2 from ConfigParser import SafeConfigParser
8 from optparse import OptionParser, OptionGroup
10 from pprint import pprint, pformat
12 from StringIO import StringIO
20 from zipfile import ZipFile
24 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
25 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
27 from htsworkflow.util import api
28 from htsworkflow.util.rdfhelp import \
36 from htsworkflow.submission.daf import \
38 MetadataLookupException, \
40 from htsworkflow.submission.results import ResultMap
41 from htsworkflow.submission.condorfastq import CondorFastqExtract
43 logger = logging.getLogger('ucsc_gather')
46 LFTP = '/usr/bin/lftp'
48 def main(cmdline=None):
49 parser = make_parser()
50 opts, args = parser.parse_args(cmdline)
59 logging.basicConfig(level = logging.DEBUG )
61 logging.basicConfig(level = logging.INFO )
63 logging.basicConfig(level = logging.WARNING )
65 apidata = api.make_auth_from_opts(opts, parser)
67 model = get_model(opts.model, opts.db_path)
70 mapper = UCSCSubmission(opts.name, opts.daf, model)
71 if opts.library_url is not None:
72 mapper.library_url = opts.library_url
73 submission_uri = get_submission_uri(opts.name)
76 if opts.load_rdf is not None:
77 if submission_uri is None:
78 parser.error("Please specify the submission name")
79 load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
81 if opts.make_ddf and opts.daf is None:
82 parser.error("Please specify your daf when making ddf files")
86 results.add_results_from_file(a)
88 if opts.make_tree_from is not None:
89 results.make_tree_from(opts.make_tree_from)
93 parser.error("Specify a submission model")
94 if mapper.daf is None:
95 parser.error("Please load a daf first")
96 mapper.link_daf(results)
99 flowcells = os.path.join(opts.sequence, 'flowcells')
100 extractor = CondorFastqExtract(opts.host, flowcells,
102 extractor.create_scripts(results)
104 if opts.scan_submission:
105 mapper.scan_submission_dirs(results)
108 if not os.path.exists(TAR):
109 parser.error("%s does not exist, please specify --tar" % (TAR,))
110 if not os.path.exists(LFTP):
111 parser.error("%s does not exist, please specify --lftp" % (LFTP,))
112 make_all_ddfs(mapper, results, opts.daf, force=opts.force)
115 zip_ddfs(mapper, results, opts.daf)
118 sparql_query(model, opts.sparql)
121 writer = get_serializer()
122 print writer.serialize_model_to_string(model)
126 parser = OptionParser()
128 model = OptionGroup(parser, 'model')
129 model.add_option('--name', help="Set submission name")
130 model.add_option('--db-path', default=None,
131 help="set rdf database path")
132 model.add_option('--model', default=None,
133 help="Load model database")
134 model.add_option('--load-rdf', default=None,
135 help="load rdf statements into model")
136 model.add_option('--sparql', default=None, help="execute sparql query")
137 model.add_option('--print-rdf', action="store_true", default=False,
138 help="print ending model state")
139 model.add_option('--tar', default=TAR,
140 help="override path to tar command")
141 model.add_option('--lftp', default=LFTP,
142 help="override path to lftp command")
143 parser.add_option_group(model)
145 commands = OptionGroup(parser, 'commands')
146 commands.add_option('--make-tree-from',
147 help="create directories & link data files",
149 commands.add_option('--fastq', default=False, action="store_true",
150 help="generate scripts for making fastq files")
151 commands.add_option('--scan-submission', default=False, action="store_true",
152 help="Import metadata for submission into our model")
153 commands.add_option('--link-daf', default=False, action="store_true",
154 help="link daf into submission directories")
155 commands.add_option('--make-ddf', help='make the ddfs', default=False,
157 commands.add_option('--zip-ddf', default=False, action='store_true',
158 help='zip up just the metadata')
160 parser.add_option_group(commands)
162 parser.add_option('--force', default=False, action="store_true",
163 help="Force regenerating fastqs")
164 parser.add_option('--daf', default=None, help='specify daf name')
165 parser.add_option('--library-url', default=None,
166 help="specify an alternate source for library information")
168 parser.add_option('--verbose', default=False, action="store_true",
169 help='verbose logging')
170 parser.add_option('--debug', default=False, action="store_true",
171 help='debug logging')
173 api.add_auth_options(parser)
178 def make_all_ddfs(view_map, library_result_map, daf_name, make_condor=True, force=False):
180 for lib_id, result_dir in library_result_map.items():
181 submissionNode = view_map.get_submission_node(result_dir)
183 make_ddf(view_map, submissionNode, daf_name, make_condor, result_dir)
186 if make_condor and len(dag_fragment) > 0:
187 dag_filename = 'submission.dagman'
188 if not force and os.path.exists(dag_filename):
189 logger.warn("%s exists, please delete" % (dag_filename,))
191 f = open(dag_filename,'w')
192 f.write( os.linesep.join(dag_fragment))
193 f.write( os.linesep )
197 def make_ddf(view_map, submissionNode, daf_name, make_condor=False, outdir=None):
199 Make ddf files, and bonus condor file
201 query_template = """PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
202 PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
203 PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
205 select ?submitView ?files ?md5sum ?view ?cell ?antibody ?sex ?control ?strain ?controlId ?labExpId ?labVersion ?treatment ?protocol ?readType ?insertLength ?replicate ?mapAlgorithm
207 ?file ucscDaf:filename ?files ;
208 ucscDaf:md5sum ?md5sum .
209 ?submitView ucscDaf:has_file ?file ;
210 ucscDaf:view ?dafView ;
211 ucscDaf:submission <%(submission)s> .
212 ?dafView ucscDaf:name ?view .
213 <%(submission)s> submissionOntology:library ?library ;
215 OPTIONAL { ?library libraryOntology:antibody ?antibody }
216 OPTIONAL { ?library libraryOntology:cell_line ?cell }
217 OPTIONAL { <%(submission)s> ucscDaf:control ?control }
218 OPTIONAL { <%(submission)s> ucscDaf:controlId ?controlId }
219 OPTIONAL { ?library ucscDaf:sex ?sex }
220 OPTIONAL { ?library libraryOntology:library_id ?labExpId }
221 OPTIONAL { ?library libraryOntology:library_id ?labVersion }
222 OPTIONAL { ?library libraryOntology:replicate ?replicate }
223 OPTIONAL { ?library libraryOntology:condition_term ?treatment }
224 OPTIONAL { ?library ucscDaf:protocol ?protocol }
225 OPTIONAL { ?library ucscDaf:readType ?readType }
226 OPTIONAL { ?library ucscDaf:strain ?strain }
227 OPTIONAL { ?library libraryOntology:insert_size ?insertLength }
228 OPTIONAL { ?library ucscDaf:mapAlgorithm ?mapAlgorithm }
230 ORDER BY ?submitView"""
233 name = fromTypedNode(view_map.model.get_target(submissionNode, submissionOntology['name']))
235 logger.error("Need name for %s" % (str(submissionNode)))
238 ddf_name = make_ddf_name(name)
239 if outdir is not None:
240 outfile = os.path.join(outdir, ddf_name)
241 output = open(outfile,'w')
246 formatted_query = query_template % {'submission': str(submissionNode.uri)}
248 query = RDF.SPARQLQuery(formatted_query)
249 results = query.execute(view_map.model)
251 # filename goes first
252 variables = view_map.get_daf_variables()
254 output.write('\t'.join(variables))
255 output.write(os.linesep)
260 viewname = fromTypedNode(row['view'])
261 current = all_views.setdefault(viewname, {})
262 for variable_name in variables:
263 value = str(fromTypedNode(row[variable_name]))
264 if value is None or value == 'None':
265 logger.warn("{0}: {1} was None".format(outfile, variable_name))
266 if variable_name in ('files', 'md5sum'):
267 current.setdefault(variable_name,[]).append(value)
269 current[variable_name] = value
271 for view in all_views.keys():
273 for variable_name in variables:
274 if variable_name in ('files', 'md5sum'):
275 line.append(','.join(all_views[view][variable_name]))
277 line.append(all_views[view][variable_name])
278 output.write("\t".join(line))
279 output.write(os.linesep)
280 all_files.extend(all_views[view]['files'])
283 "Examined {0}, found files: {1}".format(
284 str(submissionNode), ", ".join(all_files)))
286 all_files.append(daf_name)
287 all_files.append(ddf_name)
290 archive_condor = make_condor_archive_script(name, all_files, outdir)
291 upload_condor = make_condor_upload_script(name, outdir)
293 dag_fragments.extend(
294 make_dag_fragment(name, archive_condor, upload_condor)
300 def zip_ddfs(view_map, library_result_map, daf_name):
301 """zip up just the ddf & daf files
303 rootdir = os.getcwd()
304 for lib_id, result_dir in library_result_map:
305 submissionNode = view_map.get_submission_node(result_dir)
306 nameNode = view_map.model.get_target(submissionNode,
307 submissionOntology['name'])
308 name = fromTypedNode(nameNode)
310 logger.error("Need name for %s" % (str(submissionNode)))
313 zip_name = '../{0}.zip'.format(lib_id)
314 os.chdir(os.path.join(rootdir, result_dir))
315 with ZipFile(zip_name, 'w') as stream:
316 stream.write(make_ddf_name(name))
317 stream.write(daf_name)
321 def make_condor_archive_script(name, files, outdir=None):
322 script = """Universe = vanilla
325 arguments = czvhf ../%(archivename)s %(filelist)s
327 Error = compress.out.$(Process).log
328 Output = compress.out.$(Process).log
329 Log = /tmp/submission-compress-%(user)s.log
330 initialdir = %(initialdir)s
331 environment="GZIP=-3"
339 pathname = os.path.join(outdir, f)
340 if not os.path.exists(pathname):
341 raise RuntimeError("Missing %s from %s" % (f,outdir))
343 context = {'archivename': make_submission_name(name),
344 'filelist': " ".join(files),
345 'initialdir': os.path.abspath(outdir),
346 'user': os.getlogin(),
349 condor_script = os.path.join(outdir, make_condor_name(name, 'archive'))
350 condor_stream = open(condor_script,'w')
351 condor_stream.write(script % context)
352 condor_stream.close()
356 def make_condor_upload_script(name, lftp, outdir=None):
357 script = """Universe = vanilla
359 Executable = %(lftp)s
360 arguments = -c put %(archivename)s -o ftp://%(ftpuser)s:%(ftppassword)s@%(ftphost)s/%(archivename)s
362 Error = upload.out.$(Process).log
363 Output = upload.out.$(Process).log
364 Log = /tmp/submission-upload-%(user)s.log
365 initialdir = %(initialdir)s
372 auth = netrc.netrc(os.path.expanduser("~diane/.netrc"))
374 encodeftp = 'encodeftp.cse.ucsc.edu'
375 ftpuser = auth.hosts[encodeftp][0]
376 ftppassword = auth.hosts[encodeftp][2]
377 context = {'archivename': make_submission_name(name),
378 'initialdir': os.path.abspath(outdir),
379 'user': os.getlogin(),
381 'ftppassword': ftppassword,
382 'ftphost': encodeftp,
385 condor_script = os.path.join(outdir, make_condor_name(name, 'upload'))
386 condor_stream = open(condor_script,'w')
387 condor_stream.write(script % context)
388 condor_stream.close()
389 os.chmod(condor_script, stat.S_IREAD|stat.S_IWRITE)
394 def make_dag_fragment(ininame, archive_condor, upload_condor):
396 Make the couple of fragments compress and then upload the data.
398 cur_dir = os.getcwd()
399 archive_condor = os.path.join(cur_dir, archive_condor)
400 upload_condor = os.path.join(cur_dir, upload_condor)
401 job_basename = make_base_name(ininame)
404 fragments.append('JOB %s_archive %s' % (job_basename, archive_condor))
405 fragments.append('JOB %s_upload %s' % (job_basename, upload_condor))
406 fragments.append('PARENT %s_archive CHILD %s_upload' % (job_basename, job_basename))
411 def make_base_name(pathname):
412 base = os.path.basename(pathname)
413 name, ext = os.path.splitext(base)
417 def make_submission_name(ininame):
418 name = make_base_name(ininame)
422 def make_ddf_name(pathname):
423 name = make_base_name(pathname)
427 def make_condor_name(pathname, run_type=None):
428 name = make_base_name(pathname)
430 if run_type is not None:
431 elements.append(run_type)
432 elements.append("condor")
433 return ".".join(elements)
436 def parse_filelist(file_string):
437 return file_string.split(",")
440 def validate_filelist(files):
442 Die if a file doesn't exist in a file list
445 if not os.path.exists(f):
446 raise RuntimeError("%s does not exist" % (f,))
448 if __name__ == "__main__":