Dear all, We have a modified Galaxy server with tools for virtual screening. You can access is at http://lisis.cs.ucy.ac.cy.
We created a composite datatype (auto_primary_file) to handle PDBQT files for proteins and their config file requested by AutoDock Vina, in simple words is a composite datatype consisted of two files, a pdbqt file and a text file. We have the following problems: 1. Uploading the files needed to create such a composite datatype via the Upload Tool, stacks in upload phase, as shown in the following figure http://prntscr.com/xbosn 1. As you can see in the figure, uploading individual files works 2. In this figure http://prntscr.com/xbp6k you can see the upload options for this composite datatype. 2. Uploading composite datatypes within a data library does not provide the same functionality as the Upload Tool. Regarding problem 1 what do you think is the underlying problem? Following is the source code of this composite datatype class: class PDBQT_Protein(Html): """PDBQT Protein files, ASCII protein information files.""" MetadataElement(name = "base_name", desc = "Base name for all transformed versions of this PDBQT protein dataset", default = 'protein', readonly = False, set_in_upload = True) composite_type = 'auto_primary_file' allow_datatype_change = False file_ext = 'pdbqt_protein' def __init__(self, **kwd): Text.__init__(self, **kwd) self.add_composite_file('%s.pdbqt', description = 'PDBQT Protein File', substitute_name_with_metadata = 'base_name', mimetype = 'text/plain', is_binary = False) self.add_composite_file('%s_config.txt', description = 'PDBQT Config File', substitute_name_with_metadata = 'base_name', mimetype = 'text/plain', is_binary = False) def generate_primary_file(self, dataset = None): if dataset.metadata.base_name == "protein" and \ dataset.metadata.base_name != dataset.name: dataset.metadata.base_name = dataset.name rval = ['<html><head><title>PDBQT Protein Galaxy/LiSIs Composite Dataset</title></head>'] rval.append('<body><div>This %s composite dataset is composed of the following files:<ul>' % (dataset.metadata.base_name)) for composite_name, composite_file in self.get_composite_files(dataset = dataset).iteritems(): fn = composite_name opt_text = '' if composite_file.optional: opt_text = ' (optional)' if composite_file.get('description'): rval.append('<li><a href="%s">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text)) else: rval.append('<li><a href="%s">%s</a>%s</li>' % (fn, fn, opt_text)) rval.append('</ul></div></body></html>') return "\n".join(rval) def regenerate_primary_file(self, dataset): """ cannot do this until we are setting metadata """ bn = dataset.metadata.base_name efp = dataset.extra_files_path flist = os.listdir(efp) rval = ['<html><head><title>PDBQT Protein Galaxy/LiSIs Composite Dataset</title></head>'] rval.append('<body><div>This %s composite dataset is composed of the following files:<ul>' % (bn)) for i, fname in enumerate(flist): sfname = os.path.split(fname)[-1] rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname)) rval.append('</ul></div></body></html>') f = file(dataset.file_name, 'w') f.write("\n".join(rval)) f.write('\n') f.close() def set_meta(self, dataset, **kwd): """ Set metadata... """ Text.set_meta(self, dataset, **kwd) if dataset.metadata.base_name == "protein" and \ dataset.metadata.base_name != dataset.name: dataset.metadata.base_name = dataset.name log.debug('@@@ PDBQT_Protein set_meta changed dataset.metadata.base_name to: %s' % (dataset.metadata.base_name)) if kwd.get('overwrite') == False: log.debug('@@@ PDBQT_Protein set_meta called with overwrite = False') return True try: efp = dataset.extra_files_path except: log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s has no extra_files_path ?' % (sys.exc_info()[0], dataset.name)) return False try: flist = os.listdir(efp) except: log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s has no extra_files_path ?' % (sys.exc_info()[0], dataset.name)) return False if len(flist) == 0: log.debug('@@@ PDBQT_Protein set_meta failed - %s extra_files_path %s is empty?' % (dataset.name, efp)) return False self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy/LiSIs %s PDBQT Protein datatype object' % (dataset.metadata.base_name) if not dataset.blurb: dataset.blurb = 'Composite file - %s PDBQT Protein Galaxy/LiSIs datatype' % (dataset.metadata.base_name) return True Thanks in advance, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.chris...@ucy.ac.cy kannas.chris...@cs.ucy.ac.cy chriskan...@gmail.com Mob: (+357) 99530608
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