1 from __future__ import absolute_import, print_function, unicode_literals
10 from django.conf import settings
11 from django.core import urlresolvers
12 from django.utils import timezone
13 from django.db import models
14 from django.db.models.signals import pre_save
16 from samples.models import Library, HTSUser
17 from htsworkflow.util.conversion import parse_flowcell_id
18 from htsworkflow.pipelines import runfolder
22 LOGGER = logging.getLogger(__name__)
25 default_pM = int(settings.DEFAULT_PM)
26 except AttributeError as e:
27 LOGGER.error("invalid value for default_pm")
29 # how many days to wait before trying to re-import a runfolder
32 RESCAN_DELAY = int(settings.RESCAN_DELAY)
33 except (ValueError, AttributeError):
34 LOGGER.error("Missing or invalid settings.RESCAN_DELAY, "\
35 "defaulting to %s" % (RESCAN_DELAY,))
37 RUN_STATUS_CHOICES = (
38 (0, 'Sequencer running'), # Solexa Data Pipeline Not Yet Started'),
39 (1, 'Data Pipeline Started'),
40 (2, 'Data Pipeline Interrupted'),
41 (3, 'Data Pipeline Finished'),
42 (4, 'Collect Results Started'),
43 (5, 'Collect Results Finished'),
48 RUN_STATUS_REVERSE_MAP = dict(((v, k) for k, v in RUN_STATUS_CHOICES))
51 class ClusterStation(models.Model):
52 """List of cluster stations"""
53 name = models.CharField(max_length=50, unique=True)
54 isdefault = models.BooleanField(default=False, null=False)
57 ordering = ["-isdefault", "name"]
63 def update_isdefault(sender, instance, **kwargs):
64 """Clear default if needed
66 if instance.isdefault:
67 for c in ClusterStation.objects.filter(isdefault=True).all():
68 if c.id != instance.id:
72 def cluster_station_default():
73 d = ClusterStation.objects.filter(isdefault=True).all()
76 d = ClusterStation.objects.order_by('-id').all()
81 pre_save.connect(ClusterStation.update_isdefault, sender=ClusterStation)
83 class Sequencer(models.Model):
84 """Sequencers we've owned
86 name = models.CharField(max_length=50, db_index=True)
87 instrument_name = models.CharField(max_length=50, db_index=True)
88 serial_number = models.CharField(max_length=50, db_index=True)
89 model = models.CharField(max_length=255)
90 active = models.BooleanField(default=True, null=False)
91 isdefault = models.BooleanField(default=False, null=False)
92 comment = models.CharField(max_length=255)
95 ordering = ["-isdefault", "-active", "name"]
98 name = [str(self.name)]
99 if self.instrument_name is not None:
100 name.append("(%s)" % (str(self.instrument_name),))
101 return " ".join(name)
103 def get_absolute_url(self):
104 return urlresolvers.reverse('sequencer',
105 kwargs={'sequencer_id': self.id})
108 def update_isdefault(sender, instance, **kwargs):
109 """Clear default if needed
111 if instance.isdefault:
112 for s in Sequencer.objects.filter(isdefault=True).all():
113 if s.id != instance.id:
117 pre_save.connect(Sequencer.update_isdefault, sender=Sequencer)
119 def sequencer_default():
120 d = Sequencer.objects.filter(isdefault=True).all()
123 d = Sequencer.objects.order_by('active', '-id').all()
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,
148 default=cluster_station_default)
149 sequencer = models.ForeignKey(Sequencer, default=sequencer_default)
151 notes = models.TextField(blank=True)
154 return str(self.flowcell_id)
158 for lane in self.lane_set.order_by('lane_number'):
159 cluster_estimate = lane.cluster_estimate
160 if cluster_estimate is not None:
161 cluster_estimate = "%s k" % ((int(cluster_estimate) / 1000), )
163 cluster_estimate = 'None'
164 library_id = lane.library_id
165 library = lane.library
166 element = '<tr><td>%d</td>'\
167 '<td><a href="%s">%s</a></td><td>%s</td></tr>'
168 html.append(element % (lane.lane_number,
169 library.get_admin_url(),
172 html.append('</table>')
173 return "\n".join(html)
174 Lanes.allow_tags = True
177 ordering = ["-run_date"]
179 def get_admin_url(self):
180 # that's the django way... except it didn't work
181 return urlresolvers.reverse('admin:experiments_flowcell_change',
184 def flowcell_type(self):
185 """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 urlresolvers.reverse('flowcell_detail', args=[str(flowcell_id)])
196 def get_raw_data_directory(self):
197 """Return location of where the raw data is stored"""
198 flowcell_id, status = parse_flowcell_id(self.flowcell_id)
200 return os.path.join(settings.RESULT_HOME_DIR, flowcell_id)
202 def update_sequencing_runs(self):
203 result_root = self.get_raw_data_directory()
204 LOGGER.debug("Update data runs flowcell root: %s" % (result_root,))
205 if result_root is None:
208 run_xml_re = re.compile(glob.fnmatch.translate('run*.xml'))
210 for dirpath, dirnames, filenames in os.walk(result_root):
211 for filename in filenames:
212 if run_xml_re.match(filename):
213 # we have a run directory
214 relative_pathname = get_relative_pathname(dirpath)
215 self.import_sequencing_run(relative_pathname, filename)
217 def import_sequencing_run(self, relative_pathname, run_xml_name, force=False):
218 """Given a result directory import files"""
220 run_dir = get_absolute_pathname(relative_pathname)
221 run_xml_path = os.path.join(run_dir, run_xml_name)
223 runs = SequencingRun.objects.filter(result_dir = relative_pathname)
225 run = SequencingRun()
228 raise RuntimeError("Too many data runs for %s" % (
234 if created or force or (now-run.last_update_time).days > RESCAN_DELAY:
235 LOGGER.debug("Importing run from %s" % (relative_pathname,))
236 run_xml_data = runfolder.load_pipeline_run_xml(run_xml_path)
238 run.status = RUN_STATUS_REVERSE_MAP['DONE']
239 run.result_dir = relative_pathname
240 run.runfolder_name = run_xml_data.runfolder_name
241 run.cycle_start = run_xml_data.image_analysis.start
242 run.cycle_stop = run_xml_data.image_analysis.stop
243 naive_run_start_time = datetime.datetime.fromordinal(run_xml_data.image_analysis.date.toordinal())
244 run.run_start_time = pytz.timezone(settings.TIME_ZONE).localize(naive_run_start_time)
245 run.image_software = run_xml_data.image_analysis.software
246 run.image_version = run_xml_data.image_analysis.version
247 run.basecall_software = run_xml_data.bustard.software
248 run.basecall_version = run_xml_data.bustard.version
249 # we're frequently not running alignments
250 if run_xml_data.gerald:
251 run.alignment_software = run_xml_data.gerald.software
252 run.alignment_version = run_xml_data.gerald.version
254 run.last_update_time = timezone.now()
257 run.update_result_files()
260 # FIXME: should we automatically update sequencing run?
261 # Or should we expect someone to call update_sequencing_runs?
262 #def update_flowcell_sequencingruns(sender, instance, *args, **kwargs):
263 # """Update our sequencing rungs
265 # if not os.path.exists(settings.RESULT_HOME_DIR):
268 # instance.update_sequencing_runs()
269 #post_init.connect(update_flowcell_sequencingruns, sender=FlowCell)
271 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)
301 def get_absolute_url(self):
302 return urlresolvers.reverse('flowcell_lane_detail',
303 kwargs={'lane_pk': str(self.id)})
306 return self.flowcell.flowcell_id + ':' + str(self.lane_number)
309 class SequencingRun(models.Model):
310 flowcell = models.ForeignKey(FlowCell, verbose_name="Flowcell Id")
311 runfolder_name = models.CharField(max_length=50)
312 result_dir = models.CharField(max_length=255)
313 last_update_time = models.DateTimeField()
314 run_start_time = models.DateTimeField()
315 cycle_start = models.IntegerField(null=True, blank=True)
316 cycle_stop = models.IntegerField(null=True, blank=True)
317 run_status = models.IntegerField(choices=RUN_STATUS_CHOICES,
318 null=True, blank=True)
319 image_software = models.CharField(max_length=50)
320 image_version = models.CharField(max_length=50)
321 basecall_software = models.CharField(max_length=50)
322 basecall_version = models.CharField(max_length=50)
323 alignment_software = models.CharField(max_length=50)
324 alignment_version = models.CharField(max_length=50)
325 comment = models.TextField(blank=True)
327 def update_result_files(self):
328 abs_result_dir = get_absolute_pathname(self.result_dir)
330 for dirname, dirnames, filenames in os.walk(abs_result_dir):
331 for filename in filenames:
332 pathname = os.path.join(dirname, filename)
333 relative_pathname = get_relative_pathname(pathname)
334 datafiles = self.datafile_set.filter(
336 relative_pathname=relative_pathname)
337 if len(datafiles) > 0:
340 metadata = find_file_type_metadata_from_filename(filename)
341 if metadata is not None:
342 metadata['filename'] = filename
344 newfile.sequencing_run = self
345 newfile.file_type = metadata['file_type']
346 newfile.relative_pathname = relative_pathname
348 lane_number = metadata.get('lane', None)
349 if lane_number is not None:
350 lane = self.flowcell.lane_set.get(
351 lane_number=lane_number)
352 newfile.library = lane.library
355 self.datafile_set.add(newfile)
357 self.last_update_time = timezone.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.TextField(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)
425 """Helper function to set default UUID in DataFile"""
426 return str(uuid.uuid1())
429 class DataFile(models.Model):
430 """Store map from random ID to filename"""
431 random_key = models.CharField(max_length=64,
434 sequencing_run = models.ForeignKey(SequencingRun, db_index=True, null=True)
435 library = models.ForeignKey(Library, db_index=True, null=True, blank=True)
436 file_type = models.ForeignKey(FileType)
437 relative_pathname = models.CharField(max_length=255, db_index=True)
439 def _get_attributes(self):
440 return self.file_type.parse_filename(self.relative_pathname)
441 attributes = property(_get_attributes)
443 def _get_pathname(self):
444 return get_absolute_pathname(self.relative_pathname)
445 pathname = property(_get_pathname)
447 def get_absolute_url(self):
448 return urlresolvers.reverse('read_result_file', (), {'key': self.random_key})
451 def find_file_type_metadata_from_filename(pathname):
452 path, filename = os.path.split(pathname)
454 for file_type in FileType.objects.all():
455 result = file_type.parse_filename(filename)
456 if result is not None:
457 result['file_type'] = file_type
463 def get_relative_pathname(abspath):
464 """Strip off the result home directory from a path
466 result_home_dir = os.path.join(settings.RESULT_HOME_DIR, '')
467 relative_pathname = abspath.replace(result_home_dir, '')
468 return relative_pathname
471 def get_absolute_pathname(relative_pathname):
472 """Attach relative path to results home directory"""
473 return os.path.join(settings.RESULT_HOME_DIR, relative_pathname)