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[hg] galaxy 2887: rename composite files and rewrite the html li...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cbe28b41fb9d changeset: 2887:cbe28b41fb9d user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Thu Oct 15 10:48:38 2009 -0400 description: rename composite files and rewrite the html links if base_name changed in the upload form - this should probably happen in the upload logic 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (63 lines): diff -r 79fe45b43b4e -r cbe28b41fb9d lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Thu Oct 15 07:54:10 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Oct 15 10:48:38 2009 -0400 @@ -238,6 +238,59 @@ rval.append( '<li><a href="%s" type="application/binary">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) rval.append( '</ul></div></html>' ) return "\n".join( rval ) + + def regenerate_primary_file(self,dataset): + """cannot do this until we are setting metadata + """ + def fix(oldpath,newbase): + old,e = os.path.splitext(oldpath) + head,rest = os.path.split(old) + newpath = os.path.join(head,newbase) + newpath = '%s%s' % (newpath,e) + shutil.move(oldpath,newpath) + return newpath + bn = dataset.metadata.base_name + efp = dataset.extra_files_path + flist = os.listdir(efp) + proper_base = bn + rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)] + for i,fname in enumerate(flist): + newpath = fix(os.path.join(efp,fname),proper_base) + sfname = os.path.split(newpath)[-1] + rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) ) + rval.append( '</ul></html>' ) + f = file(dataset.file_name,'w') + f.write("\n".join( rval )) + f.write('\n') + f.close() + + def set_meta( self, dataset, **kwd ): + + """ + NOTE we apply the tabular machinary to the phenodata extracted + from a BioC eSet or affybatch. + + """ + try: + flist = os.listdir(dataset.extra_files_path) + except: + gal_Log.debug('@@@rgenetics set_meta failed - no dataset?') + return + bn = None + for f in flist: + n = os.path.splitext(f)[0] + if not bn: + bn = n + dataset.metadata.base_name = bn + if not bn: + bn = '?' + self.regenerate_primary_file(dataset) + if not dataset.info: + dataset.info = 'Galaxy genotype datatype object' + if not dataset.blurb: + dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit' + return True + class SNPMatrix(Rgenetics): """fake class to distinguish different species of Rgenetics data collections

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[hg] galaxy 2886: remove debug and clean up genetics.py
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/79fe45b43b4e changeset: 2886:79fe45b43b4e user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Thu Oct 15 07:54:10 2009 -0400 description: remove debug and clean up genetics.py 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (504 lines): diff -r 7f5489d7c3d8 -r 79fe45b43b4e lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Wed Oct 14 18:43:38 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Oct 15 07:54:10 2009 -0400 @@ -1,463 +1,3 @@ -<<<<<<< local -""" -rgenetics datatypes -Use at your peril -Ross Lazarus -for the rgenetics and galaxy projects - -genome graphs datatypes derived from Interval datatypes -genome graphs datasets have a header row with appropriate columnames -The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps -subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or 'NA') values -ross lazarus for rgenetics -august 20 2007 -""" - -import logging, os, sys, time, tempfile, shutil -import data -from galaxy import util -from cgi import escape -import urllib -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 - -log = logging.getLogger(__name__) - - - -class GenomeGraphs( Tabular ): - """Tab delimited data containing a marker id and any number of numeric values""" - - """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' - - 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" - #i don't think set_meta should not be called here, it should be called separately - self.set_meta( dataset ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - 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') - - 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! - if dataset.has_data: - 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%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), 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") - sl.append(ggtail) - s = urllib.quote_plus( ''.join(sl) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, s, display_url ) - ret_val.append( (site_name, link) ) - return ret_val - - def validate( self, dataset ): - """Validate a gg file - all numeric after header row""" - errors = list() - infile = open(dataset.file_name, "r") - header= infile.next() # header - for i,row in enumerate(infile): - ll = row.strip().split('\t') - badvals = [] - 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 repair_methods( self, dataset ): - """Return options for removing errors along with a description""" - return [("lines","Remove erroneous lines")] - - -class rgTabList(Tabular): - """ for sampleid and for featureid lists of exclusions or inclusions in the clean tool - featureid subsets on statistical criteria -> specialized display such as gg - """ - file_ext = "rgTList" - - - def __init__(self, **kwd): - """Initialize featurelistt datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = [] - - 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 ) ) - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - 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 - -class rgSampleList(rgTabList): - """ for sampleid exclusions or inclusions in the clean tool - output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,... - since they can be uploaded, should be flexible - but they are persistent at least - same infrastructure for expression? - """ - file_ext = "rgSList" - - def __init__(self, **kwd): - """Initialize samplelist datatype""" - rgTabList.__init__( self, **kwd ) - self.column_names[0] = 'FID' - self.column_names[1] = 'IID' - # this is what Plink wants as at 2009 - - -class rgFeatureList( rgTabList ): - """ for featureid lists of exclusions or inclusions in the clean tool - output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,... - featureid subsets on statistical criteria -> specialized display such as gg - same infrastructure for expression? - """ - file_ext = "rgFList" - - def __init__(self, **kwd): - """Initialize featurelist datatype""" - rgTabList.__init__( self, **kwd ) - for i,s in enumerate(['#FeatureId', 'Chr', 'Genpos', 'Mappos']): - self.column_names[i] = s - - - -class Rgenetics(Html): - """class to use for rgenetics""" - """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True, set_in_upload=True) - - file_ext="html" - composite_type = 'auto_primary_file' - allow_datatype_change = False - - def missing_meta( self, dataset=None, **kwargs): - """Checks for empty meta values""" - for key, value in dataset.metadata.items(): - if not value: - return True - return False - - def generate_primary_file( self, dataset = None ): - rval = ['<html><head><title>Files for Composite Dataset (%s)</title></head><p/>This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext ) ] - for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): - opt_text = '' - if composite_file.optional: - opt_text = ' (optional)' - rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) - rval.append( '</ul></html>' ) - return "\n".join( rval ) - -class SNPMatrix(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="snpmatrix" - - def set_peek( self, dataset ): - if not dataset.dataset.purged: - dataset.peek = "Binary RGenetics file" - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - -class Lped(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="lped" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True ) - - -class Pphe(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="pphe" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name' ) - - -class Lmap(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="lmap" - -class Fphe(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="fphe" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.fphe', description = 'FBAT Phenotype File', substitute_name_with_metadata = 'base_name' ) - -class Phe(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="phe" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' ) - - - -class Fped(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="fped" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' ) - - -class Pbed(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="pbed" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = True ) - -class Eigenstratgeno(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="eigenstratgeno" - - def __init__( self, **kwd ): - Rgenetics.__init__( self, **kwd ) - self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True ) - - - -class Eigenstratpca(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="eigenstratpca" - -class Snptest(Rgenetics): - """fake class to distinguish different species of Rgenetics data collections - """ - file_ext="snptest" - -class RexpBase( Html ): - """base class for BioC data structures in Galaxy - must be constructed with the pheno data in place since that - goes into the metadata for each instance""" - - """Add metadata elements""" - MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="column_names", default=[], desc="Column names", readonly=True,visible=True ) - MetadataElement( name="base_name", - desc="base name for all transformed versions of this genetic dataset", readonly=True, default='galaxy', set_in_upload=True) - ### Do we really need these below? can we rely on dataset.extra_files_path: os.path.join( dataset.extra_files_path, '%s.phenodata' % dataset.metadata.base_name ) ? - ### Do these have a different purpose? Ross will need to clarify - ### Uploading these datatypes will not work until this is sorted out (set_peek fails)... - MetadataElement( name="pheno_path", - desc="Path to phenotype data for this experiment", readonly=True) - MetadataElement( name="pheno", - desc="Phenotype data for this experiment", readonly=True) - - file_ext = None - - is_binary = True - - allow_datatype_change = False - - composite_type = 'basic' - - def __init__( self, **kwd ): - Html.__init__( self, **kwd ) - self.add_composite_file( '%s.phenodata', substitute_name_with_metadata = 'base_name', is_binary = True ) - self.metadata.pheno_path = '%s.phenodata' % (self.metadata.base_name) - - def missing_meta( self, dataset=None, **kwargs): - """Checks for empty meta values""" - for key, value in dataset.metadata.items(): - if not value: - return True - return False - - def get_pheno(self,dataset): - """expects a .pheno file in the extra_files_dir - ugh - note that R is wierd and does not include the row.name in - the header. why?""" - p = file(dataset.metadata.pheno_path,'r').readlines() #this fails - head = p[0].strip().split('\t') - head.insert(0,'ChipFileName') # fix R write.table b0rken-ness - p[0] = '\t'.join(head) - p = '\n'.join(p) - return p - - def set_peek( self, dataset ): - """expects a .pheno file in the extra_files_dir - ugh - note that R is wierd and does not include the row.name in - the header. why?""" - p = self.get_pheno(dataset) - dataset.peek = p[:20] - dataset.info = p[0] - dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' - - # stolen from Tabular - # class Tabular( data.Text ): - """Tab delimited data""" - - """Add metadata elements""" - def init_meta( self, dataset, copy_from=None ): - if copy_from: - dataset.metadata = copy_from.metadata - - def set_readonly_meta( self, dataset, **kwd ): - """Resets the values of readonly metadata elements.""" - RexpBase.set_meta( self, dataset ) - - def set_meta( self, dataset, **kwd ): - - """ - NOTE we apply the tabular machinary to the phenodata extracted - from a BioC eSet or affybatch. - - """ - if not dataset.peek: - dataset.set_peek() - pk = dataset.get_pheno # read the basename.phenodata in the extra_files_path - ###this is probably not the best source, can we just access the raw data directly? - if pk: - p = pk.split('\n') - h = p[0].strip().split('\t') # hope is header - h = [escape(x) for x in h] - dataset.metadata.column_names = h - dataset.metadata.columns = len(h) - else: - dataset.metadata.column_names = [] - dataset.metadata.columns = 0 - - def make_html_table( self, dataset): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">',] - try: - # Generate column header - pk = dataset.peek - p = pk.split('\n') - for i,row in enumerate(p): - lrow = row.strip().split('\t') - if i == 0: - orow = ['<th>%s</th>' % escape(x) for x in lrow] - orow.insert(0,'<tr>') - orow.append('</tr>') - else: - orow = ['<td>%s</td>' % escape(x) for x in lrow] - orow.insert(0,'<tr>') - orow.append('</tr>') - out.append(''.join(orow)) - out.append( '</table>' ) - out = "\n".join( out ) - except Exception, exc: - out = "Can't create peek %s" % str( exc ) - return out - - def display_peek( self, dataset ): - """Returns formatted html of peek""" - if not dataset.peek: - dataset.set_peek() - return self.make_html_table( dataset ) - - def get_mime(self): - """Returns the mime type of the datatype""" - return 'application/gzip' - - -class AffyBatch( RexpBase ): - """derived class for BioC data structures in Galaxy """ - file_ext = "affybatch" - - -class ESet( RexpBase ): - """derived class for BioC data structures in Galaxy """ - file_ext = "eset" - - -class MAList( RexpBase ): - """derived class for BioC data structures in Galaxy """ - file_ext = "malist" - - -if __name__ == '__main__': - import doctest, sys - doctest.testmod(sys.modules[__name__]) - -======= """ rgenetics datatypes Use at your peril @@ -957,7 +497,6 @@ p = file(pp,'r').readlines() except: p = ['##failed to find %s' % pp,] - gal_Log.debug('@@@rexpression set_peek, dataset.name=%s,\npp=%s,\np=%s' % (dataset.name,pp,p[:3])) dataset.peek = ''.join(p[:5]) dataset.blurb = 'Galaxy Rexpression composite file' else: @@ -972,7 +511,6 @@ p = file(pp,'r').readlines() except: p = ['##failed to find %s' % pp] - gal_Log.debug('@@@rexpression get_peek, dataset.file_name=%s,\npp=%s,\np=%s' % (dataset.file_name,pp,p[:3])) return ''.join(p[:5]) def get_file_peek(self,filename): @@ -996,7 +534,6 @@ sfname = os.path.split(fname)[-1] rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) ) rval.append( '</ul></html>' ) - gal_Log.debug('rexpression regenerate primary file, writing %s' % rval) f = file(dataset.file_name,'w') f.write("\n".join( rval )) f.write('\n') @@ -1054,7 +591,6 @@ dataset.info = 'Galaxy Expression datatype object' if not dataset.blurb: dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' - gal_Log.debug('@@@rexpression set_meta on dsn=%s, pf=%s, peek=%s' % (dataset.file_name,''.join(pf[:5]),dataset.peek)) return True def make_html_table( self, pp='nothing supplied from peek\n'): @@ -1125,4 +661,3 @@ doctest.testmod(sys.modules[__name__]) ->>>>>>> other

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[hg] galaxy 2884: adding three LGPL ECMA script helpers for rgGR...
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c2d042ba8cd0 changeset: 2884:c2d042ba8cd0 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Wed Oct 14 15:47:58 2009 -0400 description: adding three LGPL ECMA script helpers for rgGRR interactive SVG. 4 file(s) affected in this change: lib/galaxy/datatypes/genetics.py static/scripts/checkbox_and_radiobutton.js static/scripts/helper_functions.js static/scripts/timer.js diffs (1724 lines): diff -r 878ca31a4995 -r c2d042ba8cd0 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Wed Oct 14 09:33:56 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Wed Oct 14 15:47:58 2009 -0400 @@ -1,3 +1,463 @@ +<<<<<<< local +""" +rgenetics datatypes +Use at your peril +Ross Lazarus +for the rgenetics and galaxy projects + +genome graphs datatypes derived from Interval datatypes +genome graphs datasets have a header row with appropriate columnames +The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps +subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or 'NA') values +ross lazarus for rgenetics +august 20 2007 +""" + +import logging, os, sys, time, tempfile, shutil +import data +from galaxy import util +from cgi import escape +import urllib +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 + +log = logging.getLogger(__name__) + + + +class GenomeGraphs( Tabular ): + """Tab delimited data containing a marker id and any number of numeric values""" + + """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' + + 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" + #i don't think set_meta should not be called here, it should be called separately + self.set_meta( dataset ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + 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') + + 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! + if dataset.has_data: + 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%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), 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") + sl.append(ggtail) + s = urllib.quote_plus( ''.join(sl) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, s, display_url ) + ret_val.append( (site_name, link) ) + return ret_val + + def validate( self, dataset ): + """Validate a gg file - all numeric after header row""" + errors = list() + infile = open(dataset.file_name, "r") + header= infile.next() # header + for i,row in enumerate(infile): + ll = row.strip().split('\t') + badvals = [] + 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 repair_methods( self, dataset ): + """Return options for removing errors along with a description""" + return [("lines","Remove erroneous lines")] + + +class rgTabList(Tabular): + """ for sampleid and for featureid lists of exclusions or inclusions in the clean tool + featureid subsets on statistical criteria -> specialized display such as gg + """ + file_ext = "rgTList" + + + def __init__(self, **kwd): + """Initialize featurelistt datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = [] + + 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 ) ) + if dataset.metadata.columns - len( self.column_names ) > 0: + for i in range( len( self.column_names ), dataset.metadata.columns ): + out.append( '<th>%s</th>' % str( i+1 ) ) + out.append( '</tr>' ) + 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 + +class rgSampleList(rgTabList): + """ for sampleid exclusions or inclusions in the clean tool + output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,... + since they can be uploaded, should be flexible + but they are persistent at least + same infrastructure for expression? + """ + file_ext = "rgSList" + + def __init__(self, **kwd): + """Initialize samplelist datatype""" + rgTabList.__init__( self, **kwd ) + self.column_names[0] = 'FID' + self.column_names[1] = 'IID' + # this is what Plink wants as at 2009 + + +class rgFeatureList( rgTabList ): + """ for featureid lists of exclusions or inclusions in the clean tool + output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,... + featureid subsets on statistical criteria -> specialized display such as gg + same infrastructure for expression? + """ + file_ext = "rgFList" + + def __init__(self, **kwd): + """Initialize featurelist datatype""" + rgTabList.__init__( self, **kwd ) + for i,s in enumerate(['#FeatureId', 'Chr', 'Genpos', 'Mappos']): + self.column_names[i] = s + + + +class Rgenetics(Html): + """class to use for rgenetics""" + """Add metadata elements""" + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True, set_in_upload=True) + + file_ext="html" + composite_type = 'auto_primary_file' + allow_datatype_change = False + + def missing_meta( self, dataset=None, **kwargs): + """Checks for empty meta values""" + for key, value in dataset.metadata.items(): + if not value: + return True + return False + + def generate_primary_file( self, dataset = None ): + rval = ['<html><head><title>Files for Composite Dataset (%s)</title></head><p/>This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext ) ] + for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): + opt_text = '' + if composite_file.optional: + opt_text = ' (optional)' + rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) + rval.append( '</ul></html>' ) + return "\n".join( rval ) + +class SNPMatrix(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="snpmatrix" + + def set_peek( self, dataset ): + if not dataset.dataset.purged: + dataset.peek = "Binary RGenetics file" + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + +class Lped(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="lped" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True ) + + +class Pphe(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="pphe" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name' ) + + +class Lmap(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="lmap" + +class Fphe(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="fphe" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.fphe', description = 'FBAT Phenotype File', substitute_name_with_metadata = 'base_name' ) + +class Phe(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="phe" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' ) + + + +class Fped(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="fped" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' ) + + +class Pbed(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="pbed" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = True ) + +class Eigenstratgeno(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="eigenstratgeno" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True ) + + + +class Eigenstratpca(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="eigenstratpca" + +class Snptest(Rgenetics): + """fake class to distinguish different species of Rgenetics data collections + """ + file_ext="snptest" + +class RexpBase( Html ): + """base class for BioC data structures in Galaxy + must be constructed with the pheno data in place since that + goes into the metadata for each instance""" + + """Add metadata elements""" + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="column_names", default=[], desc="Column names", readonly=True,visible=True ) + MetadataElement( name="base_name", + desc="base name for all transformed versions of this genetic dataset", readonly=True, default='galaxy', set_in_upload=True) + ### Do we really need these below? can we rely on dataset.extra_files_path: os.path.join( dataset.extra_files_path, '%s.phenodata' % dataset.metadata.base_name ) ? + ### Do these have a different purpose? Ross will need to clarify + ### Uploading these datatypes will not work until this is sorted out (set_peek fails)... + MetadataElement( name="pheno_path", + desc="Path to phenotype data for this experiment", readonly=True) + MetadataElement( name="pheno", + desc="Phenotype data for this experiment", readonly=True) + + file_ext = None + + is_binary = True + + allow_datatype_change = False + + composite_type = 'basic' + + def __init__( self, **kwd ): + Html.__init__( self, **kwd ) + self.add_composite_file( '%s.phenodata', substitute_name_with_metadata = 'base_name', is_binary = True ) + self.metadata.pheno_path = '%s.phenodata' % (self.metadata.base_name) + + def missing_meta( self, dataset=None, **kwargs): + """Checks for empty meta values""" + for key, value in dataset.metadata.items(): + if not value: + return True + return False + + def get_pheno(self,dataset): + """expects a .pheno file in the extra_files_dir - ugh + note that R is wierd and does not include the row.name in + the header. why?""" + p = file(dataset.metadata.pheno_path,'r').readlines() #this fails + head = p[0].strip().split('\t') + head.insert(0,'ChipFileName') # fix R write.table b0rken-ness + p[0] = '\t'.join(head) + p = '\n'.join(p) + return p + + def set_peek( self, dataset ): + """expects a .pheno file in the extra_files_dir - ugh + note that R is wierd and does not include the row.name in + the header. why?""" + p = self.get_pheno(dataset) + dataset.peek = p[:20] + dataset.info = p[0] + dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' + + # stolen from Tabular + # class Tabular( data.Text ): + """Tab delimited data""" + + """Add metadata elements""" + def init_meta( self, dataset, copy_from=None ): + if copy_from: + dataset.metadata = copy_from.metadata + + def set_readonly_meta( self, dataset, **kwd ): + """Resets the values of readonly metadata elements.""" + RexpBase.set_meta( self, dataset ) + + def set_meta( self, dataset, **kwd ): + + """ + NOTE we apply the tabular machinary to the phenodata extracted + from a BioC eSet or affybatch. + + """ + if not dataset.peek: + dataset.set_peek() + pk = dataset.get_pheno # read the basename.phenodata in the extra_files_path + ###this is probably not the best source, can we just access the raw data directly? + if pk: + p = pk.split('\n') + h = p[0].strip().split('\t') # hope is header + h = [escape(x) for x in h] + dataset.metadata.column_names = h + dataset.metadata.columns = len(h) + else: + dataset.metadata.column_names = [] + dataset.metadata.columns = 0 + + def make_html_table( self, dataset): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">',] + try: + # Generate column header + pk = dataset.peek + p = pk.split('\n') + for i,row in enumerate(p): + lrow = row.strip().split('\t') + if i == 0: + orow = ['<th>%s</th>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + else: + orow = ['<td>%s</td>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + out.append(''.join(orow)) + out.append( '</table>' ) + out = "\n".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + def display_peek( self, dataset ): + """Returns formatted html of peek""" + if not dataset.peek: + dataset.set_peek() + return self.make_html_table( dataset ) + + def get_mime(self): + """Returns the mime type of the datatype""" + return 'application/gzip' + + +class AffyBatch( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "affybatch" + + +class ESet( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "eset" + + +class MAList( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "malist" + + +if __name__ == '__main__': + import doctest, sys + doctest.testmod(sys.modules[__name__]) + +======= """ rgenetics datatypes Use at your peril @@ -665,3 +1125,4 @@ doctest.testmod(sys.modules[__name__]) +>>>>>>> other diff -r 878ca31a4995 -r c2d042ba8cd0 static/scripts/checkbox_and_radiobutton.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/checkbox_and_radiobutton.js Wed Oct 14 15:47:58 2009 -0400 @@ -0,0 +1,347 @@ +/* +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 878ca31a4995 -r c2d042ba8cd0 static/scripts/helper_functions.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/helper_functions.js Wed Oct 14 15:47:58 2009 -0400 @@ -0,0 +1,817 @@ +/** + * @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 878ca31a4995 -r c2d042ba8cd0 static/scripts/timer.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/timer.js Wed Oct 14 15:47:58 2009 -0400 @@ -0,0 +1,74 @@ +// 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

1 0

[hg] galaxy 2885: pack the new scripts for rgenetics
by Greg Von Kuster 20 Oct '09

20 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7f5489d7c3d8 changeset: 2885:7f5489d7c3d8 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Oct 14 18:43:38 2009 -0400 description: pack the new scripts for rgenetics 3 file(s) affected in this change: static/scripts/packed/checkbox_and_radiobutton.js static/scripts/packed/helper_functions.js static/scripts/packed/timer.js diffs (18 lines): diff -r c2d042ba8cd0 -r 7f5489d7c3d8 static/scripts/packed/checkbox_and_radiobutton.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/checkbox_and_radiobutton.js Wed Oct 14 18:43:38 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 c2d042ba8cd0 -r 7f5489d7c3d8 static/scripts/packed/helper_functions.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/helper_functions.js Wed Oct 14 18:43:38 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 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1 0

Running tools on command line
by SHAUN WEBB 16 Oct '09

16 Oct '09

Hi, I want to run a few of the interval operation tools on the command line, however I am getting the following error: Traceback (most recent call last): File "/home/swebb/galaxy/galaxy_dist/tools/new_operations/gops_join.py", line 11, in <module> from galaxy import eggs ImportError: No module named galaxy I assume I may need to alter some Environmental variables. Any help appreciated. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

Writing functional test for galaxy tool.
by Vipin Thankam Sreedharan 16 Oct '09

16 Oct '09

To whom it may concern, Here is my test code. ******************************************************** <tests> <test> <param name="source" value="From current history" /> <param name="fasta_input" value="chr4.fas" ftype="fasta" /> <param name="organism" value="Arabidopsis thaliana (TAIR9)" /> <output name="output" file="tair9_test.txt" /> </test> </tests> ******************************************************** And I am getting a failure result for my test. The error message is ******************************************************* 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 363, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 3 different than expected, difference: --- local_file +++ history_data @@ -1,0 +1,14 @@ ***************************************************** It will be great if you can suggest a way for me to solve the problem. Many thanks in advance, Vipin T S

2 2

request: dedicated python files for user datatypes
by Assaf Gordon 14 Oct '09

14 Oct '09

Hello, I'd like to request a small change: to create a dedicated python file for user customizable datatypes - something like "user_intervals.py" along side "intervals.py" (in /lib/galaxy/datatypes). The reason is that we have our own custom types, with special column assignment. So for example, I've added the following class to the bottom of "intervals.py": ========= class Foobar ( Interval ): """Foobar results""" """Add metadata elements""" MetadataElement( name="chromCol", default=2, 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", default=3, desc="Strand column", param=metadata.ColumnParameter ) MetadataElement( name="nameCol", default=1, desc="Name/Identifier column", param=metadata.ColumnParameter ) MetadataElement( name="columns", default=6, desc="Number of columns", readonly=True, visible=False ) =========== It's a simple text file containing intervals, but with different column assignment. I also updated <datatypes_conf.xml>, and this way, if my tool outputs a "foobar" format - the columns assignment works perfectly. The only problem is merging: If the "intervals.py" file is changed in the main repository - automatic merging doesn't work cleanly. It needs to merge an old intervals.py (with my custom types) together with a new intervals.py (without my custom types). Maybe I'm doing something wrong, but I always end up having to manually resolve the conflicts. My suggestion is to have an empty "user_intervals.py" (or other datatypes, too), which will be monitored in the repository, but will not contain any Galaxy official types. That will keep a clear separation between galaxy types and user types. If this is already possible somehow, please let me know. Thanks! gordon.

2 1

[hg] galaxy 2883: Remove a debug statement, slight cleanup.
by Greg Von Kuster 14 Oct '09

14 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/878ca31a4995 changeset: 2883:878ca31a4995 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Oct 14 09:33:56 2009 -0400 description: Remove a debug statement, slight cleanup. 3 file(s) affected in this change: lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py diffs (37 lines): diff -r ca816e66ec69 -r 878ca31a4995 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Wed Oct 14 02:22:11 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Wed Oct 14 09:33:56 2009 -0400 @@ -135,7 +135,6 @@ renaming fields, adding/deleting fields, changing fields attributes. ''' params = util.Params( kwd ) - log.debug( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) try: diff -r ca816e66ec69 -r 878ca31a4995 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Wed Oct 14 02:22:11 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Wed Oct 14 09:33:56 2009 -0400 @@ -114,7 +114,8 @@ created_ldda_ids = params.get( 'created_ldda_ids', '' ) hidden_folder_ids = util.listify( util.restore_text( params.get( 'hidden_folder_ids', '' ) ) ) if created_ldda_ids and not msg: - msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). Please do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the upload(s) change from the \"uploading\" state." % ( len( created_ldda_ids.split(',') ), library.name ) + msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). " % ( len( created_ldda_ids.split(',') ), library.name ) + msg += "Do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons ( on this tab ) until the upload(s) change from the \"uploading\" state." messagetype = "info" return trans.fill_template( '/library/browse_library.mako', library=library, diff -r ca816e66ec69 -r 878ca31a4995 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Wed Oct 14 02:22:11 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Oct 14 09:33:56 2009 -0400 @@ -50,7 +50,8 @@ messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) if created_ldda_ids and not msg: - msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). Please do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the upload(s) change from the \"uploading\" state." % ( len( created_ldda_ids.split(',') ), library.name ) + msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). " % ( len( created_ldda_ids.split( ',' ) ), library.name ) + msg += "Do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons ( on this tab ) until the upload(s) change from the \"uploading\" state." messagetype = "info" return trans.fill_template( '/admin/library/browse_library.mako', library=library,

1 0

[hg] galaxy 2882: Forms & request controllers
by Greg Von Kuster 14 Oct '09

14 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ca816e66ec69 changeset: 2882:ca816e66ec69 user: rc date: Wed Oct 14 02:22:11 2009 -0400 description: Forms & request controllers - refactored to work on main - cleanup Added more functional tests 12 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/framework/__init__.py templates/admin/forms/edit_form.mako templates/admin/forms/show_form_read_only.mako templates/admin/requests/show_request.mako templates/requests/show_request.mako templates/user/address.mako test/base/twilltestcase.py test/functional/test_forms_and_requests.py diffs (2308 lines): diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Oct 13 18:15:06 2009 -0400 +++ b/lib/galaxy/model/__init__.py Wed Oct 14 02:22:11 2009 -0400 @@ -1090,11 +1090,12 @@ types = Bunch( REQUEST = 'Sequencing Request Form', SAMPLE = 'Sequencing Sample Form', LIBRARY_INFO_TEMPLATE = 'Library information template' ) - def __init__(self, name=None, desc=None, fields=[], current_form=None, form_type=None, layout=None): + def __init__(self, name=None, desc=None, fields=[], + form_definition_current=None, form_type=None, layout=None): self.name = name self.desc = desc self.fields = fields - self.form_definition_current = current_form + self.form_definition_current = form_definition_current self.type = form_type self.layout = layout def fields_of_grid(self, layout_grid_name): @@ -1263,20 +1264,26 @@ self.postal_code = postal_code self.country = country self.phone = phone - def display(self): - return self.name+'<br/>'+ \ - self.institution+'<br/>'+ \ - self.address+'<br/>'+ \ - self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \ - self.country+'<br/>'+ \ - 'Phone: '+self.phone def get_html(self): - return self.name+'<br/>'+ \ - self.institution+'<br/>'+ \ - self.address+'<br/>'+ \ - self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \ - self.country+'<br/>'+ \ - 'Phone: '+self.phone + html = '' + if self.name: + html = html + self.name + if self.institution: + html = html + '<br/>' + self.institution + if self.address: + html = html + '<br/>' + self.address + if self.city: + html = html + '<br/>' + self.city + if self.state: + html = html + ' ' + self.state + if self.postal_code: + html = html + ' ' + self.postal_code + if self.country: + html = html + '<br/>' + self.country + if self.phone: + html = html + '<br/>' + 'Phone: ' + self.phone + return html + class Page( object ): def __init__( self ): diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Oct 13 18:15:06 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Wed Oct 14 02:22:11 2009 -0400 @@ -12,6 +12,14 @@ log = logging.getLogger( __name__ ) class Forms( BaseController ): + # Empty form field + empty_field = { 'label': '', + 'helptext': '', + 'visible': True, + 'required': False, + 'type': BaseField.form_field_types()[0], + 'selectlist': [], + 'layout': 'none' } @web.expose @web.require_admin def index( self, trans, **kwd ): @@ -84,19 +92,12 @@ action='edit', form_id=fd.id, add_field_button='Add field', - num_fields=0, name=fd.name, description=fd.desc, form_type_selectbox=fd.type ) ) - self.current_form = {} - self.current_form[ 'name' ] = 'New Form' - self.current_form[ 'desc' ] = '' - self.current_form[ 'type' ] = params.get( 'form_type', 'none' ) - self.current_form[ 'layout' ] = [ 'Main' ] - self.current_form[ 'fields' ] = [] - inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), - ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), - ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ), + inputs = [ ( 'Name', TextField( 'name', 40, 'New Form' ) ), + ( 'Description', TextField( 'description', 40, '' ) ), + ( 'Type', self.__form_types_widget(trans, selected=params.get( 'form_type', 'none' )) ), ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', inputs=inputs, @@ -134,102 +135,156 @@ renaming fields, adding/deleting fields, changing fields attributes. ''' params = util.Params( kwd ) + log.debug( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - form_id = params.get( 'form_id', None ) - if not form_id: - msg = 'Invalid form id %s' % str( form_id ) - trans.response.send_redirect( web.url_for( controller='forms', - action='manage', - msg=msg, - messagetype='error' ) ) - fd = trans.app.model.FormDefinition.get( int( params.form_id ) ) + try: + fd = trans.app.model.FormDefinition.get( int( params.get( 'form_id', None ) ) ) + except: + return trans.response.send_redirect( web.url_for( controller='forms', + action='manage', + msg='Invalid form', + messagetype='error' ) ) + # # Show the form for editing + # if params.get( 'show_form', False ): - self.__get_saved_form( fd ) - # The following two dicts store the unsaved select box options - self.del_options = {} - self.add_options = {} - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - #Add a layout grid + current_form = self.__get_saved_form( fd ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # + # Add a layout grid + # elif params.get( 'add_layout_grid', False ): - self.__update_current_form( trans, **kwd ) - self.__add_layout_grid() + current_form = self.__get_form( trans, **kwd ) + current_form['layout'].append('') # show the form again - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # # Delete a layout grid + # elif params.get( 'remove_layout_grid_button', False ): - self.__update_current_form( trans, **kwd ) + current_form = self.__get_form( trans, **kwd ) index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1 - self.__remove_layout_grid( index ) - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + del current_form['layout'][index] + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # + # Add a field + # + elif params.get( 'add_field_button', False ): + current_form = self.__get_form( trans, **kwd ) + current_form['fields'].append( self.empty_field ) + # show the form again with one empty field + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # # Delete a field + # elif params.get( 'remove_button', False ): - self.__update_current_form( trans, **kwd ) + current_form = self.__get_form( trans, **kwd ) + # find the index of the field to be removed from the remove button label index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1 - self.__remove_field( index ) - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + del current_form['fields'][index] + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # # Save changes + # elif params.get( 'save_changes_button', False ): - self.__update_current_form( trans, **kwd ) - fd_new, msg = self.__save_form( trans, fd.form_definition_current.id, **kwd ) + fd_new, msg = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd ) + # if validation error encountered while saving the form, show the + # unsaved form, with the error message if not fd_new: - return self.__show( trans=trans, form=fd, msg=msg, messagetype='error', **kwd ) - else: - fd = fd_new + current_form = self.__get_form( trans, **kwd ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype='error', **kwd ) + # everything went fine. form saved successfully. Show the saved form + fd = fd_new + current_form = self.__get_saved_form( fd ) msg = "The form '%s' has been updated with the changes." % fd.name - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - #Add a field - elif params.get( 'add_field_button', False ): - self.__update_current_form( trans, **kwd ) - self.__add_field() - # show the form again with one empty field - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + # # Show form read-only + # elif params.get( 'read_only', False ): return trans.fill_template( '/admin/forms/show_form_read_only.mako', form=fd, msg=msg, messagetype=messagetype ) - # Refresh page, SelectField is selected/deselected as the type of a field + # + # Add SelectField option + # + elif 'Add' in kwd.values(): + return self.__add_selectbox_option(trans, fd, msg, messagetype, **kwd) + # + # Remove SelectField option + # + elif 'Remove' in kwd.values(): + return self.__remove_selectbox_option(trans, fd, msg, messagetype, **kwd) + # + # Refresh page + # elif params.get( 'refresh', False ): - self.__update_current_form( trans, **kwd ) - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - # Remove SelectField option - elif params.get( 'select_box_options', False ) == 'remove': - index = int( kwd[ 'field_index' ] ) - option = int( kwd[ 'option_index' ] ) - del self.current_form[ 'fields' ][ index ][ 'selectlist' ][ option ] - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - # Add SelectField option - elif params.get( 'select_box_options', False ) == 'add': - index = int( kwd[ 'field_index' ] ) - self.current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - def __add_layout_grid(self): - self.current_form['layout'].append('') - def __remove_layout_grid(self, index): - del self.current_form['layout'][index] - def __remove_field(self, index): - del self.current_form['fields'][index] - def __add_field(self): + current_form = self.__get_form( trans, **kwd ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + + def __add_selectbox_option( self, trans, fd, msg, messagetype, **kwd ): ''' - add an empty field to the fields list + This method adds a selectbox option. The kwd dict searched for + the field index which needs to be removed ''' - empty_field = { 'label': '', - 'helptext': '', - 'visible': True, - 'required': False, - 'type': BaseField.form_field_types()[0], - 'selectlist': [], - 'layout': 'none' } - self.current_form['fields'].append(empty_field) + current_form = self.__get_form( trans, **kwd ) + index = -1 + for k, v in kwd.items(): + if v == 'Add': + # extract the field index from the + # button name of format: 'addoption_<field>' + index = int(k.split('_')[1]) + break + if index == -1: + # something wrong happened + return self.__show( trans=trans, form=fd, current_form=current_form, + msg='Error in adding selectfield option', + messagetype='error', **kwd ) + # add an empty option + current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + def __remove_selectbox_option( self, trans, fd, msg, messagetype, **kwd ): + ''' + This method removes a selectbox option. The kwd dict searched for + the field index and option index which needs to be removed + ''' + current_form = self.__get_form( trans, **kwd ) + option = -1 + for k, v in kwd.items(): + if v == 'Remove': + # extract the field & option indices from the + # button name of format: 'removeoption_<field>_<option>' + index = int(k.split('_')[1]) + option = int(k.split('_')[2]) + break + if option == -1: + # something wrong happened + return self.__show( trans=trans, form=fd, current_form=current_form, + msg='Error in removing selectfield option', + messagetype='error', **kwd ) + # remove the option + del current_form[ 'fields' ][ index ][ 'selectlist' ][ option ] + return self.__show( trans=trans, form=fd, current_form=current_form, + msg=msg, messagetype=messagetype, **kwd ) + + def __get_field(self, index, **kwd): + ''' + This method retrieves all the user-entered details of a field and + returns a dict. + ''' params = util.Params( kwd ) - #TODO: RC this needs to be handled so that it does not throw an exception. - # To reproduce, create a new form, click the "add field" button, click the - # browser back arrow, then click the "add field" button again. - # You should never attempt to "restore_text()" on a None object... name = util.restore_text( params.get( 'field_name_%i' % index, '' ) ) helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) ) required = params.get( 'field_required_%i' % index, False ) @@ -266,57 +321,54 @@ else: return sb_options def __get_saved_form(self, fd): - self.current_form = {} - self.current_form['name'] = fd.name - self.current_form['desc'] = fd.desc - self.current_form['type'] = fd.type - self.current_form['layout'] = list(copy.deepcopy(fd.layout)) - self.current_form['fields'] = list(copy.deepcopy(fd.fields)) - def __validate_form(self, **kwd): ''' - This method checks the following text inputs are filled out by the user - - the name of form - - name of all the fields + This retrieves the saved form and returns a dictionary containing the name, + desc, type, layout & fields of the form ''' - params = util.Params( kwd ) - # form name - if not util.restore_text( params.name ): - return None, 'Form name must be filled.' - # form type - if util.restore_text( params.form_type_selectbox ) == 'none': - return None, 'Form type must be selected.' - # fields -# for i in range( len(self.current_form['fields']) ): -# if not util.restore_text(params.get( 'field_name_%i' % i, None )): -# return None, "All the field label(s) must be completed." - return True, '' + return dict(name = fd.name, + desc = fd.desc, + type = fd.type, + layout = list(copy.deepcopy(fd.layout)), + fields = list(copy.deepcopy(fd.fields))) def __get_form(self, trans, **kwd): + ''' + This method gets all the user-entered form details and returns a + dictionary containing the name, desc, type, layout & fields of the form + ''' params = util.Params( kwd ) name = util.restore_text( params.name ) desc = util.restore_text( params.description ) or "" form_type = util.restore_text( params.form_type_selectbox ) + # get the user entered layout grids layout = [] - if form_type == trans.app.model.FormDefinition.types.SAMPLE: - for index in range(len(self.current_form[ 'layout' ])): - layout.append(params.get( 'grid_layout%i' % index, '' )) + index = 0 + while True: + grid_name = util.restore_text( params.get( 'grid_layout%i' % index, '' ) ) + if grid_name: + layout.append( grid_name ) + index = index + 1 + else: + break + # for csv file import csv_file = params.get( 'file_data', '' ) + fields = [] if csv_file == '': - # set form fields - fields = [] - for i in range( len(self.current_form['fields']) ): - fields.append(self.__get_field(i, **kwd)) + # get the user entered fields + index = 0 + while True: + if params.get( 'field_name_%i' % index, False ): + fields.append( self.__get_field( index, **kwd ) ) + index = index + 1 + else: + break fields = fields else: fields, layout = self.__import_fields(trans, csv_file, form_type) - return name, desc, form_type, layout, fields - def __update_current_form(self, trans, **kwd): - name, desc, form_type, layout, fields = self.__get_form(trans, **kwd) - self.current_form = {} - self.current_form['name'] = name - self.current_form['desc'] = desc - self.current_form['type'] = form_type - self.current_form['layout'] = layout - self.current_form['fields'] = fields + return dict(name = name, + desc = desc, + type = form_type, + layout = layout, + fields = fields) def __import_fields(self, trans, csv_file, form_type): ''' @@ -356,7 +408,20 @@ **kwd)) self.__imported_from_file = True return fields, list(layouts) - + def __validate_form(self, **kwd): + ''' + This method checks the following text inputs are filled out by the user + - the name of form + - form type + ''' + params = util.Params( kwd ) + # form name + if not util.restore_text( params.name ): + return None, 'Form name must be filled.' + # form type + if util.restore_text( params.form_type_selectbox ) == 'none': + return None, 'Form type must be selected.' + return True, '' def __save_form(self, trans, fdc_id=None, **kwd): ''' This method saves the current form @@ -365,13 +430,18 @@ flag, msg = self.__validate_form(**kwd) if not flag: return None, msg - name, desc, form_type, layout, fields = self.__get_form(trans, **kwd) + current_form = self.__get_form( trans, **kwd ) # validate fields - for field in fields: + for field in current_form[ 'fields' ]: if not field[ 'label' ]: return None, "All the field label(s) must be completed." - fd = trans.app.model.FormDefinition(name, desc, fields, current_form=None, - form_type=form_type, layout=layout ) + # create a new form definition + fd = trans.app.model.FormDefinition(name=current_form[ 'name' ], + desc=current_form[ 'desc' ], + fields=current_form[ 'fields' ], + form_definition_current=None, + form_type=current_form[ 'type' ], + layout=current_form[ 'layout' ] ) if fdc_id: # save changes to the existing form # change the pointer in the form_definition_current table to point # to this new record @@ -467,7 +537,7 @@ def label(self): return str(self.index)+'.'+self.label - def __show( self, trans, form, msg='', messagetype='done', **kwd ): + def __show( self, trans, form, current_form, msg='', messagetype='done', **kwd ): ''' This method displays the form and any of the changes made to it, The empty_form param allows for this method to simulate clicking @@ -476,18 +546,18 @@ ''' params = util.Params( kwd ) # name & description - form_details = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), - ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), - ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ) ] + form_details = [ ( 'Name', TextField( 'name', 40, current_form[ 'name' ] ) ), + ( 'Description', TextField( 'description', 40, current_form[ 'desc' ] ) ), + ( 'Type', self.__form_types_widget(trans, selected=current_form[ 'type' ]) ) ] form_layout = [] - if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE: - for index, lg in enumerate(self.current_form['layout']): + if current_form[ 'type' ] == trans.app.model.FormDefinition.types.SAMPLE: + for index, lg in enumerate(current_form[ 'layout' ]): form_layout.append( TextField( 'grid_layout%i' % index, 40, lg )) # fields field_details = [] - for index, field in enumerate( self.current_form[ 'fields' ] ): - if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE: - field_ui = self.FieldUI( self.current_form['layout'], index, field ) + for index, field in enumerate( current_form[ 'fields' ] ): + if current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE: + field_ui = self.FieldUI( current_form['layout'], index, field ) else: field_ui = self.FieldUI( None, index, field ) field_details.append( field_ui.get() ) @@ -498,7 +568,7 @@ field_types=BaseField.form_field_types(), msg=msg, messagetype=messagetype, - current_form_type=self.current_form['type'], + current_form_type=current_form[ 'type' ], layout_grids=form_layout ) # Common methods for all components that use forms diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Oct 13 18:15:06 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Wed Oct 14 02:22:11 2009 -0400 @@ -115,20 +115,17 @@ status='error', message="Invalid request ID", **kwd) ) - self.current_samples = [] - self.edit_mode = False + current_samples = [] for s in request.samples: - self.current_samples.append([s.name, s.values.content]) + current_samples.append([s.name, s.values.content]) if add_sample: - self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]]) - self.details_state = 'Show request details' + current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]]) return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details='hide', edit_mode='False') def request_details(self, trans, id): ''' Shows the request details @@ -186,25 +183,34 @@ value=request.values.content[index], helptext=field['helptext']+' ('+req+')')) return request_details - def __update_samples(self, request, **kwd): + ''' + This method retrieves all the user entered sample information and + returns an list of all the samples and their field values + ''' params = util.Params( kwd ) - num_samples = len(self.current_samples) - self.current_samples = [] + current_samples = [] for s in request.samples: - self.current_samples.append([s.name, s.values.content]) - for index in range(num_samples-len(request.samples)): - sample_index = index + len(request.samples) - sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) - sample_values = [] - for field_index in range(len(request.type.sample_form.fields)): - sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) - self.current_samples.append([sample_name, sample_values]) - - def __copy_sample(self): + current_samples.append([s.name, s.values.content]) + index = len(request.samples) + while True: + if params.get( 'sample_%i_name' % index, '' ): + sample_index = index + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + current_samples.append([sample_name, sample_values]) + index = index + 1 + else: + break + details = params.get( 'details', 'hide' ) + edit_mode = params.get( 'edit_mode', 'False' ) + return current_samples, details, edit_mode + def __copy_sample(self, current_samples): copy_list = SelectField('copy_sample') copy_list.add_option('None', -1, selected=True) - for i, s in enumerate(self.current_samples): + for i, s in enumerate(current_samples): copy_list.add_option(s[0], i) return copy_list @web.expose @@ -221,20 +227,22 @@ status='error', message="Invalid request ID", **kwd) ) + # get the user entered sample details + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) if params.get('import_samples_button', False) == 'Import samples': try: file_obj = params.get('file_data', '') import csv reader = csv.reader(file_obj.file) for row in reader: - self.current_samples.append([row[0], row[1:]]) + current_samples.append([row[0], row[1:]]) return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) except: return trans.response.send_redirect( web.url_for( controller='requests', action='list', @@ -242,39 +250,35 @@ message='Error in importing samples file', **kwd)) elif params.get('add_sample_button', False) == 'Add New': - # save the all (saved+unsaved) sample info in 'current_samples' - self.__update_samples(request, **kwd) # add an empty or filled sample # if the user has selected a sample no. to copy then copy the contents # of the src sample to the new sample else an empty sample src_sample_index = int(params.get( 'copy_sample', -1 )) if src_sample_index == -1: # empty sample - self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]]) + current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]]) else: - self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1), - [val for val in self.current_samples[src_sample_index][1]]]) + current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1), + [val for val in current_samples[src_sample_index][1]]]) return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) elif params.get('save_samples_button', False) == 'Save': - # update current_samples - self.__update_samples(request, **kwd) # check for duplicate sample names msg = '' - for index in range(len(self.current_samples)-len(request.samples)): + for index in range(len(current_samples)-len(request.samples)): sample_index = index + len(request.samples) - sample_name = self.current_samples[sample_index][0] + sample_name = current_samples[sample_index][0] if not sample_name.strip(): msg = 'Please enter the name of sample number %i' % sample_index break count = 0 - for i in range(len(self.current_samples)): - if sample_name == self.current_samples[i][0]: + for i in range(len(current_samples)): + if sample_name == current_samples[i][0]: count = count + 1 if count > 1: msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) @@ -283,12 +287,13 @@ return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), details_state=self.details_state, + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, edit_mode=edit_mode, messagetype='error', msg=msg) # save all the new/unsaved samples entered by the user - if not self.edit_mode: - for index in range(len(self.current_samples)-len(request.samples)): + if edit_mode == 'False': + for index in range(len(current_samples)-len(request.samples)): sample_index = index + len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] @@ -299,9 +304,9 @@ s = trans.app.model.Sample(sample_name, '', request, form_values) s.flush() else: - for index in range(len(self.current_samples)): + for index in range(len(current_samples)): sample_index = index - sample_name = self.current_samples[sample_index][0] + sample_name = current_samples[sample_index][0] new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): @@ -318,14 +323,14 @@ operation='show_request', id=trans.security.encode_id(request.id)) ) elif params.get('edit_samples_button', False) == 'Edit samples': - self.edit_mode = True + edit_mode = 'True' return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) elif params.get('cancel_changes_button', False) == 'Cancel': return trans.response.send_redirect( web.url_for( controller='requests', action='list', @@ -340,21 +345,22 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) request = trans.app.model.Request.get(int(params.get('request_id', 0))) + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) sample_index = int(params.get('sample_id', 0)) - sample_name = self.current_samples[sample_index][0] + sample_name = current_samples[sample_index][0] s = request.has_sample(sample_name) if s: s.delete() s.flush() request.flush() - del self.current_samples[sample_index] + del current_samples[sample_index] return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) @web.expose @web.require_login( "create/submit sequencing requests" ) @@ -363,17 +369,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) request = trans.app.model.Request.get(int(params.get('request_id', 0))) - if self.details_state == 'Show request details': - self.details_state = 'Hide request details' - elif self.details_state == 'Hide request details': - self.details_state = 'Show request details' + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) def __select_request_type(self, trans, rtid): rt_ids = ['none'] for rt in trans.app.model.RequestType.query().all(): @@ -476,17 +479,22 @@ msg=msg, messagetype=messagetype) def __library_ui(self, trans, request=None, **kwd): + ''' + This method creates the data library & folder selectbox for new & + editing requests. First we get a list of all the libraries accessible to + the current user and display it in a selectbox. If the user has select an + existing library then display all the accessible sub folders of the selected + data library. + ''' params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - # if editing a request selected_lib = None + # if editing a request and the user has already associated a library to + # this request, then set the selected_lib to the request.library if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) selected_lib = request.library - else: - # new request - selected_lib = None # get all permitted libraries for this user all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ .order_by( trans.app.model.Library.name ).all() @@ -497,15 +505,16 @@ can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) if can_show: libraries[ library ] = hidden_folder_ids + # create data library selectbox with refresh on change enabled lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()] lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list ) - # fill up the options in the Library selectfield - # first option + # fill up the options in the Library selectbox + # first option 'none' is the value for "Select one" option if lib_id == 'none': lib_list.add_option('Select one', 'none', selected=True) else: lib_list.add_option('Select one', 'none') - # all the libraries available to the user + # add all the libraries available to the user to the library selectbox for lib, hidden_folder_ids in libraries.items(): if str(lib.id) == lib_id: lib_list.add_option(lib.name, lib.id, selected=True) @@ -524,14 +533,21 @@ helptext='Data library where the resultant dataset will be stored.') # show the folder widget only if the user has selected a valid library above if selected_lib: - # when editing a request + # when editing a request, either the user has already selected a subfolder or not if request: if request.folder: current_fid = request.folder.id - else: - current_fid = request.library.root_folder.id + else: + # when a folder not yet associated with the request then the + # the current folder is set to the root_folder of the + # parent data library if present. + if request.library: + current_fid = request.library.root_folder.id + else: + current_fid = params.get( 'folder_id', 'none' ) else: current_fid = params.get( 'folder_id', 'none' ) + # create the folder selectbox folder_list = SelectField( 'folder_id') # first option if lib_id == 'none': @@ -543,6 +559,7 @@ selected_lib, actions_to_check, selected_hidden_folder_ids ) + # add all the folders to the folder selectbox for f in showable_folders: if str(f.id) == str(current_fid): folder_list.add_option(f.name, f.id, selected=True) @@ -568,8 +585,6 @@ Validates the request entered by the user ''' empty_fields = [] -# if not request.library: -# empty_fields.append('Data library') # check rest of the fields of the form for index, field in enumerate(request.type.request_form.fields): if field['required'] == 'required' and request.values.content[index] in ['', None]: diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Oct 13 18:15:06 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Oct 14 02:22:11 2009 -0400 @@ -10,6 +10,10 @@ from galaxy.web.controllers.forms import get_all_forms log = logging.getLogger( __name__ ) + +# +# ---- Request Grid ------------------------------------------------------------ +# class RequestsListGrid( grids.Grid ): title = "Sequencing Requests" @@ -60,6 +64,11 @@ else: return query + +# +# ---- Request Controller ------------------------------------------------------ +# + class Requests( BaseController ): request_grid = RequestsListGrid() @@ -67,6 +76,7 @@ @web.require_admin def index( self, trans ): return trans.fill_template( "/admin/requests/index.mako" ) + @web.expose @web.require_admin def list( self, trans, **kwargs ): @@ -104,51 +114,26 @@ self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) # Render the list view return self.request_grid( trans, **kwargs ) - @web.expose - @web.require_admin - def edit(self, trans, **kwd): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + def __show_request(self, trans, id, messagetype, msg): try: - request = trans.app.model.Request.get(int(params.get('request_id', None))) + request = trans.app.model.Request.get(id) except: return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", **kwd) ) - if params.get('show', False) == 'True': - return self.__edit_request(trans, request.id, **kwd) - elif params.get('save_changes_request_button', False) == 'Save changes' \ - or params.get('edit_samples_button', False) == 'Edit samples': - request_type = trans.app.model.RequestType.get(int(params.select_request_type)) - if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg - kwd['show'] = 'True' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='edit', - **kwd) ) - request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name - if params.get('save_changes_request_button', False) == 'Save changes': - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - message=msg , - status='done') ) - elif params.get('edit_samples_button', False) == 'Edit samples': - new_kwd = {} - new_kwd['request_id'] = request.id - new_kwd['edit_samples_button'] = 'Edit samples' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='show_request', - msg=msg , - messagetype='done', - **new_kwd) ) - elif params.get('refresh', False) == 'true': - return self.__edit_request(trans, request.id, **kwd) + current_samples = [] + for s in request.samples: + current_samples.append([s.name, s.values.content]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, id), + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details='hide', edit_mode='False', + msg=msg, messagetype=messagetype) + def __edit_request(self, trans, id, **kwd): try: request = trans.app.model.Request.get(id) @@ -276,317 +261,10 @@ action='list', show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) - @web.expose - @web.require_admin - def submit_request(self, trans, **kwd): - params = util.Params( kwd ) - try: - id = int(params.get('id', False)) - request = trans.app.model.Request.get(id) - except: - msg = "Invalid request ID" - log.warn( msg ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - message=msg, - **kwd) ) - msg = self.__validate(trans, request) - if msg: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='edit', - messagetype='error', - msg=msg, - request_id=request.id, - show='True') ) - # get the new state - new_state = request.type.states[0] - for s in request.samples: - event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') - event.flush() - # change request's submitted field - request.state = request.states.SUBMITTED - request.flush() - kwd['id'] = trans.security.encode_id(request.id) - kwd['status'] = 'done' - kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - show_filter=trans.app.model.Request.states.SUBMITTED, - **kwd) ) - def __copy_sample(self): - copy_list = SelectField('copy_sample') - copy_list.add_option('None', -1, selected=True) - for i, s in enumerate(self.current_samples): - copy_list.add_option(s[0], i) - return copy_list - def __update_samples(self, request, **kwd): - params = util.Params( kwd ) - num_samples = len(self.current_samples) - self.current_samples = [] - for s in request.samples: - self.current_samples.append([s.name, s.values.content]) - for index in range(num_samples-len(request.samples)): - sample_index = index + len(request.samples) - sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) - sample_values = [] - for field_index in range(len(request.type.sample_form.fields)): - sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) - self.current_samples.append([sample_name, sample_values]) - def __show_request(self, trans, id, messagetype, msg): - try: - request = trans.app.model.Request.get(id) - except: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - message="Invalid request ID", - **kwd) ) - self.current_samples = [] - self.edit_mode = False - for s in request.samples: - self.current_samples.append([s.name, s.values.content]) - self.details_state = 'Show request details' - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode, - msg=msg, messagetype=messagetype) - @web.expose - @web.require_admin - def show_request(self, trans, **kwd): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - try: - request = trans.app.model.Request.get(int(params.get('request_id', None))) - except: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - message="Invalid request ID", - **kwd) ) - if params.get('import_samples_button', False) == 'Import samples': - try: - file_obj = params.get('file_data', '') - import csv - reader = csv.reader(file_obj.file) - for row in reader: - self.current_samples.append([row[0], row[1:]]) - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) - except: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - operation='show_request', - id=trans.security.encode_id(request.id), - message='Error in importing samples from the given file.', - **kwd)) - elif params.get('add_sample_button', False) == 'Add New': - # save the all (saved+unsaved) sample info in 'current_samples' - self.__update_samples(request, **kwd) - # add an empty or filled sample - # if the user has selected a sample no. to copy then copy the contents - # of the src sample to the new sample else an empty sample - src_sample_index = int(params.get( 'copy_sample', -1 )) - if src_sample_index == -1: - # empty sample - self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]]) - else: - self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1), - [val for val in self.current_samples[src_sample_index][1]]]) - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) - elif params.get('save_samples_button', False) == 'Save': - # update current_samples - self.__update_samples(request, **kwd) - # check for duplicate sample names - msg = '' - for index in range(len(self.current_samples)-len(request.samples)): - sample_index = index + len(request.samples) - sample_name = self.current_samples[sample_index][0] - if not sample_name.strip(): - msg = 'Please enter the name of sample number %i' % sample_index - break - count = 0 - for i in range(len(self.current_samples)): - if sample_name == self.current_samples[i][0]: - count = count + 1 - if count > 1: - msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) - break - if msg: - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), details_state=self.details_state, - messagetype='error', msg=msg) - # save all the new/unsaved samples entered by the user - if not self.edit_mode: - for index in range(len(self.current_samples)-len(request.samples)): - sample_index = index + len(request.samples) - sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) - sample_values = [] - for field_index in range(len(request.type.sample_form.fields)): - sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) - form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) - form_values.flush() - s = trans.app.model.Sample(sample_name, '', request, form_values) - s.flush() - else: - for index in range(len(self.current_samples)): - sample_index = index - sample_name = self.current_samples[sample_index][0] - new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) - sample_values = [] - for field_index in range(len(request.type.sample_form.fields)): - sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) - sample = request.has_sample(sample_name) - if sample: - form_values = trans.app.model.FormValues.get(sample.values.id) - form_values.content = sample_values - form_values.flush() - sample.name = new_sample_name - sample.flush() - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - operation='show_request', - id=trans.security.encode_id(request.id)) ) - elif params.get('edit_samples_button', False) == 'Edit samples': - self.edit_mode = True - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples=self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) - elif params.get('cancel_changes_button', False) == 'Cancel': - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - operation='show_request', - id=trans.security.encode_id(request.id)) ) - - @web.expose - @web.require_admin - def delete_sample(self, trans, **kwd): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - request = trans.app.model.Request.get(int(params.get('request_id', 0))) - sample_index = int(params.get('sample_id', 0)) - sample_name = self.current_samples[sample_index][0] - s = request.has_sample(sample_name) - if s: - s.delete() - s.flush() - request.flush() - del self.current_samples[sample_index] - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=self.__copy_sample(), - details_state=self.details_state, - edit_mode=self.edit_mode) - - @web.expose - @web.require_admin - def toggle_request_details(self, trans, **kwd): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - request = trans.app.model.Request.get(int(params.get('request_id', 0))) - if self.details_state == 'Show request details': - self.details_state = 'Hide request details' - elif self.details_state == 'Hide request details': - self.details_state = 'Show request details' - copy_list = SelectField('copy_sample') - copy_list.add_option('None', -1, selected=True) - for i, s in enumerate(self.current_samples): - copy_list.add_option(i+1, i) - return trans.fill_template( '/admin/requests/show_request.mako', - request=request, - request_details=self.request_details(trans, request.id), - current_samples = self.current_samples, - sample_copy=copy_list, details_state=self.details_state) - def request_details(self, trans, id): - ''' - Shows the request details - ''' - request = trans.app.model.Request.get(id) - # list of widgets to be rendered on the request form - request_details = [] - # main details - request_details.append(dict(label='User', - value=str(request.user.email), - helptext='')) - request_details.append(dict(label='Description', - value=request.desc, - helptext='')) - request_details.append(dict(label='Type', - value=request.type.name, - helptext='')) - request_details.append(dict(label='State', - value=request.state, - helptext='')) - request_details.append(dict(label='Date created', - value=request.create_time, - helptext='')) - # library associated - if request.library: - value=request.library.name - else: - value = None - request_details.append(dict(label='Data library', - value=value, - helptext='Data library where the resultant dataset will be stored')) - # folder associated - if request.folder: - value = request.folder.name - else: - value = None - request_details.append( dict( label='Data library folder', - value=value, - helptext='Data library folder where the resultant dataset will be stored' ) ) - - # form fields - for index, field in enumerate(request.type.request_form.fields): - if field['required']: - req = 'Required' - else: - req = 'Optional' - if field['type'] == 'AddressField': - if request.values.content[index]: - request_details.append(dict(label=field['label'], - value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(), - helptext=field['helptext']+' ('+req+')')) - else: - request_details.append(dict(label=field['label'], - value=None, - helptext=field['helptext']+' ('+req+')')) - else: - request_details.append(dict(label=field['label'], - value=request.values.content[index], - helptext=field['helptext']+' ('+req+')')) - return request_details - +# +#---- Request Creation ---------------------------------------------------------- +# def __select_request_type(self, trans, rtid): rt_ids = ['none'] for rt in trans.app.model.RequestType.query().all(): @@ -723,21 +401,22 @@ return select_user def __library_ui(self, trans, user, request=None, **kwd): - """ - Return a list of libraries for which user has the permission - to perform the LIBRARY_ADD action on any of it's folders - """ + ''' + This method creates the data library & folder selectbox for new & + editing requests. First we get a list of all the libraries accessible to + the current user and display it in a selectbox. If the user has select an + existing library then display all the accessible sub folders of the selected + data library. + ''' params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - # if editing a request + # if editing a request and the user has already associated a library to + # this request, then set the selected_lib to the request.library selected_lib = None if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) selected_lib = request.library - else: - # new request - selected_lib = None # if new request no user is selected initially, none of the libraries are # listed in the selectfield if not user: @@ -759,10 +438,11 @@ can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) if can_show: libraries[ library ] = hidden_folder_ids - # create the selectfield + # create data library selectbox with refresh on change enabled lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()] lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list ) - # first option + # fill up the options in the Library selectbox + # first option 'none' is the value for "Select one" option if lib_id == 'none': lib_list.add_option('Select one', 'none', selected=True) else: @@ -784,15 +464,23 @@ lib_widget = dict(label='Data library', widget=lib_list, helptext='Data library where the resultant dataset will be stored.') + # show the folder widget only if the user has selected a valid library above if selected_lib: - # when editing a request + # when editing a request, either the user has already selected a subfolder or not if request: if request.folder: current_fid = request.folder.id - else: - current_fid = request.library.root_folder.id + else: + # when a folder not yet associated with the request then the + # the current folder is set to the root_folder of the + # parent data library if present. + if request.library: + current_fid = request.library.root_folder.id + else: + current_fid = params.get( 'folder_id', 'none' ) else: current_fid = params.get( 'folder_id', 'none' ) + # create the folder selectbox folder_list = SelectField( 'folder_id') # first option if lib_id == 'none': @@ -828,9 +516,14 @@ ''' Validates the request entered by the user ''' + if not request.samples: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + message='Please add one or more samples to this request before submitting.', + status='error', + id=trans.security.encode_id(request.id)) ) empty_fields = [] -# if not request.library: -# empty_fields.append('Library') # check rest of the fields of the form for index, field in enumerate(request.type.request_form.fields): if field['required'] == 'required' and request.values.content[index] in ['', None]: @@ -909,6 +602,350 @@ request.folder = folder request.flush() return request + + +# +#---- Request Editing ---------------------------------------------------------- +# + @web.expose + @web.require_admin + def edit(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('show', False) == 'True': + return self.__edit_request(trans, request.id, **kwd) + elif params.get('save_changes_request_button', False) == 'Save changes' \ + or params.get('edit_samples_button', False) == 'Edit samples': + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if not util.restore_text(params.get('name', '')): + msg = 'Please enter the <b>Name</b> of the request' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['show'] = 'True' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + **kwd) ) + request = self.__save_request(trans, request, **kwd) + msg = 'The changes made to the request named %s has been saved' % request.name + if params.get('save_changes_request_button', False) == 'Save changes': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done') ) + elif params.get('edit_samples_button', False) == 'Edit samples': + new_kwd = {} + new_kwd['request_id'] = request.id + new_kwd['edit_samples_button'] = 'Edit samples' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_request', + msg=msg , + messagetype='done', + **new_kwd) ) + elif params.get('refresh', False) == 'true': + return self.__edit_request(trans, request.id, **kwd) + @web.expose + @web.require_admin + def submit_request(self, trans, **kwd): + params = util.Params( kwd ) + try: + id = int(params.get('id', False)) + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + msg = self.__validate(trans, request) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + messagetype='error', + msg=msg, + request_id=request.id, + show='True') ) + # get the new state + new_state = request.type.states[0] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') + event.flush() + # change request's submitted field + request.state = request.states.SUBMITTED + request.flush() + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, + **kwd) ) + def __update_samples(self, request, **kwd): + ''' + This method retrieves all the user entered sample information and + returns an list of all the samples and their field values + ''' + params = util.Params( kwd ) + current_samples = [] + for s in request.samples: + current_samples.append([s.name, s.values.content]) + index = len(request.samples) + while True: + if params.get( 'sample_%i_name' % index, '' ): + sample_index = index + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + current_samples.append([sample_name, sample_values]) + index = index + 1 + else: + break + details = params.get( 'details', 'hide' ) + edit_mode = params.get( 'edit_mode', 'False' ) + return current_samples, details, edit_mode + def __copy_sample(self, current_samples): + copy_list = SelectField('copy_sample') + copy_list.add_option('None', -1, selected=True) + for i, s in enumerate(current_samples): + copy_list.add_option(s[0], i) + return copy_list + @web.expose + @web.require_login( "create/submit sequencing requests" ) + def show_request(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + # get the user entered sample details + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) + if params.get('import_samples_button', False) == 'Import samples': + try: + file_obj = params.get('file_data', '') + import csv + reader = csv.reader(file_obj.file) + for row in reader: + current_samples.append([row[0], row[1:]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message='Error in importing samples file', + **kwd)) + elif params.get('add_sample_button', False) == 'Add New': + # add an empty or filled sample + # if the user has selected a sample no. to copy then copy the contents + # of the src sample to the new sample else an empty sample + src_sample_index = int(params.get( 'copy_sample', -1 )) + if src_sample_index == -1: + # empty sample + current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]]) + else: + current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1), + [val for val in current_samples[src_sample_index][1]]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) + elif params.get('save_samples_button', False) == 'Save': + # check for duplicate sample names + msg = '' + for index in range(len(current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = current_samples[sample_index][0] + if not sample_name.strip(): + msg = 'Please enter the name of sample number %i' % sample_index + break + count = 0 + for i in range(len(current_samples)): + if sample_name == current_samples[i][0]: + count = count + 1 + if count > 1: + msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + break + if msg: + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, edit_mode=edit_mode, + messagetype='error', msg=msg) + # save all the new/unsaved samples entered by the user + if edit_mode == 'False': + for index in range(len(current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) + form_values.flush() + s = trans.app.model.Sample(sample_name, '', request, form_values) + s.flush() + else: + for index in range(len(current_samples)): + sample_index = index + sample_name = current_samples[sample_index][0] + new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + sample = request.has_sample(sample_name) + if sample: + form_values = trans.app.model.FormValues.get(sample.values.id) + form_values.content = sample_values + form_values.flush() + sample.name = new_sample_name + sample.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + elif params.get('edit_samples_button', False) == 'Edit samples': + edit_mode = 'True' + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) + elif params.get('cancel_changes_button', False) == 'Cancel': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + + + @web.expose + @web.require_login( "create/submit sequencing requests" ) + def delete_sample(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request = trans.app.model.Request.get(int(params.get('request_id', 0))) + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) + sample_index = int(params.get('sample_id', 0)) + sample_name = current_samples[sample_index][0] + s = request.has_sample(sample_name) + if s: + s.delete() + s.flush() + request.flush() + del current_samples[sample_index] + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) + + @web.expose + @web.require_login( "create/submit sequencing requests" ) + def toggle_request_details(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request = trans.app.model.Request.get(int(params.get('request_id', 0))) + current_samples, details, edit_mode = self.__update_samples( request, **kwd ) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = current_samples, + sample_copy=self.__copy_sample(current_samples), + details=details, + edit_mode=edit_mode) + @web.expose + @web.require_admin + def request_details(self, trans, id): + ''' + Shows the request details + ''' + request = trans.app.model.Request.get(id) + # list of widgets to be rendered on the request form + request_details = [] + # main details + request_details.append(dict(label='User', + value=str(request.user.email), + helptext='')) + request_details.append(dict(label='Description', + value=request.desc, + helptext='')) + request_details.append(dict(label='Type', + value=request.type.name, + helptext='')) + request_details.append(dict(label='State', + value=request.state, + helptext='')) + request_details.append(dict(label='Date created', + value=request.create_time, + helptext='')) + # library associated + if request.library: + value=request.library.name + else: + value = None + request_details.append(dict(label='Data library', + value=value, + helptext='Data library where the resultant dataset will be stored')) + # folder associated + if request.folder: + value = request.folder.name + else: + value = None + request_details.append( dict( label='Data library folder', + value=value, + helptext='Data library folder where the resultant dataset will be stored' ) ) + + # form fields + for index, field in enumerate(request.type.request_form.fields): + if field['required']: + req = 'Required' + else: + req = 'Optional' + if field['type'] == 'AddressField': + if request.values.content[index]: + request_details.append(dict(label=field['label'], + value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(), + helptext=field['helptext']+' ('+req+')')) + else: + request_details.append(dict(label=field['label'], + value=None, + helptext=field['helptext']+' ('+req+')')) + else: + request_details.append(dict(label=field['label'], + value=request.values.content[index], + helptext=field['helptext']+' ('+req+')')) + return request_details @web.expose @web.require_admin def bar_codes(self, trans, **kwd): @@ -1086,7 +1123,9 @@ events_list=events_list, sample=sample, widgets=widgets, title=title) - # Request Type Stuff +## +#### Request Type Stuff ################################################### +## @web.expose @web.require_admin def manage_request_types( self, trans, **kwd ): diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Oct 13 18:15:06 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Wed Oct 14 02:22:11 2009 -0400 @@ -635,7 +635,7 @@ return None def request_types(self): - if self.app.model.RequestType.query().all(): + if self.app.model.RequestType.query().filter_by(deleted=False).all(): return True return False diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/forms/edit_form.mako --- a/templates/admin/forms/edit_form.mako Tue Oct 13 18:15:06 2009 -0400 +++ b/templates/admin/forms/edit_form.mako Wed Oct 14 02:22:11 2009 -0400 @@ -36,16 +36,20 @@ <% options = field_attr[2] %> <div class="repeat-group-item"> <div class="form-row"> - <label> Options</label> - %for i, option in enumerate(options): - <b> ${i+1}</b> - ${option[1].get_html()} - <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br> - %endfor + <label> Options</label> + %for i, option in enumerate(options): + <div class="form-row"> + <b> ${i+1}</b> + ${option[1].get_html()} + ##<a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br> + <input type="submit" name="removeoption_${index}_${i}" value="Remove"/> + </div> + %endfor + <input type="hidden" name="field_index" value="${index}"/> </div> </div> <div class="form-row"> - <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='add', field_index=index )}">Add</a> + <input type="submit" name="addoption_${index}" value="Add"/> </div> %endif %endif @@ -81,7 +85,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit form definition "${form.name}"</div> - <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" > + <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id )}" method="post" > %for label, input in form_details: <div class="form-row"> <label>${label}</label> diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/forms/show_form_read_only.mako --- a/templates/admin/forms/show_form_read_only.mako Tue Oct 13 18:15:06 2009 -0400 +++ b/templates/admin/forms/show_form_read_only.mako Wed Oct 14 02:22:11 2009 -0400 @@ -63,9 +63,19 @@ <div class="toolForm"> %if form.desc: - <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div> + <div class="toolFormTitle">${form.name} - <i>${form.desc}</i> + <a id="form-${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">${form.name}</div> + <div class="toolFormTitle">${form.name} + <a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="form-${form.id}-popup"> + <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a> + </div> + </div> %endif <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" > %if form.type == trans.app.model.FormDefinition.types.SAMPLE: @@ -77,58 +87,27 @@ %endfor %endif %else: - <table class = "grid"> - <tbody> - %for index, field in enumerate(form.fields): - <tr> - <td> - <div class="form-row"> - <label>${1+index}. Label</label> - <a>${field['label']}</a> - %if field['type'] == 'SelectField': - <a id="${field['label']}-popup" class="popup-arrow" style="display: none;">▼</a> - %for option in field['selectlist']: - <div popupmenu="${field['label']}-type-popup"> - <a class="action-button" href="" >${option}</a> - </div> - %endfor - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Help text </label> - %if not field['helptext']: - <a><i>No helptext</i></a> - %else: - <a>${field['helptext']}</a> - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Type:</label> - <a>${field['type']}</a> - %if field['type'] == 'SelectField': - <a id="fieldtype-popup" class="popup-arrow" style="display: none;">▼</a> - %for option in field['selectlist']: - <div popupmenu="type-popup"> - <a class="action-button" href="" >${option}</a> - </div> - %endfor - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Required?</label> - <a>${field['required']}</a> - </div> - </td> - </tr> - %endfor - </tbody> - </table> + %for index, field in enumerate(form.fields): + <div class="form-row"> + <label>${field['label']}</label> + %if field['helptext']: + <div class="toolParamHelp" style="clear: both;"> + <i>${field['helptext']}</i> + </div> + %endif + <div>${field['required']}</div> + <i>Type: </i> ${field['type']} + %if field['type'] == 'SelectField': + <div> + <div><i>Options:</i></div> + %for option in field['selectlist']: + <div>${option}</div> + %endfor + </div> + %endif + </div> + <div style="clear: both"></div> + %endfor %endif </form> </div> diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Tue Oct 13 18:15:06 2009 -0400 +++ b/templates/admin/requests/show_request.mako Wed Oct 14 02:22:11 2009 -0400 @@ -58,6 +58,8 @@ </select> %elif field['type'] == 'CheckboxField': <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %elif field['type'] == 'NumberField': + <input type=int name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> %endif <div class="toolParamHelp" style="clear: both;"> <i>${'('+field['required']+')' }</i> @@ -91,35 +93,41 @@ </%def> <div class="toolForm"> - <div class="form-row"> - <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a> - </div> - %if details_state == "Hide request details": - %for index, rd in enumerate(request_details): + <div class="form-row"> + %if details == "show": + <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="hide" )}">Hide request details</a> + </div> + %for index, rd in enumerate(request_details): + <div class="form-row"> + <label>${rd['label']}</label> + %if not rd['value']: + <i>None</i> + %else: + %if rd['label'] == 'Data library': + %if rd['value']: + <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a> + %else: + <i>None</i> + %endif + %else: + ${rd['value']} + %endif + %endif + </div> + <div style="clear: both"></div> + %endfor <div class="form-row"> - <label>${rd['label']}</label> - %if not rd['value']: - <i>None</i> - %else: - %if rd['label'] == 'Data library': - <a href="${h.url_for( controller='library_admin', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a> - %else: - ${rd['value']} - %endif - %endif - </div> - <div style="clear: both"></div> - %endfor - <div class="form-row"> <ul class="manage-table-actions"> <li> <a class="action-button" href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}"> <span>Edit request details</span></a> </li> </ul> + </div> </div> + %else: + <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="show" )}">Show request details</a> %endif - </div> </div> <%def name="render_grid( grid_index, grid_name, fields_dict )"> @@ -151,13 +159,13 @@ request.refresh() %> %for sample_index, sample in enumerate(current_samples): - %if edit_mode: + %if edit_mode == 'True': <tr> <td>${sample_index+1}</td> ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} <td> %if request.unsubmitted() and grid_index == 0: - <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> <img src="${h.url_for('/static/images/delete_icon.png')}" /> <span></span></a> %endif @@ -173,7 +181,7 @@ %endif <td> %if request.unsubmitted() and grid_index == 0: - <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> <img src="${h.url_for('/static/images/delete_icon.png')}" /> <span></span></a> %endif @@ -201,7 +209,7 @@ <label>There are no samples.</label> %endif </div> - %if not edit_mode: + %if edit_mode == 'False': <table class="grid"> <tbody> <tr> @@ -238,7 +246,7 @@ <div style="clear: both"></div> </div> <div class="form-row"> - %if edit_mode: + %if edit_mode == 'True': <input type="submit" name="save_samples_button" value="Save"/> <input type="submit" name="cancel_changes_button" value="Cancel"/> %elif request.unsubmitted(): diff -r b16a6d767e65 -r ca816e66ec69 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Tue Oct 13 18:15:06 2009 -0400 +++ b/templates/requests/show_request.mako Wed Oct 14 02:22:11 2009 -0400 @@ -92,41 +92,43 @@ </%def> <div class="toolForm"> - <div class="form-row"> - <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a> - </div> - %if details_state == "Hide request details": - %for index, rd in enumerate(request_details): - <div class="form-row"> - <label>${rd['label']}</label> - %if not rd['value']: - <i>None</i> - %else: - %if rd['label'] == 'Data library': - %if rd['value']: - <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a> + <div class="form-row"> + %if details == "show": + <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="hide" )}">Hide request details</a> + </div> + %for index, rd in enumerate(request_details): + <div class="form-row"> + <label>${rd['label']}</label> + %if not rd['value']: + <i>None</i> + %else: + %if rd['label'] == 'Data library': + %if rd['value']: + <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a> + %else: + <i>None</i> + %endif %else: - <i>None</i> + ${rd['value']} %endif - %else: - ${rd['value']} %endif - %endif - </div> - <div style="clear: both"></div> - %endfor - %if request.unsubmitted(): - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}"> - <span>Edit request details</span></a> - </li> - </ul> - </div> - %endif + </div> + <div style="clear: both"></div> + %endfor + %if request.unsubmitted(): + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}"> + <span>Edit request details</span></a> + </li> + </ul> + </div> + %endif + </div> + %else: + <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="show" )}">Show request details</a> %endif - </div> </div> <%def name="render_grid( grid_index, grid_name, fields_dict )"> @@ -158,7 +160,7 @@ request.refresh() %> %for sample_index, sample in enumerate(current_samples): - %if edit_mode: + %if edit_mode == 'True': <tr> <td>${sample_index+1}</td> ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} @@ -194,7 +196,7 @@ <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> - <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request' )}" enctype="multipart/form-data" method="post" > + <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: %if not request.type.sample_form.layout: @@ -211,7 +213,7 @@ %endif </div> - %if request.unsubmitted() and not edit_mode: + %if request.unsubmitted() and edit_mode == 'False': <table class="grid"> <tbody> <tr> @@ -251,7 +253,7 @@ </div> <div class="form-row"> <input type="submit" name="save_samples_button" value="Save"/> - %if edit_mode: + %if edit_mode == 'True': <input type="submit" name="cancel_changes_button" value="Cancel"/> %endif </div> diff -r b16a6d767e65 -r ca816e66ec69 templates/user/address.mako --- a/templates/user/address.mako Tue Oct 13 18:15:06 2009 -0400 +++ b/templates/user/address.mako Wed Oct 14 02:22:11 2009 -0400 @@ -46,7 +46,7 @@ <td> <div class="form-row"> <label>${address.desc}</label> - ${address.display()} + ${address.get_html()} </div> <div class="form-row"> <ul class="manage-table-actions"> diff -r b16a6d767e65 -r ca816e66ec69 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Oct 13 18:15:06 2009 -0400 +++ b/test/base/twilltestcase.py Wed Oct 14 02:22:11 2009 -0400 @@ -1059,8 +1059,15 @@ tc.fv( "1", field_name, field_contents ) tc.fv( "1", field_help_name, field_help_contents ) tc.submit( "save_changes_button" ) + if num_fields: check_str = "The form '%s' has been updated with the changes." % name - self.check_page_for_string( check_str ) + self.check_page_for_string( check_str ) + else: + self.home() + self.visit_url( "%s/forms/manage" % self.url ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + self.check_page_for_string( formtype ) self.home() def edit_form( self, form_id, form_name, new_form_name="Form One's Name (Renamed)", new_form_desc="This is Form One's description (Re-described)"): """ @@ -1074,7 +1081,7 @@ tc.submit( "save_changes_button" ) self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name ) self.home() - def form_add_field( self, form_id, form_name, field_index, fields): + def form_add_field( self, form_id, form_name, form_desc, form_type, field_index, fields): """ Add a new fields to the form definition """ @@ -1088,13 +1095,18 @@ tc.fv( "1", "field_helptext_%i" % index, field['desc'] ) tc.fv( "1", "field_type_%i" % index, field['type'] ) tc.fv( "1", "field_required_%i" % index, field['required'] ) -# if field['type'] == 'SelectField': -# for option_index, option in enumerate(field['selectlist']): -# self.visit_url( "%s/forms/edit?select_box_options=add&form_id=%i&field_index=%i" % \ -# (self.url, form_id, index)) -# #data = self.last_page() -# #file( "rc.html", 'wb' ).write(data) -# tc.fv( "1", "field_%i_option_%i" % (index, option_index), option ) + if field['type'] == 'SelectField': + options = '' + for option_index, option in enumerate(field['selectlist']): + url_str = "%s/forms/edit?description=%s&form_id=%i&form_type_selectbox=%s&addoption_%i=Add&name=%s&field_name_%i=%s&field_helptext_%i=%s&field_type_%i=%s" % \ + (self.url, form_desc.replace(" ", "+"), form_id, form_type.replace(" ", "+"), + index, form_name.replace(" ", "+"), index, field['name'].replace(" ", "+"), + index, field['desc'].replace(" ", "+"), index, field['type']) + self.visit_url( url_str + options ) + data = self.last_page() + file( "rc.html", 'wb' ).write(data) + tc.fv( "1", "field_%i_option_%i" % (index, option_index), option ) + options = options + "&field_%i_option_%i=%s" % (index, option_index, option) tc.submit( "save_changes_button" ) check_str = "The form '%s' has been updated with the changes." % form_name self.check_page_for_string( check_str ) @@ -1130,18 +1142,22 @@ self.check_page_for_string( "Request type <b>%s</b> has been created" % name ) def create_request( self, request_type_id, name, desc, library_id, folder_id, fields ): self.home() - self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.visit_url( "%s/requests/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, + request_type_id, + library_id ) ) self.check_page_for_string( 'Add a new request' ) tc.fv( "1", "name", name ) tc.fv( "1", "desc", desc ) tc.fv( "1", "library_id", str(library_id) ) - #tc.fv( "1", "folder_id", str(folder_id) ) + tc.fv( "1", "folder_id", str(folder_id) ) for index, field_value in enumerate(fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "create_request_button" ) def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ): self.home() - self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, + request_type_id, + library_id ) ) self.check_page_for_string( 'Add a new request' ) tc.fv( "1", "select_user", str(user_id) ) tc.fv( "1", "name", name ) diff -r b16a6d767e65 -r ca816e66ec69 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Oct 13 18:15:06 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Wed Oct 14 02:22:11 2009 -0400 @@ -42,12 +42,7 @@ name = form_one_name desc = "This is Form One's description" formtype = galaxy.model.FormDefinition.types.REQUEST - self.create_form( name=name, desc=desc, formtype=formtype ) - self.home() - self.visit_page( 'forms/manage' ) - self.check_page_for_string( name ) - self.check_page_for_string( desc ) - self.check_page_for_string( formtype ) + self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 ) # Get the form_definition object for later tests form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name, galaxy.model.FormDefinition.table.c.desc==desc, @@ -66,24 +61,21 @@ """Testing adding fields to a form definition""" fields = [dict(name='Test field name one', desc='Test field description one', - type='TextField', - required='required'), + type='SelectField', + required='optional', + selectlist=['option1', 'option2']), dict(name='Test field name two', desc='Test field description two', type='AddressField', - required='optional')] + required='optional'), + dict(name='Test field name three', + desc='Test field description three', + type='TextField', + required='required')] form_one = get_latest_form(form_one_name) - self.form_add_field(form_one.id, form_one.name, field_index=len(form_one.fields), fields=fields) + self.form_add_field(form_one.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields) form_one_latest = get_latest_form(form_one_name) assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) -#This following test has been commented out as it is causing: -#TwillException: multiple matches to "remove_button" -# def test_010_remove_form_fields( self ): -# """Testing removing fields from a form definition""" -# form_one = get_latest_form(form_one_name) -# self.form_remove_field( form_one.id, form_one.name, 'Test field name one' ) -# form_one_latest = get_latest_form(form_one_name) -# assert len(form_one_latest.fields) == len(form_one.fields)-1 def test_015_create_sample_form( self ): """Testing creating another form (for samples)""" global form_two_name @@ -186,10 +178,10 @@ self.logout() self.login( email='test1(a)bx.psu.edu' ) # set field values - fields = ['field one value', 'field two value', str(user_address.id)] + fields = ['option1', str(user_address.id), 'field three value'] # create the request request_name, request_desc = 'Request One', 'Request One Description' - self.create_request(request_type.id, request_name, request_desc, library_one.id, folder_one.id, fields) + self.create_request(request_type.id, request_name, request_desc, library_one.id, 'none', fields) self.check_page_for_string( request_name ) self.check_page_for_string( request_desc ) global request_one @@ -208,8 +200,9 @@ for field_value in fields: self.check_page_for_string( field_value ) # edit this request - fields = ['field one value (edited)', 'field two value (edited)', str(user_address.id)] - self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) + fields = ['option2', str(user_address.id), 'field three value (edited)'] + self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', + request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) request_one.refresh() self.check_page_for_string( request_name+' (Renamed)' ) self.check_page_for_string( request_desc+' (Re-described)' ) @@ -261,8 +254,8 @@ self.login( email='test(a)bx.psu.edu' ) request_name = "RequestTwo" # simulate request creation - url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_1=%s&field_2=%i' \ - % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_1_value", user_address.id ) + url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_2=%s&field_0=%s&field_1=%i' \ + % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_2_value", 'option1', user_address.id ) self.home() self.visit_url( url_str ) self.check_page_for_string( "The new request named %s has been created" % request_name ) @@ -299,10 +292,3 @@ self.visit_url( '%s/requests_admin/list?show_filter=All' % self.url ) self.check_page_for_string( request_one.name ) self.check_page_for_string( request_two.name ) - - - - - - - \ No newline at end of file

1 0

[hg] galaxy 2881: Add 2 rgenetics test files I missed for testin...
by Greg Von Kuster 14 Oct '09

14 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b16a6d767e65 changeset: 2881:b16a6d767e65 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Oct 13 18:15:06 2009 -0400 description: Add 2 rgenetics test files I missed for testing uploading composite data types. 2 file(s) affected in this change: test-data/rgenetics.map test-data/rgenetics.ped diffs (108 lines): diff -r 738085dcc542 -r b16a6d767e65 test-data/rgenetics.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgenetics.map Tue Oct 13 18:15:06 2009 -0400 @@ -0,0 +1,10 @@ +22 rs5992809 16.5965 16596539 +22 rs12168131 16.6573 16657262 +22 rs390041 16.6629 16662916 +22 rs437633 16.6697 16669684 +22 rs450960 16.6909 16690858 +22 rs450975 16.6909 16690887 +22 rs451740 16.6912 16691174 +22 rs8139723 16.6917 16691696 +22 rs405490 16.6922 16692175 +22 rs415170 16.6935 16693517 diff -r 738085dcc542 -r b16a6d767e65 test-data/rgenetics.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgenetics.ped Tue Oct 13 18:15:06 2009 -0400 @@ -0,0 +1,90 @@ +CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C +CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C +CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C +CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C +CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C +CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C +CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C +CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C +CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C +CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C +CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C +CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C +CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C +CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C +CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C +CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C +CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C +CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C +CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C +CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C +CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C +CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C +CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C +CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C +CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C +CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C +CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C +CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C +CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C +CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C +CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C +CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C +CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C +CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C +CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C +JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C +JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C +JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C +JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C +JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C +JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C +JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C +JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C +JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C +JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C +JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C +JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C +JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C +JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C +JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C +JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G +JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C +JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C +JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C +JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C +JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C +JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C +JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C +JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G +JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C +JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G +JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C +JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C +JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C +JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C +JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C +JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C +JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C +JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C +JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C +JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C +JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C +JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C +JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C +JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C +JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C

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