from django.db import models from django.core.files import File from django.core.files.storage import FileSystemStorage from datetime import datetime import urllib import os imagefs = FileSystemStorage(location='/b7_1/exports/leica/images') class PI(models.Model): """ Store PI name. Names must be entered manually """ sunetid = models.CharField('PI sunetid', max_length=32, primary_key=True, db_index=True ) first = models.CharField('first name', max_length=32) last = models.CharField('surname', max_length=32, null=True, blank=True) fullname = models.CharField('Full name', max_length=65, null=True, blank=True) aliases = models.CharField('aliases', max_length=128, null=True, blank=True) def save(self): self.fullname = self.first + " " + self.last self.aliases = self.first + " " + self.last super(PI, self).save() class Meta: verbose_name = "PI" ordering = ['last', 'first'] def __unicode__(self): if len(self.fullname): return self.fullname else: return self.sunetid class User(models.Model): """Store user name and sunetid. When first encountered, only the sunetid is used. Names must be entered manually """ sunetid = models.CharField('PI sunetid', max_length=32, primary_key=True, db_index=True ) first = models.CharField('first name', max_length=32) last = models.CharField('surname', max_length=32) defaultPI = models.ForeignKey(PI, null=True, blank=True) class Meta: ordering = ['last', 'first'] def __unicode__(self): if len(self.first + " " + self.last) > 1: return self.last + ", " + self.first else: return self.sunetid class SampleSpecies(models.Model): name = models.CharField('species name', max_length=32, primary_key=True ) aliases = models.CharField('species aliases', max_length=128, default='', null=True, blank=True ) class Meta: verbose_name = "Sample specie" def __unicode__(self): return self.name class C1Instrument(models.Model): name = models.CharField('C1 id name', max_length=30, primary_key=True ) location = models.CharField('location', max_length=16) serialnumber = models.CharField('serial number', max_length=16, null = True, blank = True) aliases = models.CharField('name used in Leica program', max_length=30, null = True, blank = True ) def __unicode__(self): return self.name class ChipType(models.Model): type = models.CharField('chip protocol', max_length=64, primary_key=True ) def __unicode__(self): return self.type class SampleType(models.Model): type = models.CharField('chip protocol', max_length=64, primary_key=True ) def __unicode__(self): return self.type class ChipSize(models.Model): size = models.CharField('cell capture size', max_length=64, primary_key=True ) def __unicode__(self): return self.size class SortMethod(models.Model): name = models.CharField('sort method', max_length=64, primary_key=True ) def __unicode__(self): return self.name class SerialMapping(models.Model): serial_prefix = models.CharField('serial number digits that encode chip type to be mapped', max_length=4, primary_key=True ) type = models.ForeignKey(ChipType) size = models.ForeignKey(ChipSize) def __unicode__(self): return self.serial_prefix class ImageType(models.Model): name = models.CharField('Imaging method', max_length=10, primary_key=True ) def __unicode__(self): return self.name class Tissue(models.Model): name = models.CharField('source tissue', max_length = 32, primary_key=True ) class Meta: ordering = ['name'] def __unicode__(self): return self.name class StorageLocation(models.Model): name = models.CharField('Storage Location', max_length=16, primary_key=True ) class Meta: ordering = ['name'] def __unicode__(self): return self.name class CaptureArray(models.Model): chipid = models.CharField('unique, 10-digit barcode', max_length=10, primary_key=True ) type = models.ForeignKey(ChipType, null=True, blank=True) size = models.ForeignKey(ChipSize, null=True, blank=True) pi = models.ForeignKey(PI, null=True, blank=True) user = models.ForeignKey(User, null=True, blank=True) species = models.ForeignKey(SampleSpecies, null=True, blank=True) instrument = models.ForeignKey(C1Instrument, null=True, blank=True) sampletype = models.ForeignKey(SampleType, null=True, blank=True) tissue = models.ForeignKey(Tissue, null=True, blank=True) sortmethod = models.ForeignKey(SortMethod, null=True, blank=True) description = models.TextField('Sample description', max_length=1024, null=True, blank=True) capturetime = models.DateTimeField('time and date of image capture', null=True, blank=True) revisiontime = models.DateTimeField('time and date of last data update', null=True, blank=True) location = models.ForeignKey(StorageLocation, null=True, blank=True) mosaicimage = models.ImageField('mosaic image', max_length=255, null = True, blank = True) mosaicthumb = models.ImageField('mosaic thumbnail', max_length=255, null = True, blank = True) cirmproject = models.BooleanField('Associated with CIRM Cell Atlas Project', default = False) cirmxfer = models.BooleanField('Transferred to CIRM Cell Atlas Repository', default = False) datesearch = models.CharField('date and time string for admin search',max_length=128, blank=True, null=True) class Meta: ordering = ['chipid'] def save(self): try: prefix = self.chipid[0:4] obj = SerialMapping.objects.filter(serial_prefix=prefix)[0] self.type = obj.type self.size = obj.size except: pass try: self.datesearch = self.capturetime.strftime('%Y%m%d%H%M%S') except: pass super(CaptureArray, self).save() def __unicode__(self): return self.chipid class CellPresent(models.Model): evaluation = models.CharField('user evaluation', null = True, blank = True, default = "No response", max_length = 16) value = models.IntegerField('encoded value') class Meta: verbose_name = "user evaluation" def __unicode__(self): return self.evaluation class HarvestWell(models.Model): name = models.CharField('cell capture site name', max_length = 3, primary_key=True ) class Meta: ordering = ['name'] def __unicode__(self): return self.name class ChipSite(models.Model): name = models.CharField('cell capture site name', max_length = 4, primary_key=True ) harvestwell = models.ForeignKey(HarvestWell, null=True, blank=True) alias = models.CharField('cell capture site alias', max_length = 4, null=True, blank=True) def save(self): try: self.alias = "C" + self.name[2:] super(ChipSite, self).save() except: pass class Meta: ordering = ['name'] def __unicode__(self): if self.alias: return self.alias else: return self.name class CellImage(models.Model): chipid = models.ForeignKey(CaptureArray, null=True, blank=True) cellsite = models.ForeignKey(ChipSite, null=True, blank=True) harvestwell = models.ForeignKey(HarvestWell, null=True, blank=True) imagetype = models.ForeignKey(ImageType, null=True, blank=True) gain = models.FloatField('gain', null=True, blank=True) magnification = models.IntegerField('magnification', default=20, null=True, blank=True) exposure = models.FloatField('exposure', null=True, blank=True) cellsize = models.FloatField('cell size', null=True, blank=True) cellpresent = models.ForeignKey(CellPresent, null=True, blank=True) image = models.ImageField('cell image', max_length=255, null = True, blank = True, upload_to='cellcapture/cellimages') thumbnail = models.ImageField('thumbnail image', max_length=255, null = True, blank = True, upload_to='cellcapture/cellimages') reference = models.CharField('unique reference', max_length=255, unique=True, blank=True, null=True ) class Meta: ordering = ('chipid','cellsite','imagetype') def save(self): # work-around failed three-way unique_together try: self.reference = u'%s:%s:%s'%(self.chipid, self.cellsite, self.imagetype) super(CellImage, self).save() except: pass def __unicode__(self): return u'%s:%s:%s'%(self.chipid, self.cellsite, self.imagetype) class SortMarker(models.Model): name = models.CharField('unique, sort marker', max_length=32, unique=True, blank=True, null=True ) #name = models.CharField('unique, sort marker', max_length=32, default='None', blank=True, null=True ) aliases = models.CharField('Marker aliases', max_length=128, default='', blank=True, null=True) class Meta: ordering = ['name'] def __unicode__(self): return self.name class SortMarkerEntry(models.Model): sortmarker = models.ForeignKey(SortMarker, null=True, blank=True) chipid = models.ForeignKey(CaptureArray, null=True, blank=True) class Meta: ordering = ['sortmarker'] # unique_together = ['sortmarker', 'chipid'] def __unicode__(self): return u'%s:%s'%(self.chipid, self.sortmarker)