e) - shutil.move(oldpath,newpath) + if oldpath <> newpath: + shutil.move(oldpath,newpath) return newpath bn = dataset.metadata.base_name efp = dataset.extra_files_path @@ -266,20 +268,32 @@ def set_meta( self, dataset, **kwd ): - """ - NOTE we apply the tabular machinary to the phenodata extracted - from a BioC eSet or affybatch. + """for lped/pbed eg """ + if kwd.get('overwrite') == False: + if verbose: + gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False') + return True try: - flist = os.listdir(dataset.extra_files_path) - except: - gal_Log.debug('@@@rgenetics set_meta failed - no dataset?') - return + efp = dataset.extra_files_path + except: + if verbose: + gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) + return False + try: + flist = os.listdir(efp) + except: + if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) + return False + if len(flist) == 0: + if verbose: + gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) + return False bn = None for f in flist: - n = os.path.splitext(f)[0] - if not bn: + n,e = os.path.splitext(f)[0] + if (not bn) and e in ('.ped','.map','.bim','.fam'): bn = n dataset.metadata.base_name = bn if not bn: @@ -607,8 +621,9 @@ try: flist = os.listdir(dataset.extra_files_path) except: - gal_Log.debug('@@@rexpression set_meta failed - no dataset?') - return + if verbose: + gal_Log.debug('@@@rexpression set_meta failed - no dataset?') + return False bn = None for f in flist: n = os.path.splitext(f)[0] diff -r cbe28b41fb9d -r e945dcdfd578 scripts/check_eggs.py --- a/scripts/check_eggs.py Thu Oct 15 10:48:38 2009 -0400 +++ b/scripts/check_eggs.py Thu Oct 15 19:01:07 2009 -0400 @@ -1,3 +1,4 @@ +#! /usr/bin/python """ usage: check_eggs.py """ diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/checkbox_and_radiobutton.js --- a/static/scripts/checkbox_and_radiobutton.js Thu Oct 15 10:48:38 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,347 +0,0 @@ -/* -Scripts to create interactive checkboxes and radio buttons in SVG using ECMA script -Copyright (C) <2007> <Andreas Neumann> -Version 1.1.3, 2007-08-09 -neumann(a)karto.baug.ethz.ch -http://www.carto.net/ -http://www.carto.net/neumann/ - -Credits: -* Guy Morton for providing a fix to let users toggle checkboxes by clicking on text labels -* Bruce Rindahl for providing the bugfix described in version 1.1.2 -* Simon Shutter for providing a fix for the ASV in IE crash when reloading the SVG file after calling the .remove() method on a checkbox - ----- - -Documentation: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ - ----- - -current version: 1.1.3 - -version history: -1.0 (2006-03-13) -initial version - -1.1 (2006-07-11) -text labels are now clickable (thanks to Guy Morton) -added method .moveTo() to move checkbox to a different location -introduced new constructor parameter labelYOffset to allow more flexible placement of the text label - -1.1.1 (2007-02-06) -added cursor pointer to the text label and use element representing the checkBox - -1.1.2 (2007-04-19) -bug fix: this.selectedIndex was not correctly initialized in method addCheckBox of the radioButtonGroup object - -1.1.3 (2007-08-09) -bug fix: the method .remove() was slightly modified (using removeEventListener) for avoiding a crash related to the method after reloading the SVG file - -------- - - -This ECMA script library is free software; you can redistribute it and/or -modify it under the terms of the GNU Lesser General Public -License as published by the Free Software Foundation; either -version 2.1 of the License, or (at your option) any later version. - -This library is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -Lesser General Public License for more details. - -You should have received a copy of the GNU Lesser General Public -License along with this library (lesser_gpl.txt); if not, write to the Free Software -Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - ----- - -original document site: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ -Please contact the author in case you want to use code or ideas commercially. -If you use this code, please include this copyright header, the included full -LGPL 2.1 text and read the terms provided in the LGPL 2.1 license -(http://www.gnu.org/copyleft/lesser.txt) - -------------------------------- - -Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch -If you use this control, please link to the original (http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/) -somewhere in the source-code-comment or the "about" of your project and give credits, thanks! - -*/ - -function checkBox(id,parentNode,x,y,checkboxId,checkcrossId,checkedStatus,labelText,textStyles,labelDistance,labelYOffset,radioButtonGroup,functionToCall) { - var nrArguments = 13; - var createCheckbox= true; - if (arguments.length == nrArguments) { - this.id = id; //an internal id, this id is not used in the SVG Dom tree - this.parentNode = parentNode; //the parentNode, string or nodeReference - this.x = x; //the center of the checkBox - this.y = y; //the center of the checkBox - this.checkboxId = checkboxId; //the id of the checkbox symbol (background) - this.checkcrossId = checkcrossId; //the id of the checkbox symbol (foreground), pointer-events should be set to "none" - this.checkedStatus = checkedStatus; //a status variable (true|false), indicates if checkbox is on or off - this.labelText = labelText; //the text of the checkbox label to be displayed, use undefined or empty string if you don't need a label text - this.textStyles = textStyles; //an array of literals containing the text settings - if (!this.textStyles["font-size"]) { - this.textStyles["font-size"] = 12; - } - this.labelDistance = labelDistance; //a distance defined from the center of the checkbox to the left of the text of the label - this.labelYOffset = labelYOffset; //a y offset value for the text label in relation to the checkbox symbol center - this.radioButtonGroup = radioButtonGroup; //a reference to a radio button group, if this is a standalone checkBox, just use the parameter undefined - this.functionToCall = functionToCall; //the function to call after triggering checkBox - this.exists = true; //status that indicates if checkbox exists or not, is set to false after method .remove() was called - this.label = undefined; //later a reference to the label text node - } - else { - createCheckbox = false; - alert("Error in checkbox ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); - } - if (createCheckbox) { - //timer stuff - this.timer = new Timer(this); //a Timer instance for calling the functionToCall - if (this.radioButtonGroup) { - this.timerMs = 0; - } - else { - this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms - } - //create checkbox - this.createCheckBox(); - } - else { - alert("Could not create checkbox with id '"+id+"' due to errors in the constructor parameters"); - } -} - -//this method creates all necessary checkbox geometry -checkBox.prototype.createCheckBox = function() { - if (typeof(this.parentNode) == "string") { - this.parentNode = document.getElementById(this.parentNode); - } - //create checkbox - this.checkBox = document.createElementNS(svgNS,"use"); - this.checkBox.setAttributeNS(null,"x",this.x); - this.checkBox.setAttributeNS(null,"y",this.y); - this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId); - this.checkBox.addEventListener("click",this,false); - this.checkBox.setAttributeNS(null,"cursor","pointer"); - this.parentNode.appendChild(this.checkBox); - //create checkcross - this.checkCross = document.createElementNS(svgNS,"use"); - this.checkCross.setAttributeNS(null,"x",this.x); - this.checkCross.setAttributeNS(null,"y",this.y); - this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId); - this.parentNode.appendChild(this.checkCross); - if (this.checkedStatus == false) { - this.checkCross.setAttributeNS(null,"display","none"); - } - //create label, if any - if (this.labelText) { - if (this.labelText.length > 0) { - this.label = document.createElementNS(svgNS,"text"); - for (var attrib in this.textStyles) { - var value = this.textStyles[attrib]; - if (attrib == "font-size") { - value += "px"; - } - this.label.setAttributeNS(null,attrib,value); - } - this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); - this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); - this.label.setAttributeNS(null,"cursor","pointer"); - var labelTextNode = document.createTextNode(this.labelText); - this.label.appendChild(labelTextNode); - this.label.setAttributeNS(null,"pointer-events","all"); - this.label.addEventListener("click",this,false); - this.parentNode.appendChild(this.label); - } - } - if (this.radioButtonGroup) { - this.radioButtonGroup.addCheckBox(this); - } -} - -checkBox.prototype.handleEvent = function(evt) { - if (evt.type == "click") { - if (this.checkedStatus == true) { - this.checkCross.setAttributeNS(null,"display","none"); - this.checkedStatus = false; - } - else { - this.checkCross.setAttributeNS(null,"display","inline"); - this.checkedStatus = true; - } - } - this.timer.setTimeout("fireFunction",this.timerMs); -} - -checkBox.prototype.fireFunction = function() { - if (this.radioButtonGroup) { - this.radioButtonGroup.selectById(this.id,true); - } - else { - if (typeof(this.functionToCall) == "function") { - this.functionToCall(this.id,this.checkedStatus,this.labelText); - } - if (typeof(this.functionToCall) == "object") { - this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText); - } - if (typeof(this.functionToCall) == undefined) { - return; - } - } -} - -checkBox.prototype.check = function(FireFunction) { - this.checkCross.setAttributeNS(null,"display","inherit"); - this.checkedStatus = true; - if (FireFunction) { - this.timer.setTimeout("fireFunction",this.timerMs); - } -} - -checkBox.prototype.uncheck = function(FireFunction) { - this.checkCross.setAttributeNS(null,"display","none"); - this.checkedStatus = false; - if (FireFunction) { - this.timer.setTimeout("fireFunction",this.timerMs); - } -} - -//move checkbox to a different position -checkBox.prototype.moveTo = function(moveX,moveY) { - this.x = moveX; - this.y = moveY; - //move checkbox - this.checkBox.setAttributeNS(null,"x",this.x); - this.checkBox.setAttributeNS(null,"y",this.y); - //move checkcross - this.checkCross.setAttributeNS(null,"x",this.x); - this.checkCross.setAttributeNS(null,"y",this.y); - //move text label - if (this.labelText) { - this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); - this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); - } -} - -checkBox.prototype.remove = function(FireFunction) { - this.checkBox.removeEventListener("click",this,false); - this.parentNode.removeChild(this.checkBox); - this.parentNode.removeChild(this.checkCross); - if (this.label) { - this.parentNode.removeChild(this.label); - } - this.exists = false; -} - -checkBox.prototype.setLabelText = function(labelText) { - this.labelText = labelText - if (this.label) { - this.label.firstChild.nodeValue = labelText; - } - else { - if (this.labelText.length > 0) { - this.label = document.createElementNS(svgNS,"text"); - for (var attrib in this.textStyles) { - value = this.textStyles[attrib]; - if (attrib == "font-size") { - value += "px"; - } - this.label.setAttributeNS(null,attrib,value); - } - this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); - this.label.setAttributeNS(null,"y",(this.y + this.textStyles["font-size"] * 0.3)); - var labelTextNode = document.createTextNode(this.labelText); - this.label.appendChild(labelTextNode); - this.parentNode.appendChild(this.label); - } - } -} - -/* start of the radioButtonGroup object */ - -function radioButtonGroup(id,functionToCall) { - var nrArguments = 2; - if (arguments.length == nrArguments) { - this.id = id; - if (typeof(functionToCall) == "function" || typeof(functionToCall) == "object" || typeof(functionToCall) == undefined) { - this.functionToCall = functionToCall; - } - else { - alert("Error in radiobutton with ("+id+"): argument functionToCall is not of type 'function', 'object' or undefined!"); - } - this.checkBoxes = new Array(); //this array will hold checkbox objects - this.selectedId = undefined; //holds the id of the active radio button - this.selectedIndex = undefined; //holds the index of the active radio button - //timer stuff - this.timer = new Timer(this); //a Timer instance for calling the functionToCall - this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms - } - else { - alert("Error in radiobutton with ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); - } -} - -radioButtonGroup.prototype.addCheckBox = function(checkBoxObj) { - this.checkBoxes.push(checkBoxObj); - if (checkBoxObj.checkedStatus) { - this.selectedId = checkBoxObj.id; - this.selectedIndex = this.checkBoxes.length - 1; - } -} - -//change radio button selection by id -radioButtonGroup.prototype.selectById = function(cbId,fireFunction) { - var found = false; - for (var i=0;i<this.checkBoxes.length;i++) { - if (this.checkBoxes[i].id == cbId) { - this.selectedId = cbId; - this.selectedIndex = i; - if (this.checkBoxes[i].checkedStatus == false) { - this.checkBoxes[i].check(false); - } - found = true; - } - else { - this.checkBoxes[i].uncheck(false); - } - } - if (found) { - if (fireFunction) { - this.timer.setTimeout("fireFunction",this.timerMs); - } - } - else { - alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+cbId+"'"); - } -} - -//change radio button selection by label name -radioButtonGroup.prototype.selectByLabelname = function(labelName,fireFunction) { - var id = -1; - for (var i=0;i<this.checkBoxes.length;i++) { - if (this.checkBoxes[i].labelText == labelName) { - id = this.checkBoxes[i].id; - } - } - if (id == -1) { - alert("Error in radiobutton with ("+this.id+"): could not find checkbox with label '"+labelName+"'"); - } - else { - this.selectById(id,fireFunction); - } -} - -radioButtonGroup.prototype.fireFunction = function() { - if (typeof(this.functionToCall) == "function") { - this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); - } - if (typeof(this.functionToCall) == "object") { - this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); - } - if (typeof(this.functionToCall) == undefined) { - return; - } -} \ No newline at end of file diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/helper_functions.js --- a/static/scripts/helper_functions.js Thu Oct 15 10:48:38 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,817 +0,0 @@ -/** - * @fileoverview - * - * ECMAScript <a href="http://www.carto.net/papers/svg/resources/helper_functions.html">helper functions</a>, main purpose is to serve in SVG mapping or other SVG based web applications - * - * This ECMA script library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public - * License as published by the Free Software Foundation; either - * version 2.1 of the License, or (at your option) any later version. - * - * This library is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this library (http://www.carto.net/papers/svg/resources/lesser_gpl.txt) if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - * - * Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch - * If you use these scripts, please link to the original (http://www.carto.net/papers/svg/resources/helper_functions.html) - * somewhere in the source-code-comment or the "about" of your project and give credits, thanks! - * - * See <a href="js_docs_out/overview-summary-helper_functions.js.html">documentation</a>. - * - * @author Andreas Neumann a.neumann(a)carto.net - * @copyright LGPL 2.1 <a href="http://www.gnu.org/copyleft/lesser.txt">Gnu LGPL 2.1</a> - * @credits Bruce Rindahl, numerous people on svgdevelopers(a)yahoogroups.com - */ - -//global variables necessary to create elements in these namespaces, do not delete them!!!! - -/** - * This variable is a shortcut to the full URL of the SVG namespace - * @final - * @type String - */ -var svgNS = "http://www.w3.org/2000/svg"; - -/** - * This variable is a shortcut to the full URL of the XLink namespace - * @final - * @type String - */ -var xlinkNS = "http://www.w3.org/1999/xlink"; - -/** - * This variable is a shortcut to the full URL of the attrib namespace - * @final - * @type String - */ -var cartoNS = "http://www.carto.net/attrib"; - -/** - * This variable is a alias to the full URL of the attrib namespace - * @final - * @type String - */ -var attribNS = "http://www.carto.net/attrib"; - -/** - * This variable is a alias to the full URL of the Batik extension namespace - * @final - * @type String - */ -var batikNS = "http://xml.apache.org/batik/ext"; - -/** - * Returns the polar direction from a given vector - * @param {Number} xdiff the x-part of the vector - * @param {Number} ydiff the y-part of the vector - * @return direction the direction in radians - * @type Number - * @version 1.0 (2007-04-30) - * @see #toPolarDist - * @see #toRectX - * @see #toRectY - */ -function toPolarDir(xdiff,ydiff) { - var direction = (Math.atan2(ydiff,xdiff)); - return(direction); -} - -/** - * Returns the polar distance from a given vector - * @param {Number} xdiff the x-part of the vector - * @param {Number} ydiff the y-part of the vector - * @return distance the distance - * @type Number - * @version 1.0 (2007-04-30) - * @see #toPolarDir - * @see #toRectX - * @see #toRectY - */ -function toPolarDist(xdiff,ydiff) { - var distance = Math.sqrt(xdiff * xdiff + ydiff * ydiff); - return(distance); -} - -/** - * Returns the x-part of a vector from a given direction and distance - * @param {Number} direction the direction (in radians) - * @param {Number} distance the distance - * @return x the x-part of the vector - * @type Number - * @version 1.0 (2007-04-30) - * @see #toPolarDist - * @see #toPolarDir - * @see #toRectY - */ -function toRectX(direction,distance) { - var x = distance * Math.cos(direction); - return(x); -} - -/** - * Returns the y-part of the vector from a given direction and distance - * @param {Number} direction the direction (in radians) - * @param {Number} distance the distance - * @return y the y-part of the vector - * @type Number - * @version 1.0 (2007-04-30) - * @see #toPolarDist - * @see #toPolarDir - * @see #toRectX - */ -function toRectY(direction,distance) { - y = distance * Math.sin(direction); - return(y); -} - -/** - * Converts degrees to radians - * @param {Number} deg the degree value - * @return rad the radians value - * @type Number - * @version 1.0 (2007-04-30) - * @see #RadToDeg - */ -function DegToRad(deg) { - return (deg / 180.0 * Math.PI); -} - -/** - * Converts radians to degrees - * @param {Number} rad the radians value - * @return deg the degree value - * @type Number - * @version 1.0 (2007-04-30) - * @see #DegToRad - */ -function RadToDeg(rad) { - return (rad / Math.PI * 180.0); -} - -/** - * Converts decimal degrees to degrees, minutes, seconds - * @param {Number} dd the decimal degree value - * @return degrees the degree values in the following notation: {deg:degrees,min:minutes,sec:seconds} - * @type literal - * @version 1.0 (2007-04-30) - * @see #dms2dd - */ -function dd2dms(dd) { - var minutes = (Math.abs(dd) - Math.floor(Math.abs(dd))) * 60; - var seconds = (minutes - Math.floor(minutes)) * 60; - var minutes = Math.floor(minutes); - if (dd >= 0) { - var degrees = Math.floor(dd); - } - else { - var degrees = Math.ceil(dd); - } - return {deg:degrees,min:minutes,sec:seconds}; -} - -/** - * Converts degrees, minutes and seconds to decimal degrees - * @param {Number} deg the degree value - * @param {Number} min the minute value - * @param {Number} sec the second value - * @return deg the decimal degree values - * @type Number - * @version 1.0 (2007-04-30) - * @see #dd2dms - */ -function dms2dd(deg,min,sec) { - if (deg < 0) { - return deg - (min / 60) - (sec / 3600); - } - else { - return deg + (min / 60) + (sec / 3600); - } -} - -/** - * log function, missing in the standard Math object - * @param {Number} x the value where the log function should be applied to - * @param {Number} b the base value for the log function - * @return logResult the result of the log function - * @type Number - * @version 1.0 (2007-04-30) - */ -function log(x,b) { - if(b==null) b=Math.E; - return Math.log(x)/Math.log(b); -} - -/** - * interpolates a value (e.g. elevation) bilinearly based on the position within a cell with 4 corner values - * @param {Number} za the value at the upper left corner of the cell - * @param {Number} zb the value at the upper right corner of the cell - * @param {Number} zc the value at the lower right corner of the cell - * @param {Number} zd the value at the lower left corner of the cell - * @param {Number} xpos the x position of the point where a new value should be interpolated - * @param {Number} ypos the y position of the point where a new value should be interpolated - * @param {Number} ax the x position of the lower left corner of the cell - * @param {Number} ay the y position of the lower left corner of the cell - * @param {Number} cellsize the size of the cell - * @return interpol_value the result of the bilinear interpolation function - * @type Number - * @version 1.0 (2007-04-30) - */ -function intBilinear(za,zb,zc,zd,xpos,ypos,ax,ay,cellsize) { //bilinear interpolation function - var e = (xpos - ax) / cellsize; - var f = (ypos - ay) / cellsize; - - //calculation of weights - var wa = (1 - e) * (1 - f); - var wb = e * (1 - f); - var wc = e * f; - var wd = f * (1 - e); - - var interpol_value = wa * zc + wb * zd + wc * za + wd * zb; - return interpol_value; -} - -/** - * tests if a given point is left or right of a given line - * @param {Number} pointx the x position of the given point - * @param {Number} pointy the y position of the given point - * @param {Number} linex1 the x position of line's start point - * @param {Number} liney1 the y position of line's start point - * @param {Number} linex2 the x position of line's end point - * @param {Number} liney2 the y position of line's end point - * @return leftof the result of the leftOfTest, 1 means leftOf, 0 means rightOf - * @type Number (integer, 0|1) - * @version 1.0 (2007-04-30) - */ -function leftOfTest(pointx,pointy,linex1,liney1,linex2,liney2) { - var result = (liney1 - pointy) * (linex2 - linex1) - (linex1 - pointx) * (liney2 - liney1); - if (result < 0) { - var leftof = 1; //case left of - } - else { - var leftof = 0; //case left of - } - return leftof; -} - -/** - * calculates the distance between a given point and a given line - * @param {Number} pointx the x position of the given point - * @param {Number} pointy the y position of the given point - * @param {Number} linex1 the x position of line's start point - * @param {Number} liney1 the y position of line's start point - * @param {Number} linex2 the x position of line's end point - * @param {Number} liney2 the y position of line's end point - * @return distance the result of the leftOfTest, 1 means leftOf, 0 means rightOf - * @type Number - * @version 1.0 (2007-04-30) - */ -function distFromLine(xpoint,ypoint,linex1,liney1,linex2,liney2) { - var dx = linex2 - linex1; - var dy = liney2 - liney1; - var distance = (dy * (xpoint - linex1) - dx * (ypoint - liney1)) / Math.sqrt(Math.pow(dx,2) + Math.pow(dy,2)); - return distance; -} - -/** - * calculates the angle between two vectors (lines) - * @param {Number} ax the x part of vector a - * @param {Number} ay the y part of vector a - * @param {Number} bx the x part of vector b - * @param {Number} by the y part of vector b - * @return angle the angle in radians - * @type Number - * @version 1.0 (2007-04-30) - * @credits <a href="http://www.mathe-online.at/mathint/vect2/i.html#Winkel">Mathe Online (Winkel)</a> - */ -function angleBetwTwoLines(ax,ay,bx,by) { - var angle = Math.acos((ax * bx + ay * by) / (Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)) * Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)))); - return angle; -} - -/** - * calculates the bisector vector for two given vectors - * @param {Number} ax the x part of vector a - * @param {Number} ay the y part of vector a - * @param {Number} bx the x part of vector b - * @param {Number} by the y part of vector b - * @return c the resulting vector as an Array, c[0] is the x part of the vector, c[1] is the y part - * @type Array - * @version 1.0 (2007-04-30) - * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> - * see #calcBisectorAngle - * */ -function calcBisectorVector(ax,ay,bx,by) { - var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); - var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); - var c = new Array(); - c[0] = ax / betraga + bx / betragb; - c[1] = ay / betraga + by / betragb; - return c; -} - -/** - * calculates the bisector angle for two given vectors - * @param {Number} ax the x part of vector a - * @param {Number} ay the y part of vector a - * @param {Number} bx the x part of vector b - * @param {Number} by the y part of vector b - * @return angle the bisector angle in radians - * @type Number - * @version 1.0 (2007-04-30) - * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> - * see #calcBisectorVector - * */ -function calcBisectorAngle(ax,ay,bx,by) { - var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); - var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); - var c1 = ax / betraga + bx / betragb; - var c2 = ay / betraga + by / betragb; - var angle = toPolarDir(c1,c2); - return angle; -} - -/** - * calculates the intersection point of two given lines - * @param {Number} line1x1 the x the start point of line 1 - * @param {Number} line1y1 the y the start point of line 1 - * @param {Number} line1x2 the x the end point of line 1 - * @param {Number} line1y2 the y the end point of line 1 - * @return interSectPoint the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate - * @type Object - * @version 1.0 (2007-04-30) - * @credits <a href="http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/">P. Bourke</a> - */ -function intersect2lines(line1x1,line1y1,line1x2,line1y2,line2x1,line2y1,line2x2,line2y2) { - var interSectPoint = new Object(); - var denominator = (line2y2 - line2y1)*(line1x2 - line1x1) - (line2x2 - line2x1)*(line1y2 - line1y1); - if (denominator == 0) { - alert("lines are parallel"); - } - else { - var ua = ((line2x2 - line2x1)*(line1y1 - line2y1) - (line2y2 - line2y1)*(line1x1 - line2x1)) / denominator; - var ub = ((line1x2 - line1x1)*(line1y1 - line2y1) - (line1y2 - line1y1)*(line1x1 - line2x1)) / denominator; - } - interSectPoint["x"] = line1x1 + ua * (line1x2 - line1x1); - interSectPoint["y"] = line1y1 + ua * (line1y2 - line1y1); - return interSectPoint; -} - -/** - * reformats a given number to a string by adding separators at every third digit - * @param {String|Number} inputNumber the input number, can be of type number or string - * @param {String} separator the separator, e.g. ' or , - * @return newString the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate - * @type String - * @version 1.0 (2007-04-30) - */ -function formatNumberString(inputNumber,separator) { - //check if of type string, if number, convert it to string - if (typeof(inputNumber) == "Number") { - var myTempString = inputNumber.toString(); - } - else { - var myTempString = inputNumber; - } - var newString=""; - //if it contains a comma, it will be split - var splitResults = myTempString.split("."); - var myCounter = splitResults[0].length; - if (myCounter > 3) { - while(myCounter > 0) { - if (myCounter > 3) { - newString = separator + splitResults[0].substr(myCounter - 3,3) + newString; - } - else { - newString = splitResults[0].substr(0,myCounter) + newString; - } - myCounter -= 3; - } - } - else { - newString = splitResults[0]; - } - //concatenate if it contains a comma - if (splitResults[1]) { - newString = newString + "." + splitResults[1]; - } - return newString; -} - -/** - * writes a status text message out to a SVG text element's first child - * @param {String} statusText the text message to be displayed - * @version 1.0 (2007-04-30) - */ - function statusChange(statusText) { - document.getElementById("statusText").firstChild.nodeValue = "Statusbar: " + statusText; -} - -/** - * scales an SVG element, requires that the element has an x and y attribute (e.g. circle, ellipse, use element, etc.) - * @param {dom::Event} evt the evt object that triggered the scaling - * @param {Number} factor the scaling factor - * @version 1.0 (2007-04-30) - */ -function scaleObject(evt,factor) { - //reference to the currently selected object - var element = evt.currentTarget; - var myX = element.getAttributeNS(null,"x"); - var myY = element.getAttributeNS(null,"y"); - var newtransform = "scale(" + factor + ") translate(" + (myX * 1 / factor - myX) + " " + (myY * 1 / factor - myY) +")"; - element.setAttributeNS(null,'transform', newtransform); -} - -/** - * returns the transformation matrix (ctm) for the given node up to the root element - * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) - * @param {svg::SVGTransformable} node the node reference for the SVGElement the ctm is queried - * @return CTM the current transformation matrix from the given node to the root element - * @type svg::SVGMatrix - * @version 1.0 (2007-05-01) - * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> - * @see #getTransformToElement - */ -function getTransformToRootElement(node) { - try { - //this part is for fully conformant players (like Opera, Batik, Firefox, Safari ...) - var CTM = node.getTransformToElement(document.documentElement); - } - catch (ex) { - //this part is for ASV3 or other non-conformant players - // Initialize our CTM the node's Current Transformation Matrix - var CTM = node.getCTM(); - // Work our way through the ancestor nodes stopping at the SVG Document - while ( ( node = node.parentNode ) != document ) { - // Multiply the new CTM to the one with what we have accumulated so far - CTM = node.getCTM().multiply(CTM); - } - } - return CTM; -} - -/** - * returns the transformation matrix (ctm) for the given dom::Node up to a different dom::Node - * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) - * @param {svg::SVGTransformable} node the node reference for the element the where the ctm should be calculated from - * @param {svg::SVGTransformable} targetNode the target node reference for the element the ctm should be calculated to - * @return CTM the current transformation matrix from the given node to the target element - * @type svg::SVGMatrix - * @version 1.0 (2007-05-01) - * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> - * @see #getTransformToRootElement - */ -function getTransformToElement(node,targetNode) { - try { - //this part is for fully conformant players - var CTM = node.getTransformToElement(targetNode); - } - catch (ex) { - //this part is for ASV3 or other non-conformant players - // Initialize our CTM the node's Current Transformation Matrix - var CTM = node.getCTM(); - // Work our way through the ancestor nodes stopping at the SVG Document - while ( ( node = node.parentNode ) != targetNode ) { - // Multiply the new CTM to the one with what we have accumulated so far - CTM = node.getCTM().multiply(CTM); - } - } - return CTM; -} - -/** - * converts HSV to RGB values - * @param {Number} hue the hue value (between 0 and 360) - * @param {Number} sat the saturation value (between 0 and 1) - * @param {Number} val the value value (between 0 and 1) - * @return rgbArr the rgb values (associative array or object, the keys are: red,green,blue), all values are scaled between 0 and 255 - * @type Object - * @version 1.0 (2007-05-01) - * @see #rgb2hsv - */ -function hsv2rgb(hue,sat,val) { - var rgbArr = new Object(); - if ( sat == 0) { - rgbArr["red"] = Math.round(val * 255); - rgbArr["green"] = Math.round(val * 255); - rgbArr["blue"] = Math.round(val * 255); - } - else { - var h = hue / 60; - var i = Math.floor(h); - var f = h - i; - if (i % 2 == 0) { - f = 1 - f; - } - var m = val * (1 - sat); - var n = val * (1 - sat * f); - switch(i) { - case 0: - rgbArr["red"] = val; - rgbArr["green"] = n; - rgbArr["blue"] = m; - break; - case 1: - rgbArr["red"] = n; - rgbArr["green"] = val; - rgbArr["blue"] = m; - break; - case 2: - rgbArr["red"] = m; - rgbArr["green"] = val; - rgbArr["blue"] = n; - break; - case 3: - rgbArr["red"] = m; - rgbArr["green"] = n; - rgbArr["blue"] = val; - break; - case 4: - rgbArr["red"] = n; - rgbArr["green"] = m; - rgbArr["blue"] = val; - break; - case 5: - rgbArr["red"] = val; - rgbArr["green"] = m; - rgbArr["blue"] = n; - break; - case 6: - rgbArr["red"] = val; - rgbArr["green"] = n; - rgbArr["blue"] = m; - break; - } - rgbArr["red"] = Math.round(rgbArr["red"] * 255); - rgbArr["green"] = Math.round(rgbArr["green"] * 255); - rgbArr["blue"] = Math.round(rgbArr["blue"] * 255); - } - return rgbArr; -} - -/** - * converts RGB to HSV values - * @param {Number} red the hue value (between 0 and 255) - * @param {Number} green the saturation value (between 0 and 255) - * @param {Number} blue the value value (between 0 and 255) - * @return hsvArr the hsv values (associative array or object, the keys are: hue (0-360),sat (0-1),val (0-1)) - * @type Object - * @version 1.0 (2007-05-01) - * @see #hsv2rgb - */ -function rgb2hsv(red,green,blue) { - var hsvArr = new Object(); - red = red / 255; - green = green / 255; - blue = blue / 255; - myMax = Math.max(red, Math.max(green,blue)); - myMin = Math.min(red, Math.min(green,blue)); - v = myMax; - if (myMax > 0) { - s = (myMax - myMin) / myMax; - } - else { - s = 0; - } - if (s > 0) { - myDiff = myMax - myMin; - rc = (myMax - red) / myDiff; - gc = (myMax - green) / myDiff; - bc = (myMax - blue) / myDiff; - if (red == myMax) { - h = (bc - gc) / 6; - } - if (green == myMax) { - h = (2 + rc - bc) / 6; - } - if (blue == myMax) { - h = (4 + gc - rc) / 6; - } - } - else { - h = 0; - } - if (h < 0) { - h += 1; - } - hsvArr["hue"] = Math.round(h * 360); - hsvArr["sat"] = s; - hsvArr["val"] = v; - return hsvArr; -} - -/** - * populates an array such that it can be addressed by both a key or an index nr, - * note that both Arrays need to be of the same length - * @param {Array} arrayKeys the array containing the keys - * @param {Array} arrayValues the array containing the values - * @return returnArray the resulting array containing both associative values and also a regular indexed array - * @type Array - * @version 1.0 (2007-05-01) - */ -function arrayPopulate(arrayKeys,arrayValues) { - var returnArray = new Array(); - if (arrayKeys.length != arrayValues.length) { - alert("error: arrays do not have the same length!"); - } - else { - for (i=0;i<arrayKeys.length;i++) { - returnArray[arrayKeys[i]] = arrayValues[i]; - } - } - return returnArray; -} - -/** - * Wrapper object for network requests, uses getURL or XMLHttpRequest depending on availability - * The callBackFunction receives a XML or text node representing the rootElement - * of the fragment received or the return text, depending on the returnFormat. - * See also the following <a href="http://www.carto.net/papers/svg/network_requests/">documentation</a>. - * @class this is a wrapper object to provide network request functionality (get|post) - * @param {String} url the URL/IRI of the network resource to be called - * @param {Function|Object} callBackFunction the callBack function or object that is called after the data was received, in case of an object, the method 'receiveData' is called; both the function and the object's 'receiveData' method get 2 return parameters: 'node.firstChild'|text (the root element of the XML or text resource), this.additionalParams (if defined) - * @param {String} returnFormat the return format, either 'xml' or 'json' (or text) - * @param {String} method the method of the network request, either 'get' or 'post' - * @param {String|Undefined} postText the String containing the post text (optional) or Undefined (if not a 'post' request) - * @param {Object|Array|String|Number|Undefined} additionalParams additional parameters that will be passed to the callBackFunction or object (optional) or Undefined - * @return a new getData instance - * @type getData - * @constructor - * @version 1.0 (2007-02-23) - */ -function getData(url,callBackFunction,returnFormat,method,postText,additionalParams) { - this.url = url; - this.callBackFunction = callBackFunction; - this.returnFormat = returnFormat; - this.method = method; - this.additionalParams = additionalParams; - if (method != "get" && method != "post") { - alert("Error in network request: parameter 'method' must be 'get' or 'post'"); - } - this.postText = postText; - this.xmlRequest = null; //@private reference to the XMLHttpRequest object -} - -/** - * triggers the network request defined in the constructor - */ -getData.prototype.getData = function() { - //call getURL() if available - if (window.getURL) { - if (this.method == "get") { - getURL(this.url,this); - } - if (this.method == "post") { - postURL(this.url,this.postText,this); - } - } - //or call XMLHttpRequest() if available - else if (window.XMLHttpRequest) { - var _this = this; - this.xmlRequest = new XMLHttpRequest(); - if (this.method == "get") { - if (this.returnFormat == "xml") { - this.xmlRequest.overrideMimeType("text/xml"); - } - this.xmlRequest.open("GET",this.url,true); - } - if (this.method == "post") { - this.xmlRequest.open("POST",this.url,true); - } - this.xmlRequest.onreadystatechange = function() {_this.handleEvent()}; - if (this.method == "get") { - this.xmlRequest.send(null); - } - if (this.method == "post") { - //test if postText exists and is of type string - var reallyPost = true; - if (!this.postText) { - reallyPost = false; - alert("Error in network post request: missing parameter 'postText'!"); - } - if (typeof(this.postText) != "string") { - reallyPost = false; - alert("Error in network post request: parameter 'postText' has to be of type 'string')"); - } - if (reallyPost) { - this.xmlRequest.send(this.postText); - } - } - } - //write an error message if neither method is available - else { - alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!"); - } -} - -/** - * this is the callback method for the getURL() or postURL() case - * @private - */ -getData.prototype.operationComplete = function(data) { - //check if data has a success property - if (data.success) { - //parse content of the XML format to the variable "node" - if (this.returnFormat == "xml") { - //convert the text information to an XML node and get the first child - var node = parseXML(data.content,document); - //distinguish between a callback function and an object - if (typeof(this.callBackFunction) == "function") { - this.callBackFunction(node.firstChild,this.additionalParams); - } - if (typeof(this.callBackFunction) == "object") { - this.callBackFunction.receiveData(node.firstChild,this.additionalParams); - } - } - if (this.returnFormat == "json") { - if (typeof(this.callBackFunction) == "function") { - this.callBackFunction(data.content,this.additionalParams); - } - if (typeof(this.callBackFunction) == "object") { - this.callBackFunction.receiveData(data.content,this.additionalParams); - } - } - } - else { - alert("something went wrong with dynamic loading of geometry!"); - } -} - -/** - * this is the callback method for the XMLHttpRequest case - * @private - */ -getData.prototype.handleEvent = function() { - if (this.xmlRequest.readyState == 4) { - if (this.returnFormat == "xml") { - //we need to import the XML node first - var importedNode = document.importNode(this.xmlRequest.responseXML.documentElement,true); - if (typeof(this.callBackFunction) == "function") { - this.callBackFunction(importedNode,this.additionalParams); - } - if (typeof(this.callBackFunction) == "object") { - this.callBackFunction.receiveData(importedNode,this.additionalParams); - } - } - if (this.returnFormat == "json") { - if (typeof(this.callBackFunction) == "function") { - this.callBackFunction(this.xmlRequest.responseText,this.additionalParams); - } - if (typeof(this.callBackFunction) == "object") { - this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams); - } - } - } -} - -/** - * Serializes an XML node and returns a string representation. Wrapper function to hide implementation differences. - * This can be used for debugging purposes or to post data to a server or network resource. - * @param {dom::Node} node the DOM node reference - * @return textRepresentation the String representation of the XML node - * @type String - * @version 1.0 (2007-05-01) - * @see getData - */ -function serializeNode(node) { - if (typeof XMLSerializer != 'undefined') { - return new XMLSerializer().serializeToString(node); - } - else if (typeof node.xml != 'undefined') { - return node.xml; - } - else if (typeof printNode != 'undefined') { - return printNode(node); - } - else if (typeof Packages != 'undefined') { - try { - var stringWriter = new java.io.StringWriter(); - Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(node,stringWriter); - return stringWriter.toString(); - } - catch (e) { - alert("Sorry, your SVG viewer does not support the printNode/serialize function."); - return ''; - } - } - else { - alert("Sorry, your SVG viewer does not support the printNode/serialize function."); - return ''; - } -} - -/** - * Starts a SMIL animation element with the given id by triggering the '.beginElement()' method. - * This is a convenience (shortcut) function. - * @param {String} id a valid id of a valid SMIL animation element - * @version 1.0 (2007-05-01) - */ -//starts an animtion with the given id -//this function is useful in combination with window.setTimeout() -function startAnimation(id) { - document.getElementById(id).beginElement(); -} diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/timer.js --- a/static/scripts/timer.js Thu Oct 15 10:48:38 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -// source/credits: "Algorithm": http://www.codingforums.com/showthread.php?s=&threadid=10531 -// The constructor should be called with -// the parent object (optional, defaults to window). - -function Timer(){ - this.obj = (arguments.length)?arguments[0]:window; - return this; -} - -// The set functions should be called with: -// - The name of the object method (as a string) (required) -// - The millisecond delay (required) -// - Any number of extra arguments, which will all be -// passed to the method when it is evaluated. - -Timer.prototype.setInterval = function(func, msec){ - var i = Timer.getNew(); - var t = Timer.buildCall(this.obj, i, arguments); - Timer.set[i].timer = window.setInterval(t,msec); - return i; -} -Timer.prototype.setTimeout = function(func, msec){ - var i = Timer.getNew(); - Timer.buildCall(this.obj, i, arguments); - Timer.set[i].timer = window.setTimeout("Timer.callOnce("+i+");",msec); - return i; -} - -// The clear functions should be called with -// the return value from the equivalent set function. - -Timer.prototype.clearInterval = function(i){ - if(!Timer.set[i]) return; - window.clearInterval(Timer.set[i].timer); - Timer.set[i] = null; -} -Timer.prototype.clearTimeout = function(i){ - if(!Timer.set[i]) return; - window.clearTimeout(Timer.set[i].timer); - Timer.set[i] = null; -} - -// Private data - -Timer.set = new Array(); -Timer.buildCall = function(obj, i, args){ - var t = ""; - Timer.set[i] = new Array(); - if(obj != window){ - Timer.set[i].obj = obj; - t = "Timer.set["+i+"].obj."; - } - t += args[0]+"("; - if(args.length > 2){ - Timer.set[i][0] = args[2]; - t += "Timer.set["+i+"][0]"; - for(var j=1; (j+2)<args.length; j++){ - Timer.set[i][j] = args[j+2]; - t += ", Timer.set["+i+"]["+j+"]"; - }} - t += ");"; - Timer.set[i].call = t; - return t; -} -Timer.callOnce = function(i){ - if(!Timer.set[i]) return; - eval(Timer.set[i].call); - Timer.set[i] = null; -} -Timer.getNew = function(){ - var i = 0; - while(Timer.set[i]) i++; - return i; -} \ No newline at end of file diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/tools/rgenetics/checkbox_and_radiobutton.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js Thu Oct 15 19:01:07 2009 -0400 @@ -0,0 +1,1 @@ +function checkBox(d,g,m,j,n,l,c,f,k,b,h,o,a){var e=13;var i=true;if(arguments.length==e){this.id=d;this.parentNode=g;this.x=m;this.y=j;this.checkboxId=n;this.checkcrossId=l;this.checkedStatus=c;this.labelText=f;this.textStyles=k;if(!this.textStyles["font-size"]){this.textStyles["font-size"]=12}this.labelDistance=b;this.labelYOffset=h;this.radioButtonGroup=o;this.functionToCall=a;this.exists=true;this.label=undefined}else{i=false;alert("Error in checkbox ("+d+"): wrong nr of arguments! You have to pass over "+e+" parameters.")}if(i){this.timer=new Timer(this);if(this.radioButtonGroup){this.timerMs=0}else{this.timerMs=200}this.createCheckBox()}else{alert("Could not create checkbox with id '"+d+"' due to errors in the constructor parameters")}}checkBox.prototype.createCheckBox=function(){if(typeof(this.parentNode)=="string"){this.parentNode=document.getElementById(this.parentNode)}this.checkBox=document.createElementNS(svgNS,"use");this.checkBox.setAttributeNS(null,"x",this.x); this.checkBox.setAttributeNS(null,"y",this.y);this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId);this.checkBox.addEventListener("click",this,false);this.checkBox.setAttributeNS(null,"cursor","pointer");this.parentNode.appendChild(this.checkBox);this.checkCross=document.createElementNS(svgNS,"use");this.checkCross.setAttributeNS(null,"x",this.x);this.checkCross.setAttributeNS(null,"y",this.y);this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId);this.parentNode.appendChild(this.checkCross);if(this.checkedStatus==false){this.checkCross.setAttributeNS(null,"display","none")}if(this.labelText){if(this.labelText.length>0){this.label=document.createElementNS(svgNS,"text");for(var b in this.textStyles){var a=this.textStyles[b];if(b=="font-size"){a+="px"}this.label.setAttributeNS(null,b,a)}this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.labelYOffset));this.label.setAttributeNS(null,"cursor", "pointer");var c=document.createTextNode(this.labelText);this.label.appendChild(c);this.label.setAttributeNS(null,"pointer-events","all");this.label.addEventListener("click",this,false);this.parentNode.appendChild(this.label)}}if(this.radioButtonGroup){this.radioButtonGroup.addCheckBox(this)}};checkBox.prototype.handleEvent=function(a){if(a.type=="click"){if(this.checkedStatus==true){this.checkCross.setAttributeNS(null,"display","none");this.checkedStatus=false}else{this.checkCross.setAttributeNS(null,"display","inline");this.checkedStatus=true}}this.timer.setTimeout("fireFunction",this.timerMs)};checkBox.prototype.fireFunction=function(){if(this.radioButtonGroup){this.radioButtonGroup.selectById(this.id,true)}else{if(typeof(this.functionToCall)=="function"){this.functionToCall(this.id,this.checkedStatus,this.labelText)}if(typeof(this.functionToCall)=="object"){this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText)}if(typeof(this.functionToCall)==unde fined){return}}};checkBox.prototype.check=function(a){this.checkCross.setAttributeNS(null,"display","inherit");this.checkedStatus=true;if(a){this.timer.setTimeout("fireFunction",this.timerMs)}};checkBox.prototype.uncheck=function(a){this.checkCross.setAttributeNS(null,"display","none");this.checkedStatus=false;if(a){this.timer.setTimeout("fireFunction",this.timerMs)}};checkBox.prototype.moveTo=function(b,a){this.x=b;this.y=a;this.checkBox.setAttributeNS(null,"x",this.x);this.checkBox.setAttributeNS(null,"y",this.y);this.checkCross.setAttributeNS(null,"x",this.x);this.checkCross.setAttributeNS(null,"y",this.y);if(this.labelText){this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.labelYOffset))}};checkBox.prototype.remove=function(a){this.checkBox.removeEventListener("click",this,false);this.parentNode.removeChild(this.checkBox);this.parentNode.removeChild(this.checkCross);if(this.label){this.parentNode.removeChild(t his.label)}this.exists=false};checkBox.prototype.setLabelText=function(a){this.labelText=a;if(this.label){this.label.firstChild.nodeValue=a}else{if(this.labelText.length>0){this.label=document.createElementNS(svgNS,"text");for(var b in this.textStyles){value=this.textStyles[b];if(b=="font-size"){value+="px"}this.label.setAttributeNS(null,b,value)}this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.textStyles["font-size"]*0.3));var c=document.createTextNode(this.labelText);this.label.appendChild(c);this.parentNode.appendChild(this.label)}}};function radioButtonGroup(c,a){var b=2;if(arguments.length==b){this.id=c;if(typeof(a)=="function"||typeof(a)=="object"||typeof(a)==undefined){this.functionToCall=a}else{alert("Error in radiobutton with ("+c+"): argument functionToCall is not of type 'function', 'object' or undefined!")}this.checkBoxes=new Array();this.selectedId=undefined;this.selectedIndex=undefined;this.timer=ne w Timer(this);this.timerMs=200}else{alert("Error in radiobutton with ("+c+"): wrong nr of arguments! You have to pass over "+b+" parameters.")}}radioButtonGroup.prototype.addCheckBox=function(a){this.checkBoxes.push(a);if(a.checkedStatus){this.selectedId=a.id;this.selectedIndex=this.checkBoxes.length-1}};radioButtonGroup.prototype.selectById=function(c,a){var d=false;for(var b=0;b<this.checkBoxes.length;b++){if(this.checkBoxes[b].id==c){this.selectedId=c;this.selectedIndex=b;if(this.checkBoxes[b].checkedStatus==false){this.checkBoxes[b].check(false)}d=true}else{this.checkBoxes[b].uncheck(false)}}if(d){if(a){this.timer.setTimeout("fireFunction",this.timerMs)}}else{alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+c+"'")}};radioButtonGroup.prototype.selectByLabelname=function(a,b){var d=-1;for(var c=0;c<this.checkBoxes.length;c++){if(this.checkBoxes[c].labelText==a){d=this.checkBoxes[c].id}}if(d==-1){alert("Error in radiobutton with ("+this.id+ "): could not find checkbox with label '"+a+"'")}else{this.selectById(d,b)}};radioButtonGroup.prototype.fireFunction=function(){if(typeof(this.functionToCall)=="function"){this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText)}if(typeof(this.functionToCall)=="object"){this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText)}if(typeof(this.functionToCall)==undefined){return}}; \ No newline at end of file diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/tools/rgenetics/helper_functions.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/tools/rgenetics/helper_functions.js Thu Oct 15 19:01:07 2009 -0400 @@ -0,0 +1,1 @@ +var svgNS="http://www.w3.org/2000/svg";var xlinkNS="http://www.w3.org/1999/xlink";var cartoNS="http://www.carto.net/attrib";var attribNS="http://www.carto.net/attrib";var batikNS="http://xml.apache.org/batik/ext";function toPolarDir(a,c){var b=(Math.atan2(c,a));return(b)}function toPolarDist(a,b){var c=Math.sqrt(a*a+b*b);return(c)}function toRectX(b,c){var a=c*Math.cos(b);return(a)}function toRectY(a,b){y=b*Math.sin(a);return(y)}function DegToRad(a){return(a/180*Math.PI)}function RadToDeg(a){return(a/Math.PI*180)}function dd2dms(a){var b=(Math.abs(a)-Math.floor(Math.abs(a)))*60;var d=(b-Math.floor(b))*60;var b=Math.floor(b);if(a>=0){var c=Math.floor(a)}else{var c=Math.ceil(a)}return{deg:c,min:b,sec:d}}function dms2dd(c,a,b){if(c<0){return c-(a/60)-(b/3600)}else{return c+(a/60)+(b/3600)}}function log(c,a){if(a==null){a=Math.E}return Math.log(c)/Math.log(a)}function intBilinear(m,k,g,c,o,b,a,u,t){var q=(o-a)/t;var p=(b-u)/t;var n=(1-q)*(1-p);var l=q*(1-p);var j=q*p;var d=p*(1- q);var r=n*g+l*c+j*m+d*k;return r}function leftOfTest(b,j,d,g,c,f){var a=(g-j)*(c-d)-(d-b)*(f-g);if(a<0){var e=1}else{var e=0}return e}function distFromLine(e,f,d,a,c,j){var k=c-d;var g=j-a;var b=(g*(e-d)-k*(f-a))/Math.sqrt(Math.pow(k,2)+Math.pow(g,2));return b}function angleBetwTwoLines(b,a,e,c){var d=Math.acos((b*e+a*c)/(Math.sqrt(Math.pow(b,2)+Math.pow(a,2))*Math.sqrt(Math.pow(e,2)+Math.pow(c,2))));return d}function calcBisectorVector(b,a,g,e){var f=Math.sqrt(Math.pow(b,2)+Math.pow(a,2));var d=Math.sqrt(Math.pow(g,2)+Math.pow(e,2));var j=new Array();j[0]=b/f+g/d;j[1]=a/f+e/d;return j}function calcBisectorAngle(a,k,j,g){var c=Math.sqrt(Math.pow(a,2)+Math.pow(k,2));var b=Math.sqrt(Math.pow(j,2)+Math.pow(g,2));var f=a/c+j/b;var e=k/c+g/b;var d=toPolarDir(f,e);return d}function intersect2lines(l,f,k,e,n,j,m,g){var c=new Object();var d=(g-j)*(k-l)-(m-n)*(e-f);if(d==0){alert("lines are parallel")}else{var b=((m-n)*(f-j)-(g-j)*(l-n))/d;var a=((k-l)*(f-j)-(e-f)*(l-n))/d}c.x=l+b*( k-l);c.y=f+b*(e-f);return c}function formatNumberString(a,e){if(typeof(a)=="Number"){var c=a.toString()}else{var c=a}var b="";var d=c.split(".");var f=d[0].length;if(f>3){while(f>0){if(f>3){b=e+d[0].substr(f-3,3)+b}else{b=d[0].substr(0,f)+b}f-=3}}else{b=d[0]}if(d[1]){b=b+"."+d[1]}return b}function statusChange(a){document.getElementById("statusText").firstChild.nodeValue="Statusbar: "+a}function scaleObject(a,e){var d=a.currentTarget;var c=d.getAttributeNS(null,"x");var b=d.getAttributeNS(null,"y");var f="scale("+e+") translate("+(c*1/e-c)+" "+(b*1/e-b)+")";d.setAttributeNS(null,"transform",f)}function getTransformToRootElement(b){try{var c=b.getTransformToElement(document.documentElement)}catch(a){var c=b.getCTM();while((b=b.parentNode)!=document){c=b.getCTM().multiply(c)}}return c}function getTransformToElement(b,c){try{var d=b.getTransformToElement(c)}catch(a){var d=b.getCTM();while((b=b.parentNode)!=c){d=b.getCTM().multiply(d)}}return d}function hsv2rgb(j,c,b){var l=new Object();if(c==0){l.red=Math.round(b*255);l.green=Math.round(b*255);l.blue=Math.round(b*255)}else{var g=j/60;var e=Math.floor(g);var k=g-e;if(e%2==0){k=1-k}var d=b*(1-c);var a=b*(1-c*k);switch(e){case 0:l.red=b;l.green=a;l.blue=d;break;case 1:l.red=a;l.green=b;l.blue=d;break;case 2:l.red=d;l.green=b;l.blue=a;break;case 3:l.red=d;l.green=a;l.blue=b;break;case 4:l.red=a;l.green=d;l.blue=b;break;case 5:l.red=b;l.green=d;l.blue=a;break;case 6:l.red=b;l.green=a;l.blue=d;break}l.red=Math.round(l.red*255);l.green=Math.round(l.green*255);l.blue=Math.round(l.blue*255)}return l}function rgb2hsv(c,b,a){var d=new Object();c=c/255;b=b/255;a=a/255;myMax=Math.max(c,Math.max(b,a));myMin=Math.min(c,Math.min(b,a));v=myMax;if(myMax>0){s=(myMax-myMin)/myMax}else{s=0}if(s>0){myDiff=myMax-myMin;rc=(myMax-c)/myDiff;gc=(myMax-b)/myDiff;bc=(myMax-a)/myDiff;if(c==myMax){h=(bc-gc)/6}if(b==myMax){h=(2+rc-bc)/6}if(a==myMax){h=(4+gc-rc)/6}}else{h=0}if(h<0){h+=1}d.hue=Math.round(h*360);d.sat=s;d.val=v;ret urn d}function arrayPopulate(a,b){var c=new Array();if(a.length!=b.length){alert("error: arrays do not have the same length!")}else{for(i=0;i<a.length;i++){c[a[i]]=b[i]}}return c}function getData(d,c,e,f,b,a){this.url=d;this.callBackFunction=c;this.returnFormat=e;this.method=f;this.additionalParams=a;if(f!="get"&&f!="post"){alert("Error in network request: parameter 'method' must be 'get' or 'post'")}this.postText=b;this.xmlRequest=null}getData.prototype.getData=function(){if(window.getURL){if(this.method=="get"){getURL(this.url,this)}if(this.method=="post"){postURL(this.url,this.postText,this)}}else{if(window.XMLHttpRequest){var b=this;this.xmlRequest=new XMLHttpRequest();if(this.method=="get"){if(this.returnFormat=="xml"){this.xmlRequest.overrideMimeType("text/xml")}this.xmlRequest.open("GET",this.url,true)}if(this.method=="post"){this.xmlRequest.open("POST",this.url,true)}this.xmlRequest.onreadystatechange=function(){b.handleEvent()};if(this.method=="get"){this.xmlRequest .send(null)}if(this.method=="post"){var a=true;if(!this.postText){a=false;alert("Error in network post request: missing parameter 'postText'!")}if(typeof(this.postText)!="string"){a=false;alert("Error in network post request: parameter 'postText' has to be of type 'string')")}if(a){this.xmlRequest.send(this.postText)}}}else{alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!")}}};getData.prototype.operationComplete=function(b){if(b.success){if(this.returnFormat=="xml"){var a=parseXML(b.content,document);if(typeof(this.callBackFunction)=="function"){this.callBackFunction(a.firstChild,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(a.firstChild,this.additionalParams)}}if(this.returnFormat=="json"){if(typeof(this.callBackFunction)=="function"){this.callBackFunction(b.content,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(b.content,this. additionalParams)}}}else{alert("something went wrong with dynamic loading of geometry!")}};getData.prototype.handleEvent=function(){if(this.xmlRequest.readyState==4){if(this.returnFormat=="xml"){var a=document.importNode(this.xmlRequest.responseXML.documentElement,true);if(typeof(this.callBackFunction)=="function"){this.callBackFunction(a,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(a,this.additionalParams)}}if(this.returnFormat=="json"){if(typeof(this.callBackFunction)=="function"){this.callBackFunction(this.xmlRequest.responseText,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams)}}}};function serializeNode(b){if(typeof XMLSerializer!="undefined"){return new XMLSerializer().serializeToString(b)}else{if(typeof b.xml!="undefined"){return b.xml}else{if(typeof printNode!="undefined"){return printNode(b)}else{if(typeof Pac kages!="undefined"){try{var a=new java.io.StringWriter();Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(b,a);return a.toString()}catch(c){alert("Sorry, your SVG viewer does not support the printNode/serialize function.");return""}}else{alert("Sorry, your SVG viewer does not support the printNode/serialize function.");return""}}}}}function startAnimation(a){document.getElementById(a).beginElement()}; \ No newline at end of file diff -r cbe28b41fb9d -r e945dcdfd578 static/scripts/tools/rgenetics/timer.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/tools/rgenetics/timer.js Thu Oct 15 19:01:07 2009 -0400 @@ -0,0 +1,1 @@ +function Timer(){this.obj=(arguments.length)?arguments[0]:window;return this}Timer.prototype.setInterval=function(c,d){var b=Timer.getNew();var a=Timer.buildCall(this.obj,b,arguments);Timer.set[b].timer=window.setInterval(a,d);return b};Timer.prototype.setTimeout=function(b,c){var a=Timer.getNew();Timer.buildCall(this.obj,a,arguments);Timer.set[a].timer=window.setTimeout("Timer.callOnce("+a+");",c);return a};Timer.prototype.clearInterval=function(a){if(!Timer.set[a]){return}window.clearInterval(Timer.set[a].timer);Timer.set[a]=null};Timer.prototype.clearTimeout=function(a){if(!Timer.set[a]){return}window.clearTimeout(Timer.set[a].timer);Timer.set[a]=null};Timer.set=new Array();Timer.buildCall=function(e,d,b){var c="";Timer.set[d]=new Array();if(e!=window){Timer.set[d].obj=e;c="Timer.set["+d+"].obj."}c+=b[0]+"(";if(b.length>2){Timer.set[d][0]=b[2];c+="Timer.set["+d+"][0]";for(var a=1;(a+2)<b.length;a++){Timer.set[d][a]=b[a+2];c+=", Timer.set["+d+"]["+a+"]"}}c+=");";Timer.set[ d].call=c;return c};Timer.callOnce=function(i){if(!Timer.set[i]){return}eval(Timer.set[i].call);Timer.set[i]=null};Timer.getNew=function(){var a=0;while(Timer.set[a]){a++}return a}; \ No newline at end of file

1 0

[hg] galaxy 2889: Fixes and new functional tests for uploading m...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/15756ebb2b11 changeset: 2889:15756ebb2b11 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 15 20:10:32 2009 -0400 description: Fixes and new functional tests for uploading multi-byte character files and fixes for displaying multi-byte character dataset peek. 8 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/jobs/__init__.py lib/galaxy/model/__init__.py lib/galaxy/tools/actions/upload_common.py lib/galaxy/tools/parameters/grouping.py test-data/asian_chars_1.txt test/functional/test_get_data.py tools/data_source/upload.py diffs (269 lines): diff -r e945dcdfd578 -r 15756ebb2b11 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Thu Oct 15 19:01:07 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Oct 15 20:10:32 2009 -0400 @@ -136,7 +136,7 @@ line = line.strip() if not line: continue - out.append( '<tr><td>%s</td></tr>' % escape( unicode( line ) ) ) + out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc: @@ -437,8 +437,8 @@ temp.close() if file_type in [ 'gzipped', 'binary' ]: text = "%s file" % file_type - else: - text = unicode( '\n'.join( lines ), 'utf-8' ) + else: + text = unicode( '\n'.join( lines ), 'utf-8' ) return text def get_line_count(file_name): diff -r e945dcdfd578 -r 15756ebb2b11 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Oct 15 19:01:07 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Oct 15 20:10:32 2009 -0400 @@ -535,12 +535,12 @@ dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset ).filename_out ) try: assert context.get( 'line_count', None ) is not None - if self.tool.is_multi_byte: + if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: dataset.set_multi_byte_peek( line_count=context['line_count'] ) else: dataset.set_peek( line_count=context['line_count'] ) except: - if self.tool.is_multi_byte: + if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: dataset.set_multi_byte_peek() else: dataset.set_peek() diff -r e945dcdfd578 -r 15756ebb2b11 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Oct 15 19:01:07 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Oct 15 20:10:32 2009 -0400 @@ -5,7 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys +import os.path, os, errno, sys, codecs import galaxy.datatypes from galaxy.util.bunch import Bunch from galaxy import util @@ -418,7 +418,13 @@ return self.get_size() > 0 def mark_deleted( self, include_children=True ): self.deleted = True - + def is_multi_byte( self ): + if not self.has_data(): + return False + try: + return util.is_multi_byte( codecs.open( self.file_name, 'r', 'utf-8' ).read( 100 ) ) + except UnicodeDecodeError, e: + return False # FIXME: sqlalchemy will replace this def _delete(self): """Remove the file that corresponds to this data""" @@ -433,7 +439,7 @@ permitted_actions = Dataset.permitted_actions def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset = False ): + parent_id=None, validation_errors=None, visible=True, create_dataset=False ): self.name = name or "Unnamed dataset" self.id = id self.info = info @@ -519,6 +525,9 @@ def get_mime( self ): """Returns the mime type of the data""" return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) + def is_multi_byte( self ): + """Data consists of multi-byte characters""" + return self.dataset.is_multi_byte() def set_peek( self ): return self.datatype.set_peek( self ) def set_multi_byte_peek( self ): @@ -556,7 +565,7 @@ def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry) def find_conversion_destination( self, accepted_formats, **kwd ): - """Returns ( target_ext, exisiting converted dataset )""" + """Returns ( target_ext, existing converted dataset )""" return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) def add_validation_error( self, validation_error ): self.validation_errors.append( validation_error ) diff -r e945dcdfd578 -r 15756ebb2b11 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Thu Oct 15 19:01:07 2009 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Thu Oct 15 20:10:32 2009 -0400 @@ -27,7 +27,7 @@ elif type( f ) == dict and 'filename' and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) if upload_dataset['url_paste'].strip() != '': - upload_dataset['url_paste'] = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" )[0] + upload_dataset['url_paste'], is_multi_byte = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" ) else: upload_dataset['url_paste'] = None new_files.append( upload_dataset ) @@ -135,7 +135,6 @@ folder.refresh() matches = filter( lambda x: x.name == name, active_folders( trans, folder ) ) if matches: - log.debug( 'DEBUGDEBUG: In %s, found a folder name match: %s:%s' % ( folder.name, matches[0].id, matches[0].name ) ) folder = matches[0] else: new_folder = trans.app.model.LibraryFolder( name=name, description='Automatically created by upload tool' ) @@ -143,7 +142,6 @@ folder.add_folder( new_folder ) new_folder.flush() trans.app.security_agent.copy_library_permissions( folder, new_folder ) - log.debug( 'DEBUGDEBUG: In %s, created a new folder: %s:%s' % ( folder.name, new_folder.id, new_folder.name ) ) folder = new_folder if library_bunch.replace_dataset: ld = library_bunch.replace_dataset diff -r e945dcdfd578 -r 15756ebb2b11 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Thu Oct 15 19:01:07 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Thu Oct 15 20:10:32 2009 -0400 @@ -240,7 +240,7 @@ url_paste = context['url_paste'] name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) - space_to_tab = False + space_to_tab = False if context.get( 'space_to_tab', None ) not in ["None", None]: space_to_tab = True warnings = [] @@ -248,7 +248,6 @@ if file_bunch.path: file_bunch.space_to_tab = space_to_tab rval.append( file_bunch ) - #rval.append( ( type, temp_name, precreated_name, space_to_tab, dataset_name, dataset_info ) ) for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): if file_bunch.path: file_bunch.space_to_tab = space_to_tab @@ -266,11 +265,6 @@ if d_type.composite_type is not None: #handle uploading of composite datatypes #Only one Dataset can be created - - ''' - dataset = UploadedDataset() - dataset.datatype = d_type - ''' dataset = Bunch() dataset.type = 'composite' dataset.file_type = file_type @@ -279,14 +273,12 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} - #load metadata files_metadata = context.get( self.metadata_ref, {} ) for meta_name, meta_spec in d_type.metadata_spec.iteritems(): if meta_spec.set_in_upload: if meta_name in files_metadata: dataset.metadata[ meta_name ] = files_metadata[ meta_name ] - dataset_name = None dataset_info = None if dataset.datatype.composite_type == 'auto_primary_file': diff -r e945dcdfd578 -r 15756ebb2b11 test-data/asian_chars_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/asian_chars_1.txt Thu Oct 15 20:10:32 2009 -0400 @@ -0,0 +1,1 @@ +蛋白質核酸酵素:制癌性物質の化学修飾による効果の向上. \ No newline at end of file diff -r e945dcdfd578 -r 15756ebb2b11 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Thu Oct 15 19:01:07 2009 -0400 +++ b/test/functional/test_get_data.py Thu Oct 15 20:10:32 2009 -0400 @@ -93,3 +93,17 @@ self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda1.id ) ) self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda1.id ) ) self.delete_history( id=self.security.encode_id( history4.id ) ) + def test_020_upload_multibyte_character_file( self ): + """Test uploading multi-byte character file""" + # Logged in as admin_user + self.check_history_for_string( 'Your history is empty' ) + history5 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.upload_file( 'asian_chars_1.txt' ) + hda1 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda1 is not None, "Problem retrieving hda1 from database" + self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda1.hid ) ) + self.check_history_for_string( 'uploaded multi-byte char file' ) + self.delete_history( id=self.security.encode_id( history5.id ) ) diff -r e945dcdfd578 -r 15756ebb2b11 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Oct 15 19:01:07 2009 -0400 +++ b/tools/data_source/upload.py Thu Oct 15 20:10:32 2009 -0400 @@ -4,7 +4,7 @@ # WARNING: Changes in this tool (particularly as related to parsing) may need # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools -import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile +import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs from galaxy import eggs # need to import model before sniff to resolve a circular import dependency import galaxy.model @@ -129,13 +129,11 @@ if dataset.type == 'url': try: - temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( dataset.path ), prefix='url_paste' ) + temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dataset.path ), prefix='url_paste' ) except Exception, e: file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file ) return dataset.path = temp_name - dataset.is_multi_byte = is_multi_byte - # See if we have an empty file if not os.path.exists( dataset.path ): file_err( 'Uploaded temporary file (%s) does not exist.' % dataset.path, dataset, json_file ) @@ -143,11 +141,15 @@ if not os.path.getsize( dataset.path ) > 0: file_err( 'The uploaded file is empty', dataset, json_file ) return - if 'is_multi_byte' not in dir( dataset ): - dataset.is_multi_byte = util.is_multi_byte( open( dataset.path, 'r' ).read( 1024 ) ) + if not dataset.type == 'url': + # Already set is_multi_byte above if type == 'url' + try: + dataset.is_multi_byte = util.is_multi_byte( codecs.open( dataset.path, 'r', 'utf-8' ).read( 100 ) ) + except UnicodeDecodeError, e: + dataset.is_multi_byte = False if dataset.is_multi_byte: + data_type = 'multi-byte char' ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) - data_type = ext 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 ) @@ -283,24 +285,19 @@ sys.exit( 1 ) output_paths = parse_outputs( sys.argv[2:] ) - json_file = open( 'galaxy.json', 'w' ) - for line in open( sys.argv[1], 'r' ): dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) - try: output_path = output_paths[int( dataset.dataset_id )] except: print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id sys.exit( 1 ) - if dataset.type == 'composite': add_composite_file( dataset, json_file, output_path ) else: add_file( dataset, json_file, output_path ) - # clean up paramfile try: os.remove( sys.argv[1] )

1 0

[hg] galaxy 2890: Added anchors--identified by encoded id--to da...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/16a0c13c94cc changeset: 2890:16a0c13c94cc user: jeremy goecks <jeremy.goecks at emory.edu> date: Fri Oct 16 15:54:43 2009 -0400 description: Added anchors--identified by encoded id--to datasets in a history so that HDAs can be directly referenced. Clicking on a dataset in the datasets (HDAs) grid now goes to the dataset within the history. 4 file(s) affected in this change: lib/galaxy/web/controllers/root.py templates/dataset/grid.mako templates/root/history.mako templates/root/history_common.mako diffs (59 lines): diff -r 15756ebb2b11 -r 16a0c13c94cc lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 15 20:10:32 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri Oct 16 15:54:43 2009 -0400 @@ -55,7 +55,7 @@ return trans.fill_template_mako( "/my_data.mako" ) @web.expose - def history( self, trans, as_xml=False, show_deleted=False ): + def history( self, trans, as_xml=False, show_deleted=False, hda_id=None ): """ Display the current history, creating a new history if necessary. NOTE: No longer accepts "id" or "template" options for security reasons. @@ -78,6 +78,7 @@ return trans.stream_template_mako( "root/history.mako", history = history, datasets = query.all(), + hda_id = hda_id, show_deleted = show_deleted ) @web.expose diff -r 15756ebb2b11 -r 16a0c13c94cc templates/dataset/grid.mako --- a/templates/dataset/grid.mako Thu Oct 15 20:10:32 2009 -0400 +++ b/templates/dataset/grid.mako Fri Oct 16 15:54:43 2009 -0400 @@ -110,7 +110,7 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=str(ids) )}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } diff -r 15756ebb2b11 -r 16a0c13c94cc templates/root/history.mako --- a/templates/root/history.mako Thu Oct 15 20:10:32 2009 -0400 +++ b/templates/root/history.mako Fri Oct 16 15:54:43 2009 -0400 @@ -77,6 +77,10 @@ <% updateable = [data for data in reversed( datasets ) if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]] %> ${ ",".join( map(lambda data: "\"%s\" : \"%s\"" % (data.id, data.state), updateable) ) } }); + // Navigate to a dataset. + %if hda_id: + self.location = "#${hda_id}"; + %endif }); // Functionized so AJAX'd datasets can call them function initShowHide() { diff -r 15756ebb2b11 -r 16a0c13c94cc templates/root/history_common.mako --- a/templates/root/history_common.mako Thu Oct 15 20:10:32 2009 -0400 +++ b/templates/root/history_common.mako Fri Oct 16 15:54:43 2009 -0400 @@ -20,7 +20,8 @@ </div> %endif - ## Header row for history items (name, state, action buttons) + ## Header row for history items (name, state, action buttons) + <a name="${trans.security.encode_id(data.id)}"></a> <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload":

1 0