add 1.7

grandapp/management/commands/load_cancer_data.py

@@ -40,8 +40,10 @@ def handle(self, *args, **options):
             cancer.nnets     = row['nnets']
             cancer.datasets  = row['datasets']
             cancer.nnets2    = row['nnets2']
+            cancer.nnets3    = row['nnets3']
             cancer.nnetsref  = row['nnetsref']
             cancer.nnets2ref = row['nnets2ref']
+            cancer.nnets3ref = row['nnets3ref']
             cancer.cancerref = row['cancerref']
             cancer.datasets2     = row['datasets2']
             cancer.datasetsref   = row['datasetsref']

grandapp/management/commands/load_cancerbreast_data.py

@@ -32,7 +32,7 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         print("Loading cancer breast sample data!")
-        for row in DictReader(open('./static/data/metadata_breast_01292021.csv')):
+        for row in DictReader(open('./static/data/metadata_breast_01292021_bis.csv')):
             breastsample = Breastsample()
             breastsample.sample = row['gdc_cases.samples.portions.analytes.aliquots.submitter_id']
             breastsample.gender = row['gdc_cases.demographic.gender']
@@ -46,4 +46,8 @@ def handle(self, *args, **options):
             breastsample.uicc_stage = row['gdc_cases.diagnoses.tumor_stage']
             breastsample.time_to_event = row['gdc_cases.diagnoses.days_to_death']
             breastsample.vital_status = row['gdc_cases.diagnoses.vital_status']
+            breastsample.link     = row['link']
+            breastsample.size     = row['size']
+            breastsample.ss       = row['ss']
+            breastsample.submitter_id_clean = row['submitter_id_clean']
             breastsample.save()

grandapp/management/commands/load_cancerliver_data.py

@@ -32,7 +32,7 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         print("Loading cancer liver sample data!")
-        for row in DictReader(open('./static/data/metadata_liver_01232021.csv')):
+        for row in DictReader(open('./static/data/metadata_liver_01232021_bis.csv')):
             breastsample = Liversample()
             breastsample.sample = row['gdc_cases.samples.portions.analytes.aliquots.submitter_id']
             breastsample.gender = row['gdc_cases.demographic.gender']
@@ -46,4 +46,8 @@ def handle(self, *args, **options):
             breastsample.uicc_stage = row['gdc_cases.diagnoses.tumor_stage']
             breastsample.time_to_event = row['gdc_cases.diagnoses.days_to_death']
             breastsample.vital_status = row['gdc_cases.diagnoses.vital_status']
+            breastsample.link     = row['link']
+            breastsample.size     = row['size']
+            breastsample.ss       = row['ss']
+            breastsample.submitter_id_clean = row['submitter_id_clean']
             breastsample.save()

grandapp/management/commands/load_cancerpancreas_data.py

@@ -32,7 +32,7 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         print("Loading pancreas tcga sample data!")
-        for row in DictReader(open('./static/data/pancreas_tcga.csv')):
+        for row in DictReader(open('./static/data/pancreas_tcga_bis.csv')):
             pancreassample = Pancreassample()
             pancreassample.sample     = row['gdc_cases.samples.portions.analytes.aliquots.submitter_id']
             pancreassample.gender     = row['gdc_cases.demographic.gender']
@@ -44,7 +44,11 @@ def handle(self, *args, **options):
             pancreassample.time_to_event= row['gdc_cases.diagnoses.days_to_death'] 
             pancreassample.size    = row['size']
             pancreassample.link    = row['link']
+            pancreassample.size2    = row['size2']
+            pancreassample.link2    = row['link2']
             pancreassample.ethnicity = row['gdc_cases.demographic.ethnicity']
             pancreassample.vital_status = row['gdc_cases.diagnoses.vital_status']
             pancreassample.subtype = row['subtype']
+            pancreassample.ss      = row['ss']
+            pancreassample.submitter_id_clean = row['submitter_id_clean']
             pancreassample.save()

grandapp/management/commands/load_cancerpheno_data.py

@@ -32,7 +32,7 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         print("Loading cancer geo sample data!")
-        for row in DictReader(open('./data/cancerpheno.csv')):
+        for row in DictReader(open('./data/cancerpheno_extended.csv')):
             geosample = Cancerpheno()
             geosample.sample               = row['sample']
             geosample.gender               = row['gender']
@@ -42,4 +42,8 @@ def handle(self, *args, **options):
             geosample.age                  = row['age_at_initial_pathologic_diagnosis']
             geosample.days_to_last_followup= row['days_to_last_followup']
             geosample.tumorID              = row['tumorID']
+            geosample.link              = row['link']
+            geosample.size              = row['size']
+            geosample.ss                = row['ss']
+            geosample.submitter_id_clean= row['submitter_id_clean']
             geosample.save()

grandapp/management/commands/load_cancertcga_data.py

@@ -32,7 +32,7 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         print("Loading cancer sample data!")
-        for row in DictReader(open('./static/data/clinical_tcga.csv')):
+        for row in DictReader(open('./static/data/clinical_tcga_bis.csv')):
             tcgasample = Tcgasample()
             tcgasample.sample     = row['sample']
             tcgasample.platform   = row['Platform']
@@ -45,6 +45,10 @@ def handle(self, *args, **options):
             tcgasample.uicc_stage      = row['uicc_stage']
             tcgasample.time_to_event   = row['time_to_event']
             tcgasample.vital_status    = row['vital_status'] 
-            tcgasample.size    = row['size']
-            tcgasample.link    = row['link']
+            tcgasample.size     = row['size']
+            tcgasample.link     = row['link']
+            tcgasample.size2    = row['size2']
+            tcgasample.link2    = row['link2']
+            tcgasample.ss       = row['ss']
+            tcgasample.submitter_id_clean= row['submitter_id_clean']
             tcgasample.save()

grandapp/migrations/0251_auto_20241110_0009.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.5 on 2024-11-10 00:09
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0250_tissuesamplethy_decsex'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cancer',
+            name='nnets3',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='cancer',
+            name='nnets3ref',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0252_auto_20241210_0352.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.5 on 2024-12-10 03:52
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0251_auto_20241110_0009'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cancerpheno',
+            name='link',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='cancerpheno',
+            name='size',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0253_cancerpheno_ss.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.5 on 2024-12-11 15:48
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0252_auto_20241210_0352'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cancerpheno',
+            name='ss',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0254_cancerpheno_submitter_id_clean.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.5 on 2024-12-12 04:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0253_cancerpheno_ss'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cancerpheno',
+            name='submitter_id_clean',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0255_auto_20241214_2335.py

@@ -0,0 +1,61 @@
+# Generated by Django 3.2.5 on 2024-12-14 23:35
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0254_cancerpheno_submitter_id_clean'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='breastsample',
+            name='link',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='breastsample',
+            name='size',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='breastsample',
+            name='ss',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='breastsample',
+            name='submitter_id_clean',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='liversample',
+            name='link',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='liversample',
+            name='size',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='liversample',
+            name='ss',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='liversample',
+            name='submitter_id_clean',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0256_auto_20241215_0530.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.5 on 2024-12-15 05:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0255_auto_20241214_2335'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='pancreassample',
+            name='link2',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='pancreassample',
+            name='size2',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0257_pancreassample_ss.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.5 on 2024-12-15 05:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0256_auto_20241215_0530'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='pancreassample',
+            name='ss',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0258_pancreassample_submitter_id_clean.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.5 on 2024-12-15 06:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0257_pancreassample_ss'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='pancreassample',
+            name='submitter_id_clean',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]

grandapp/migrations/0259_auto_20241215_1728.py

@@ -0,0 +1,37 @@
+# Generated by Django 3.2.5 on 2024-12-15 17:28
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('grandapp', '0258_pancreassample_submitter_id_clean'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='tcgasample',
+            name='link2',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='tcgasample',
+            name='size2',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='tcgasample',
+            name='ss',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='tcgasample',
+            name='submitter_id_clean',
+            field=models.CharField(default='', max_length=200),
+            preserve_default=False,
+        ),
+    ]