9 from django.conf import settings
10 from django.core.exceptions import ObjectDoesNotExist
11 from django.core import urlresolvers
12 from django.db import models
13 from django.db.models.signals import post_init, pre_save
15 from htsworkflow.frontend.samples.models import Library
16 from htsworkflow.util.conversion import parse_flowcell_id
17 from htsworkflow.pipelines import runfolder
19 LOGGER = logging.getLogger(__name__)
22 default_pM = int(settings.DEFAULT_PM)
24 LOGGER.error("invalid value for frontend.default_pm")
26 # how many days to wait before trying to re-import a runfolder
29 RESCAN_DELAY = int(settings.RESCAN_DELAY)
30 except (ValueError, AttributeError):
31 LOGGER.error("Missing or invalid settings.RESCAN_DELAY, "\
32 "defaulting to %s" % (RESCAN_DELAY,))
34 RUN_STATUS_CHOICES = (
35 (0, 'Sequencer running'), # Solexa Data Pipeline Not Yet Started'),
36 (1, 'Data Pipeline Started'),
37 (2, 'Data Pipeline Interrupted'),
38 (3, 'Data Pipeline Finished'),
39 (4, 'Collect Results Started'),
40 (5, 'Collect Results Finished'),
45 RUN_STATUS_REVERSE_MAP = dict(((v, k) for k, v in RUN_STATUS_CHOICES))
48 class ClusterStation(models.Model):
49 """List of cluster stations"""
50 name = models.CharField(max_length=50, unique=True)
51 isdefault = models.BooleanField(default=False, null=False)
54 ordering = ["-isdefault", "name"]
56 def __unicode__(self):
57 return unicode(self.name)
61 d = cls.objects.filter(isdefault=True).all()
64 d = cls.objects.order_by('-id').all()
70 def update_isdefault(sender, instance, **kwargs):
71 """Clear default if needed
73 if instance.isdefault:
74 for c in ClusterStation.objects.filter(isdefault=True).all():
75 if c.id != instance.id:
79 pre_save.connect(ClusterStation.update_isdefault, sender=ClusterStation)
81 class Sequencer(models.Model):
82 """Sequencers we've owned
84 name = models.CharField(max_length=50, db_index=True)
85 instrument_name = models.CharField(max_length=50, db_index=True)
86 serial_number = models.CharField(max_length=50, db_index=True)
87 model = models.CharField(max_length=255)
88 active = models.BooleanField(default=True, null=False)
89 isdefault = models.BooleanField(default=False, null=False)
90 comment = models.CharField(max_length=255)
93 ordering = ["-isdefault", "-active", "name"]
95 def __unicode__(self):
96 name = [unicode(self.name)]
97 if self.instrument_name is not None:
98 name.append("(%s)" % (unicode(self.instrument_name),))
102 def get_absolute_url(self):
103 return ('htsworkflow.frontend.experiments.views.sequencer',
108 d = cls.objects.filter(isdefault=True).all()
111 d = cls.objects.order_by('active', '-id').all()
117 def update_isdefault(sender, instance, **kwargs):
118 """Clear default if needed
120 if instance.isdefault:
121 for s in Sequencer.objects.filter(isdefault=True).all():
122 if s.id != instance.id:
126 pre_save.connect(Sequencer.update_isdefault, sender=Sequencer)
129 class FlowCell(models.Model):
130 flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
131 run_date = models.DateTimeField()
132 advanced_run = models.BooleanField(default=False)
133 paired_end = models.BooleanField(default=False)
134 read_length = models.IntegerField(default=32) # Stanford is currenlty 25
135 control_lane = models.IntegerField(choices=[(1, 1),
147 cluster_station = models.ForeignKey(ClusterStation, default=ClusterStation.default)
148 sequencer = models.ForeignKey(Sequencer, default=Sequencer.default)
150 notes = models.TextField(blank=True)
152 def __unicode__(self):
153 return unicode(self.flowcell_id)
157 for lane in self.lane_set.order_by('lane_number'):
158 cluster_estimate = lane.cluster_estimate
159 if cluster_estimate is not None:
160 cluster_estimate = "%s k" % ((int(cluster_estimate) / 1000), )
162 cluster_estimate = 'None'
163 library_id = lane.library_id
164 library = lane.library
165 element = '<tr><td>%d</td>'\
166 '<td><a href="%s">%s</a></td><td>%s</td></tr>'
167 html.append(element % (lane.lane_number,
168 library.get_admin_url(),
171 html.append('</table>')
172 return "\n".join(html)
173 Lanes.allow_tags = True
176 ordering = ["-run_date"]
178 def get_admin_url(self):
179 # that's the django way... except it didn't work
180 return urlresolvers.reverse('admin:experiments_flowcell_change',
183 def flowcell_type(self):
184 """Convert our boolean 'is paired' flag to a name
192 def get_absolute_url(self):
193 flowcell_id, status = parse_flowcell_id(self.flowcell_id)
194 return ('htsworkflow.frontend.experiments.views.flowcell_detail',
197 def get_raw_data_directory(self):
198 """Return location of where the raw data is stored"""
199 flowcell_id, status = parse_flowcell_id(self.flowcell_id)
201 return os.path.join(settings.RESULT_HOME_DIR, flowcell_id)
203 def update_data_runs(self):
204 result_root = self.get_raw_data_directory()
205 LOGGER.debug("Update data runs flowcell root: %s" % (result_root,))
206 if result_root is None:
209 result_home_dir = os.path.join(settings.RESULT_HOME_DIR, '')
210 run_xml_re = re.compile(glob.fnmatch.translate('run*.xml'))
213 for dirpath, dirnames, filenames in os.walk(result_root):
214 for filename in filenames:
215 if run_xml_re.match(filename):
216 # we have a run directory
217 relative_pathname = get_relative_pathname(dirpath)
218 self.import_data_run(relative_pathname, filename)
220 def import_data_run(self, relative_pathname, run_xml_name, force=False):
221 """Given a result directory import files"""
222 now = datetime.datetime.now()
223 run_dir = get_absolute_pathname(relative_pathname)
224 run_xml_path = os.path.join(run_dir, run_xml_name)
226 runs = DataRun.objects.filter(result_dir = relative_pathname)
231 raise RuntimeError("Too many data runs for %s" % (
237 if created or force or (now-run.last_update_time).days > RESCAN_DELAY:
238 LOGGER.debug("Importing run from %s" % (relative_pathname,))
239 run_xml_data = runfolder.load_pipeline_run_xml(run_xml_path)
241 run.status = RUN_STATUS_REVERSE_MAP['DONE']
242 run.result_dir = relative_pathname
243 run.runfolder_name = run_xml_data.runfolder_name
244 run.cycle_start = run_xml_data.image_analysis.start
245 run.cycle_stop = run_xml_data.image_analysis.stop
246 run.run_start_time = run_xml_data.image_analysis.date
247 run.image_software = run_xml_data.image_analysis.software
248 run.image_version = run_xml_data.image_analysis.version
249 run.basecall_software = run_xml_data.bustard.software
250 run.basecall_version = run_xml_data.bustard.version
251 run.alignment_software = run_xml_data.gerald.software
252 run.alignment_version = run_xml_data.gerald.version
254 run.last_update_time = datetime.datetime.now()
257 run.update_result_files()
260 # FIXME: should we automatically update dataruns?
261 # Or should we expect someone to call update_data_runs?
262 #def update_flowcell_dataruns(sender, instance, *args, **kwargs):
263 # """Update our dataruns
265 # if not os.path.exists(settings.RESULT_HOME_DIR):
268 # instance.update_data_runs()
269 #post_init.connect(update_flowcell_dataruns, sender=FlowCell)
272 LANE_STATUS_CODES = [(0, 'Failed'),
275 LANE_STATUS_MAP = dict((int(k), v) for k, v in LANE_STATUS_CODES)
276 LANE_STATUS_MAP[None] = "Unknown"
279 def is_valid_lane(value):
280 if value >= 1 and value <= 8:
286 class Lane(models.Model):
287 flowcell = models.ForeignKey(FlowCell)
288 lane_number = models.IntegerField()
289 library = models.ForeignKey(Library)
290 pM = models.DecimalField(max_digits=5,
295 cluster_estimate = models.IntegerField(blank=True, null=True)
296 status = models.IntegerField(choices=LANE_STATUS_CODES,
299 comment = models.TextField(null=True, blank=True)
302 def get_absolute_url(self):
303 return ('htsworkflow.frontend.experiments.views.flowcell_lane_detail',
306 def __unicode__(self):
307 return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
310 class DataRun(models.Model):
311 flowcell = models.ForeignKey(FlowCell, verbose_name="Flowcell Id")
312 runfolder_name = models.CharField(max_length=50)
313 result_dir = models.CharField(max_length=255)
314 last_update_time = models.DateTimeField()
315 run_start_time = models.DateTimeField()
316 cycle_start = models.IntegerField(null=True, blank=True)
317 cycle_stop = models.IntegerField(null=True, blank=True)
318 run_status = models.IntegerField(choices=RUN_STATUS_CHOICES,
319 null=True, blank=True)
320 image_software = models.CharField(max_length=50)
321 image_version = models.CharField(max_length=50)
322 basecall_software = models.CharField(max_length=50)
323 basecall_version = models.CharField(max_length=50)
324 alignment_software = models.CharField(max_length=50)
325 alignment_version = models.CharField(max_length=50)
326 comment = models.TextField(blank=True)
328 def update_result_files(self):
329 abs_result_dir = get_absolute_pathname(self.result_dir)
331 for dirname, dirnames, filenames in os.walk(abs_result_dir):
332 for filename in filenames:
333 pathname = os.path.join(dirname, filename)
334 relative_pathname = get_relative_pathname(pathname)
335 datafiles = self.datafile_set.filter(
337 relative_pathname=relative_pathname)
338 if len(datafiles) > 0:
341 metadata = find_file_type_metadata_from_filename(filename)
342 if metadata is not None:
343 metadata['filename'] = filename
345 newfile.data_run = self
346 newfile.file_type = metadata['file_type']
347 newfile.relative_pathname = relative_pathname
349 lane_number = metadata.get('lane', None)
350 if lane_number is not None:
351 lane = self.flowcell.lane_set.get(
352 lane_number=lane_number)
353 newfile.library = lane.library
355 self.datafile_set.add(newfile)
357 self.last_update_time = datetime.datetime.now()
359 def lane_files(self):
362 for datafile in self.datafile_set.all():
363 metadata = datafile.attributes
364 if metadata is not None:
365 lane = metadata.get('lane', None)
367 lane_file_set = lanes.setdefault(lane, {})
368 normalized_name = datafile.file_type.normalized_name
369 lane_file_set[normalized_name] = datafile
372 def ivc_plots(self, lane):
373 ivc_name = ['IVC All', 'IVC Call',
374 'IVC Percent Base', 'IVC Percent All', 'IVC Percent Call']
377 for rel_filename, metadata in self.get_result_files():
378 if metadata.file_type.name in ivc_name:
379 plots[metadata.file_type.name] = (rel_filename, metadata)
382 class FileType(models.Model):
383 """Represent potential file types
385 regex is a pattern used to detect if a filename matches this type
386 data run currently assumes that there may be a (?P<lane>) and
387 (?P<end>) pattern in the regular expression.
389 name = models.CharField(max_length=50)
390 mimetype = models.CharField(max_length=50, null=True, blank=True)
391 # regular expression from glob.fnmatch.translate
392 regex = models.CharField(max_length=50, null=True, blank=True)
394 def parse_filename(self, pathname):
395 """Does filename match our pattern?
397 Returns None if not, or dictionary of match variables if we do.
399 path, filename = os.path.split(pathname)
400 if len(self.regex) > 0:
401 match = re.match(self.regex, filename)
402 if match is not None:
403 # These are (?P<>) names we know about from our
405 results = match.groupdict()
407 # convert int parameters
408 for attribute_name in ['lane', 'end']:
409 value = results.get(attribute_name, None)
410 if value is not None:
411 results[attribute_name] = int(value)
415 def _get_normalized_name(self):
416 """Crush data file name into identifier friendly name"""
417 return self.name.replace(' ', '_').lower()
418 normalized_name = property(_get_normalized_name)
420 def __unicode__(self):
421 #return u"<FileType: %s>" % (self.name,)
426 """Helper function to set default UUID in DataFile"""
427 return str(uuid.uuid1())
430 class DataFile(models.Model):
431 """Store map from random ID to filename"""
432 random_key = models.CharField(max_length=64,
435 data_run = models.ForeignKey(DataRun, db_index=True)
436 library = models.ForeignKey(Library, db_index=True, null=True, blank=True)
437 file_type = models.ForeignKey(FileType)
438 relative_pathname = models.CharField(max_length=255, db_index=True)
440 def _get_attributes(self):
441 return self.file_type.parse_filename(self.relative_pathname)
442 attributes = property(_get_attributes)
444 def _get_pathname(self):
445 return get_absolute_pathname(self.relative_pathname)
446 pathname = property(_get_pathname)
449 def get_absolute_url(self):
450 return ('htsworkflow.frontend.experiments.views.read_result_file',
451 (), {'key': self.random_key})
454 def find_file_type_metadata_from_filename(pathname):
455 path, filename = os.path.split(pathname)
457 for file_type in FileType.objects.all():
458 result = file_type.parse_filename(filename)
459 if result is not None:
460 result['file_type'] = file_type
466 def get_relative_pathname(abspath):
467 """Strip off the result home directory from a path
469 result_home_dir = os.path.join(settings.RESULT_HOME_DIR, '')
470 relative_pathname = abspath.replace(result_home_dir, '')
471 return relative_pathname
474 def get_absolute_pathname(relative_pathname):
475 """Attach relative path to results home directory"""
476 return os.path.join(settings.RESULT_HOME_DIR, relative_pathname)