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
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 RUN_STATUS_CHOICES = (
27 (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
28 (1, 'Data Pipeline Started'),
29 (2, 'Data Pipeline Interrupted'),
30 (3, 'Data Pipeline Finished'),
31 (4, 'Collect Results Started'),
32 (5, 'Collect Results Finished'),
37 RUN_STATUS_REVERSE_MAP = dict(((v,k) for k,v in RUN_STATUS_CHOICES))
39 class ClusterStation(models.Model):
40 name = models.CharField(max_length=50, unique=True)
42 def __unicode__(self):
43 return unicode(self.name)
45 class Sequencer(models.Model):
46 name = models.CharField(max_length=50, unique=True)
48 def __unicode__(self):
49 return unicode(self.name)
51 class FlowCell(models.Model):
52 flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
53 run_date = models.DateTimeField()
54 advanced_run = models.BooleanField(default=False)
55 paired_end = models.BooleanField(default=False)
56 read_length = models.IntegerField(default=32) #Stanford is currenlty 25
57 control_lane = models.IntegerField(choices=[(1,1),(2,2),(3,3),(4,4),(5,5),(6,6),(7,7),(8,8),(0,'All Lanes')], null=True, blank=True)
59 cluster_station = models.ForeignKey(ClusterStation, default=3)
60 sequencer = models.ForeignKey(Sequencer, default=1)
62 notes = models.TextField(blank=True)
64 def __unicode__(self):
65 return unicode(self.flowcell_id)
69 for lane in self.lane_set.all():
70 cluster_estimate = lane.cluster_estimate
71 if cluster_estimate is not None:
72 cluster_estimate = "%s k" % ((int(cluster_estimate)/1000), )
74 cluster_estimate = 'None'
75 library_id = lane.library_id
76 library = lane.library
77 element = '<tr><td>%d</td><td><a href="%s">%s</a></td><td>%s</td></tr>'
78 html.append(element % (lane.lane_number,
79 library.get_admin_url(),
82 html.append('</table>')
83 return "\n".join(html)
84 Lanes.allow_tags = True
87 ordering = ["-run_date"]
89 def get_admin_url(self):
90 # that's the django way... except it didn't work
91 return urlresolvers.reverse('admin:experiments_flowcell_change',
94 def flowcell_type(self):
96 Convert our boolean 'is paired' flag to a name
104 def get_absolute_url(self):
105 flowcell_id, status = parse_flowcell_id(self.flowcell_id)
106 return ('htsworkflow.frontend.experiments.views.flowcell_detail',
109 def get_raw_data_directory(self):
110 """Return location of where the raw data is stored"""
111 flowcell_id, status = parse_flowcell_id(self.flowcell_id)
113 return os.path.join(settings.RESULT_HOME_DIR, flowcell_id)
115 def update_data_runs(self):
116 result_root = self.get_raw_data_directory()
117 if result_root is None:
120 result_home_dir = os.path.join(settings.RESULT_HOME_DIR,'')
121 run_xml_re = re.compile(glob.fnmatch.translate('run*.xml'))
123 dataruns = self.datarun_set.all()
124 datarun_result_dirs = [ x.result_dir for x in dataruns ]
127 for dirpath, dirnames, filenames in os.walk(result_root):
128 for filename in filenames:
129 if run_xml_re.match(filename):
130 # we have a run directory
131 relative_pathname = get_relative_pathname(dirpath)
132 if relative_pathname not in datarun_result_dirs:
133 self.import_data_run(relative_pathname, filename)
135 def import_data_run(self, relative_pathname, run_xml_name):
136 """Given a result directory import files"""
137 run_dir = get_absolute_pathname(relative_pathname)
138 run_xml_path = os.path.join(run_dir, run_xml_name)
139 run_xml_data = runfolder.load_pipeline_run_xml(run_xml_path)
143 run.status = RUN_STATUS_REVERSE_MAP['DONE']
144 run.result_dir = relative_pathname
145 run.runfolder_name = run_xml_data.runfolder_name
146 run.cycle_start = run_xml_data.image_analysis.start
147 run.cycle_stop = run_xml_data.image_analysis.stop
148 run.run_start_time = run_xml_data.image_analysis.date
150 run.last_update_time = datetime.datetime.now()
153 run.update_result_files()
156 # FIXME: should we automatically update dataruns?
157 # Or should we expect someone to call update_data_runs?
158 #def update_flowcell_dataruns(sender, instance, *args, **kwargs):
159 # """Update our dataruns
161 # if not os.path.exists(settings.RESULT_HOME_DIR):
164 # instance.update_data_runs()
165 #post_init.connect(update_flowcell_dataruns, sender=FlowCell)
169 LANE_STATUS_CODES = [(0, 'Failed'),
172 LANE_STATUS_MAP = dict((int(k),v) for k,v in LANE_STATUS_CODES )
173 LANE_STATUS_MAP[None] = "Unknown"
175 def is_valid_lane(value):
176 if value >= 1 and value <= 8:
181 class Lane(models.Model):
182 flowcell = models.ForeignKey(FlowCell)
183 lane_number = models.IntegerField(validators=[is_valid_lane])
184 library = models.ForeignKey(Library)
185 pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
186 cluster_estimate = models.IntegerField(blank=True, null=True)
187 status = models.IntegerField(choices=LANE_STATUS_CODES, null=True, blank=True)
188 comment = models.TextField(null=True, blank=True)
191 def get_absolute_url(self):
192 return ('htsworkflow.frontend.experiments.views.flowcell_lane_detail',
195 def __unicode__(self):
196 return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
198 ### -----------------------
199 class DataRun(models.Model):
200 flowcell = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
201 runfolder_name = models.CharField(max_length=50)
202 result_dir = models.CharField(max_length=255)
203 last_update_time = models.DateTimeField()
204 run_start_time = models.DateTimeField()
205 cycle_start = models.IntegerField(null=True, blank=True)
206 cycle_stop = models.IntegerField(null=True, blank=True)
207 run_status = models.IntegerField(choices=RUN_STATUS_CHOICES,
208 null=True, blank=True)
209 comment = models.TextField(blank=True)
211 def update_result_files(self):
212 abs_result_dir = get_absolute_pathname(self.result_dir)
214 for dirname, dirnames, filenames in os.walk(abs_result_dir):
215 for filename in filenames:
216 pathname = os.path.join(dirname, filename)
217 relative_pathname = get_relative_pathname(pathname)
218 datafiles = self.datafile_set.filter(
220 relative_pathname=relative_pathname)
221 if len(datafiles) > 0:
224 metadata = find_file_type_metadata_from_filename(filename)
225 if metadata is not None:
226 metadata['filename'] = filename
228 newfile.data_run = self
229 newfile.file_type = metadata['file_type']
230 newfile.relative_pathname = relative_pathname
232 lane_number = metadata.get('lane', None)
233 if lane_number is not None:
234 lane = self.flowcell.lane_set.get(lane_number = lane_number)
235 newfile.library = lane.library
237 self.datafile_set.add(newfile)
239 self.last_update_time = datetime.datetime.now()
241 def lane_files(self):
244 for datafile in self.datafile_set.all():
245 metadata = datafile.attributes
246 if metadata is not None:
247 lane = metadata.get('lane', None)
249 lane_file_set = lanes.setdefault(lane, {})
250 lane_file_set[datafile.file_type.normalized_name] = datafile
253 def ivc_plots(self, lane):
254 ivc_name = ['IVC All', 'IVC Call',
255 'IVC Percent Base', 'IVC Percent All', 'IVC Percent Call']
258 for rel_filename, metadata in self.get_result_files():
259 if metadata.file_type.name in ivc_name:
260 plots[metadata.file_type.name] = (rel_filename, metadata)
262 class FileType(models.Model):
263 """Represent potential file types
265 regex is a pattern used to detect if a filename matches this type
266 data run currently assumes that there may be a (?P<lane>) and
267 (?P<end>) pattern in the regular expression.
269 name = models.CharField(max_length=50)
270 mimetype = models.CharField(max_length=50, null=True, blank=True)
271 # regular expression from glob.fnmatch.translate
272 regex = models.CharField(max_length=50, null=True, blank=True)
274 def parse_filename(self, pathname):
275 """Does filename match our pattern?
277 Returns None if not, or dictionary of match variables if we do.
279 path, filename = os.path.split(pathname)
280 if len(self.regex) > 0:
281 match = re.match(self.regex, filename)
282 if match is not None:
283 # These are (?P<>) names we know about from our default regexes.
284 results = match.groupdict()
286 # convert int parameters
287 for attribute_name in ['lane', 'end']:
288 value = results.get(attribute_name, None)
289 if value is not None:
290 results[attribute_name] = int(value)
294 def _get_normalized_name(self):
295 """Crush data file name into identifier friendly name"""
296 return self.name.replace(' ', '_').lower()
297 normalized_name = property(_get_normalized_name)
299 def __unicode__(self):
300 #return u"<FileType: %s>" % (self.name,)
304 """Helper function to set default UUID in DataFile"""
305 return str(uuid.uuid1())
307 class DataFile(models.Model):
308 """Store map from random ID to filename"""
309 random_key = models.CharField(max_length=64,
312 data_run = models.ForeignKey(DataRun, db_index=True)
313 library = models.ForeignKey(Library, db_index=True, null=True, blank=True)
314 file_type = models.ForeignKey(FileType)
315 relative_pathname = models.CharField(max_length=255, db_index=True)
317 def _get_attributes(self):
318 return self.file_type.parse_filename(self.relative_pathname)
319 attributes = property(_get_attributes)
321 def _get_pathname(self):
322 return get_absolute_pathname(self.relative_pathname)
323 pathname = property(_get_pathname)
326 def get_absolute_url(self):
327 return ('htsworkflow.frontend.experiments.views.read_result_file',
328 (), {'key': self.random_key })
330 def find_file_type_metadata_from_filename(pathname):
331 path, filename = os.path.split(pathname)
333 for file_type in FileType.objects.all():
334 result = file_type.parse_filename(filename)
335 if result is not None:
336 result['file_type'] = file_type
341 def get_relative_pathname(abspath):
342 """Strip off the result home directory from a path
344 result_home_dir = os.path.join(settings.RESULT_HOME_DIR,'')
345 relative_pathname = abspath.replace(result_home_dir,'')
346 return relative_pathname
348 def get_absolute_pathname(relative_pathname):
349 """Attach relative path to results home directory"""
350 return os.path.join(settings.RESULT_HOME_DIR, relative_pathname)