# Create your models here.
-
-class Specie(models.Model):
-
- class Admin: pass
+class Species(models.Model):
- scientific_name = models.CharField(maxlength=256, unique=True, db_index=True)
-
+ scientific_name = models.CharField(max_length=256, unique=True, db_index=True, core=True)
+ common_name = models.CharField(max_length=256, blank=True)
def __str__(self):
- return self.scientific_name
-
-#class BedFilePack(models.Model):
+ return '%s (%s)' % (self.scientific_name, self.common_name)
+
+ class Meta:
+ verbose_name_plural = "species"
+ ordering = ["scientific_name"]
+
+ class Admin:
+ fields = (
+ (None, {
+ 'fields': (('scientific_name', 'common_name'),)
+ }),
+ )
class Library(models.Model):
- class Admin: pass
-
- library_id = models.IntegerField(unique=True, db_index=True)
- library_name = models.CharField(maxlength=100, unique=True)
- library_species = models.ForeignKey(Specie)
- made_from_sample = models.ForeignKey('self', blank=True)
+ library_id = models.IntegerField(primary_key=True, db_index=True, core=True)
+ library_name = models.CharField(max_length=100, unique=True, core=True)
+ library_species = models.ForeignKey(Species, core=True)
+ RNAseq = models.BooleanField()
- made_by = models.CharField(maxlength=50, blank=True)
+ made_by = models.CharField(max_length=50, blank=True, default="Lorian")
creation_date = models.DateField(blank=True, null=True)
+ made_for = models.CharField(max_length=50, blank=True)
+
+ PROTOCOL_END_POINTS = (
+ ('?', 'Unknown'),
+ ('Sample', 'Raw sample'),
+ ('Gel', 'Ran gel'),
+ ('1A', 'Gel purification'),
+ ('2A', '2nd PCR'),
+ ('Progress', 'In progress'),
+ )
+ stopping_point = models.CharField(max_length=50, choices=PROTOCOL_END_POINTS)
+ amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
+
+ undiluted_concentration = models.DecimalField(max_digits=5, decimal_places=2, blank=True, null=True)
+ ten_nM_dilution = models.BooleanField()
+ successful_pM = models.IntegerField(blank=True, null=True)
+
notes = models.TextField(blank=True)
def __str__(self):
- return self.library_name
-
-
-class FlowCell(models.Model):
+ return '#%s: %s' % (self.library_id, self.library_name)
- class Admin: pass
+ class Meta:
+ verbose_name_plural = "libraries"
+ ordering = ["-library_id"]
- flowcell_id = models.CharField(maxlength=20, unique=True, db_index=True)
+ class Admin:
+ date_hierarchy = "creation_date"
+ save_as = True
+ save_on_top = True
+ search_fields = ['library_name']
+ list_display = ('library_id', 'library_name', 'made_for', 'creation_date', 'ten_nM_dilution', 'stopping_point', 'successful_pM')
+ list_display_links = ('library_id', 'library_name')
+ list_filter = ('stopping_point', 'ten_nM_dilution', 'library_species', 'made_for', 'made_by')
+ fields = (
+ (None, {
+ 'fields': (('library_id', 'library_name'), ('library_species', 'RNAseq'),)
+ }),
+ ('Creation Information:', {
+ 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'ten_nM_dilution', 'successful_pM'), 'notes',)
+ }),
+ )
+
+class FlowCell(models.Model):
- run_date = models.DateTimeField()
+ flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
+ run_date = models.DateTimeField(core=True)
- lane1_sample = models.CharField(maxlength=500)
- lane1_species = models.ForeignKey(Specie, related_name="lane1_species")
- lane2_sample = models.CharField(maxlength=500)
- lane2_species = models.ForeignKey(Specie, related_name="lane2_species")
- lane3_sample = models.CharField(maxlength=500)
- lane3_species = models.ForeignKey(Specie, related_name="lane3_species")
- lane4_sample = models.CharField(maxlength=500)
- lane4_species = models.ForeignKey(Specie, related_name="lane4_species")
+ lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
+ lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
+ lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
+ lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
+ lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
+ lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
+ lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
+ lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
+
+ lane_1_pM = models.IntegerField(default=4)
+ lane_2_pM = models.IntegerField(default=4)
+ lane_3_pM = models.IntegerField(default=4)
+ lane_4_pM = models.IntegerField(default=4)
+ lane_5_pM = models.IntegerField(default=4)
+ lane_6_pM = models.IntegerField(default=4)
+ lane_7_pM = models.IntegerField(default=4)
+ lane_8_pM = models.IntegerField(default=4)
- lane5_sample = models.CharField(maxlength=500)
- lane5_species = models.ForeignKey(Specie, related_name="lane5_species")
- lane6_sample = models.CharField(maxlength=500)
- lane6_species = models.ForeignKey(Specie, related_name="lane6_species")
- lane7_sample = models.CharField(maxlength=500)
- lane7_species = models.ForeignKey(Specie, related_name="lane7_species")
- lane8_sample = models.CharField(maxlength=500)
- lane8_species = models.ForeignKey(Specie, related_name="lane8_species")
+ lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
notes = models.TextField(blank=True)
def __str__(self):
- return self.flowcell_id
-
+ return '%s (%s)' % (self.flowcell_id, self.run_date)
+
+ class Meta:
+ ordering = ["run_date"]
+
+ class Admin:
+ date_hierarchy = "run_date"
+ save_on_top = True
+ search_fields = ['lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library']
+ list_display = ('flowcell_id', 'run_date', 'lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library')
+ fields = (
+ (None, {
+ 'fields': ('run_date', 'flowcell_id',)
+ }),
+ ('Lanes:', {
+ 'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
+ }),
+ (None, {
+ 'fields' : ('notes',)
+ }),
+ )
class ElandResult(models.Model):
projects / htsworkflow.git / blobdiff