details: http://www.bx.psu.edu/hg/galaxy/rev/cbe28b41fb9d changeset: 2887:cbe28b41fb9d user: Ross Lazarus ross.lazarus@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