diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json
index e569e009..c6d6c221 100644
--- a/conf/first_install_tables.json
+++ b/conf/first_install_tables.json
@@ -20298,7 +20298,7 @@
"pk": 3,
"fields": {
"label": "sample_name",
- "ontology": "GENEPIO:0001123"
+ "ontology": "NCIT:C70663"
}
},
{ "model": "core.ontologymap",
diff --git a/core/admin.py b/core/admin.py
index e78a4dfb..76788e82 100644
--- a/core/admin.py
+++ b/core/admin.py
@@ -77,7 +77,7 @@ class MoleculePreparationAdmin(admin.ModelAdmin):
"extraction_type",
"protocol_used",
"molecule_extraction_date",
- "molecule_used_for",
+ "sample_continues_on",
"reused_number",
)
list_filter = ("generated_at",)
diff --git a/core/core_config.py b/core/core_config.py
index f7990350..b0b605f7 100644
--- a/core/core_config.py
+++ b/core/core_config.py
@@ -32,7 +32,7 @@
# ## Heading values when showing pending samples at handling molecules
HEADING_FOR_DEFINED_SAMPLES = [
- "Sample extraction date",
+ "Sample defined date",
"Sample Code ID",
"Sample",
"To be included",
@@ -75,7 +75,7 @@
HEADING_FOR_SELECTING_MOLECULE_USE = [
"Sample Name",
"Extraction Code ID",
- "Sample continue on",
+ "Sample continues on",
]
# ################ PROTOCOL PARAMETER SETTINGS ##############################
diff --git a/core/models.py b/core/models.py
index 3e6da274..fce123e9 100644
--- a/core/models.py
+++ b/core/models.py
@@ -1493,7 +1493,7 @@ class MoleculeUsedFor(models.Model):
massive_use = models.BooleanField(default=False)
class Meta:
- db_table = "core_molecule_used_for"
+ db_table = "core_sample_continues_on"
def __str__(self):
return "%s" % (self.used_for)
@@ -1557,7 +1557,7 @@ class MoleculePreparation(models.Model):
UserLotCommercialKits, on_delete=models.CASCADE, null=True, blank=True
)
- molecule_used_for = models.ForeignKey(
+ sample_continues_on = models.ForeignKey(
MoleculeUsedFor, on_delete=models.CASCADE, null=True, blank=True
)
@@ -1582,10 +1582,10 @@ def get_info_for_display(self):
molecule_info.append(extraction_date)
molecule_info.append(self.extraction_type)
molecule_info.append(self.molecule_type.get_name())
- if self.molecule_used_for is None:
+ if self.sample_continues_on is None:
molecule_info.append("Not defined yet")
else:
- molecule_info.append(self.molecule_used_for.get_molecule_use_name())
+ molecule_info.append(self.sample_continues_on.get_molecule_use_name())
molecule_info.append(self.protocol_used.get_name())
molecule_info.append(self.reused_number)
return molecule_info
@@ -1629,10 +1629,10 @@ def get_user_lot_kit_obj(self):
return self.user_lot_kit_id
def set_molecule_use(self, use_for_molecule, app_name):
- self.molecule_used_for_obj = MoleculeUsedFor.objects.filter(
+ self.sample_continues_on_obj = MoleculeUsedFor.objects.filter(
used_for__exact=use_for_molecule, apps_name__exact=app_name
).last()
- self.used_for_massive_sequencing = self.molecule_used_for_obj.get_massive()
+ self.used_for_massive_sequencing = self.sample_continues_on_obj.get_massive()
self.save()
return self
diff --git a/core/utils/samples.py b/core/utils/samples.py
index 0e990cea..193d784e 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -706,7 +706,7 @@ def create_table_molecule_pending_use(sample_list, app_name):
use_type = {}
use_type["data"] = list(
core.models.MoleculePreparation.objects.filter(
- molecule_used_for=None,
+ sample_continues_on=None,
sample__in=sample_list,
state__molecule_state_name="assigned_parameters",
).values_list("sample__sample_name", "molecule_code_id", "pk")
@@ -1532,9 +1532,10 @@ def get_selection_from_excel_data(data, heading, check_field, field_id):
excel_data = json.loads(data)
# Convert excel list-list to dictionary with field_names
excel_json_data = core.utils.common.jspreadsheet_to_dict(heading, excel_data)
+
for row in excel_json_data:
if check_field is not None:
- if row[check_field] is True:
+ if row[check_field] is not False and row[check_field] != "":
selected.append(row[field_id])
selected_row.append(row)
else:
@@ -2085,7 +2086,7 @@ def set_molecule_use(molecule_use_data, app_name):
}
for molecule in molecule_use_data:
molecule_obj = get_molecule_obj_from_id(molecule["m_id"])
- molecule_obj.set_molecule_use(molecule["Molecule use for"], app_name)
+ molecule_obj.set_molecule_use(molecule["Sample continues on"], app_name)
sample_obj = molecule_obj.get_sample_obj()
if molecule_obj.get_used_for_massive():
sample_obj.set_state("Library preparation")
@@ -2095,7 +2096,7 @@ def set_molecule_use(molecule_use_data, app_name):
[
molecule["Sample Name"],
molecule["Extraction Code ID"],
- molecule["Molecule use for"],
+ molecule["Sample continues on"],
]
)
return molecule_update
diff --git a/test/test_data.json b/test/test_data.json
index 116817e1..f81d46aa 100644
--- a/test/test_data.json
+++ b/test/test_data.json
@@ -5224,7 +5224,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0575_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5243,7 +5243,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0586_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5262,7 +5262,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0585_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5281,7 +5281,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0584_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5300,7 +5300,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0583_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5319,7 +5319,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0582_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5338,7 +5338,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0581_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5357,7 +5357,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0580_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5376,7 +5376,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0579_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5395,7 +5395,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0578_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5414,7 +5414,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0577_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5433,7 +5433,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0576_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5452,7 +5452,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0587_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5471,7 +5471,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0574_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5490,7 +5490,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0573_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5509,7 +5509,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0572_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5528,7 +5528,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0554_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5547,7 +5547,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0553_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5566,7 +5566,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0552_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5585,7 +5585,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0551_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5604,7 +5604,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0550_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5623,7 +5623,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0548_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5642,7 +5642,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0547_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5661,7 +5661,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0599_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5680,7 +5680,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Entb0091_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5699,7 +5699,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Ent0085_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5718,7 +5718,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0004_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5737,7 +5737,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0008_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5756,7 +5756,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0007_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5775,7 +5775,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0006_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5794,7 +5794,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0005_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5813,7 +5813,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Sm0003_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5832,7 +5832,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0601_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5851,7 +5851,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0600_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5870,7 +5870,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0546_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5889,7 +5889,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0598_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5908,7 +5908,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0597_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5927,7 +5927,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0595_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5946,7 +5946,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0594_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5965,7 +5965,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0593_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -5984,7 +5984,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0592_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6003,7 +6003,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0591_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6022,7 +6022,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0590_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6041,7 +6041,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0589_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6060,7 +6060,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0588_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6079,7 +6079,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0189_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6098,7 +6098,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0523_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6117,7 +6117,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Entb0090_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6136,7 +6136,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Entb0089_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6155,7 +6155,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Entb0088_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6174,7 +6174,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Entb0011_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6193,7 +6193,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0196_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6212,7 +6212,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0195_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6231,7 +6231,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0194_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6250,7 +6250,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0193_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6269,7 +6269,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0192_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6288,7 +6288,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0524_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6307,7 +6307,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0188_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6326,7 +6326,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0187_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6345,7 +6345,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0186_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6364,7 +6364,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0185_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6383,7 +6383,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0184_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6402,7 +6402,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0178_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6421,7 +6421,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0177_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6440,7 +6440,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0176_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6459,7 +6459,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0175_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6478,7 +6478,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23Eco0173_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6497,7 +6497,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0535_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6516,7 +6516,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0545_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6535,7 +6535,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0544_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6554,7 +6554,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0543_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6573,7 +6573,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0542_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6592,7 +6592,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0541_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6611,7 +6611,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0540_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6630,7 +6630,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0539_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6649,7 +6649,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0538_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6668,7 +6668,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0537_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6687,7 +6687,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0536_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6706,7 +6706,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_22K0483_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6725,7 +6725,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0534_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6744,7 +6744,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0533_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6763,7 +6763,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0532_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6782,7 +6782,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0531_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6801,7 +6801,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0530_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6820,7 +6820,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0529_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6839,7 +6839,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0528_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6858,7 +6858,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0527_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6877,7 +6877,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0526_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
@@ -6896,7 +6896,7 @@
"state": 5,
"molecule_user": 1,
"user_lot_kit_id": 1,
- "molecule_used_for": 9,
+ "sample_continues_on": 9,
"molecule_code_id": "admin_23K0525_E1",
"extraction_type": "Manual",
"molecule_extraction_date": "2023-07-26T00:00:00",
diff --git a/wetlab/templates/wetlab/create_pool.html b/wetlab/templates/wetlab/create_pool.html
index 43083768..3925777d 100644
--- a/wetlab/templates/wetlab/create_pool.html
+++ b/wetlab/templates/wetlab/create_pool.html
@@ -109,7 +109,7 @@ Samples included in pool
- {% for s_name, s_index in display_list.incompatible_index %}
+ {% for s_name, s_index in display_list.duplicated_index.incompatible_index %}
| {{s_name}} |
{{s_index}} |
diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html
index 9af67a77..08fe8e28 100644
--- a/wetlab/templates/wetlab/handling_molecules.html
+++ b/wetlab/templates/wetlab/handling_molecules.html
@@ -503,7 +503,7 @@ Not molecule uses have been defined yet
var table_data3 = table3.getData()
var data_json = JSON.stringify(table_data3)
$("").attr("type", "hidden")
- .attr("name", "molecule_used_for")
+ .attr("name", "sample_continues_on")
.attr("value", data_json)
.appendTo("#requestMoleculeUse");
$("#btnSubmit").attr("disabled", true);
diff --git a/wetlab/utils/pool.py b/wetlab/utils/pool.py
index 9b49e7c6..cef608d4 100644
--- a/wetlab/utils/pool.py
+++ b/wetlab/utils/pool.py
@@ -39,10 +39,13 @@ def check_if_duplicated_index(lib_prep_ids):
Input:
lib_prep_ids # library preparation id list
Return:
- True if unique indexes are used.
- a dictionary with 'incompatible_index' as key and the list of samples names as value.
+ True if unique indexes are used and empty incompatible_samples
+ False and a dictionary with 'incompatible_index' as key and the list of samples names as value.
"""
index_values = {}
+ incompatible_samples = {}
+ incompatible_index = []
+
for lib_prep_id in lib_prep_ids:
lib_prep_obj = wetlab.models.LibPrepare.objects.get(pk__exact=lib_prep_id)
# lib_prep_count += 1
@@ -58,23 +61,18 @@ def check_if_duplicated_index(lib_prep_ids):
index_values[combined_index] = []
index_values[combined_index].append(lib_prep_id)
if len(index_values) == len(lib_prep_ids):
- return "True"
+ return True, incompatible_samples
else:
- incompatible_samples = {}
- incompatible_index = []
# check which index
for key, values in index_values.items():
if len(values) > 1:
- s_name = []
for value in values:
- s_name.append(
- wetlab.models.LibPrepare.objects.get(
- pk__exact=value
- ).get_sample_name()
- )
- incompatible_index.append([" and ".join(s_name), key])
+ s_name = wetlab.models.LibPrepare.objects.get(
+ pk__exact=value
+ ).get_sample_name()
+ incompatible_index.append([s_name, key])
incompatible_samples["incompatible_index"] = incompatible_index
- return incompatible_samples
+ return False, incompatible_samples
def get_single_paired(lib_prep_ids):
@@ -132,14 +130,14 @@ def define_new_pool(form_data, user_obj):
heading_with_hidden, excel_json_data
)
for row in c_data:
- if row["Include in Pool"] == "True":
+ if row["Include in Pool"] is True:
lib_prep_ids.append(row["lib_prep_id"])
if len(lib_prep_ids) == 0:
error["ERROR"] = wetlab.config.ERROR_NOT_LIBRARY_PREPARATION_SELECTED
return error
- duplicated_index = check_if_duplicated_index(lib_prep_ids)
- if "incompatible_index" in duplicated_index:
+ valid, duplicated_index = check_if_duplicated_index(lib_prep_ids)
+ if not valid:
error["duplicated_index"] = duplicated_index
return error
# check that all library preparation use the same adapter
diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py
index a7b04e1b..3af12cc5 100644
--- a/wetlab/utils/samplesheet.py
+++ b/wetlab/utils/samplesheet.py
@@ -275,7 +275,7 @@ def get_sample_sheet_data(file_read):
file_lines = file_read.split("\n")
for line in file_lines:
- if "IEMFileVersion" in line:
+ if "iemfileversion" in line.lower():
sample_sheet_data["iem_version"] = line.split(",")[1]
break
# get assay information
diff --git a/wetlab/views.py b/wetlab/views.py
index fbffdc80..d8df2004 100644
--- a/wetlab/views.py
+++ b/wetlab/views.py
@@ -2991,7 +2991,7 @@ def handling_library_preparation(request):
samples_in_lib_prep = wetlab.utils.library.get_samples_for_library_preparation(
request.user, True
)
-
+ request.session["samples_in_lib_prep"] = samples_in_lib_prep
if request.method == "POST" and request.POST["action"] == "assignProtocol":
samples_in_lib_prep_protocol = (
wetlab.utils.library.extract_protocol_library_preparation_form(request.POST)
@@ -3090,7 +3090,7 @@ def handling_library_preparation(request):
"wetlab/handling_library_preparation.html",
{
"error_message": data["ERROR"],
- "samples_in_lib_prep": samples_in_lib_prep,
+ "samples_in_lib_prep": request.session.get("samples_in_lib_prep"),
},
)
user_in_description = wetlab.utils.common.get_configuration_value(
@@ -3112,7 +3112,9 @@ def handling_library_preparation(request):
"wetlab/handling_library_preparation.html",
{
"error_message": user_id_in_s_sheet["ERROR"],
- "samples_in_lib_prep": samples_in_lib_prep,
+ "samples_in_lib_prep": request.session.get(
+ "samples_in_lib_prep"
+ ),
},
)
else:
@@ -3130,7 +3132,7 @@ def handling_library_preparation(request):
"wetlab/handling_library_preparation.html",
{
"error_message": valid_data["ERROR"],
- "samples_in_lib_prep": samples_in_lib_prep,
+ "samples_in_lib_prep": request.session.get("samples_in_lib_prep"),
},
)
@@ -3172,8 +3174,8 @@ def handling_library_preparation(request):
request,
"wetlab/handling_library_preparation.html",
{
- "error_message": valid_data["ERROR"],
- "samples_in_lib_prep": samples_in_lib_prep,
+ "error_message": store_data_result["ERROR"],
+ "samples_in_lib_prep": request.session.get("samples_in_lib_prep"),
},
)
stored_index = "True"
@@ -3347,7 +3349,7 @@ def handling_molecules(request):
heading = core.core_config.HEADING_FOR_SELECTING_MOLECULE_USE.copy()
heading.insert(-1, "m_id")
molecules, select_use = core.utils.samples.get_selection_from_excel_data(
- request.POST["molecule_used_for"], heading, "Molecule use for", "m_id"
+ request.POST["sample_continues_on"], heading, "Sample continues on", "m_id"
)
if len(molecules) == 0:
return redirect("handling_molecules")