def validate_species(jsondata, method):
missing = expect(jsondata, ["name", "aliases"])
if len(missing):
return {"missing values": [f"Missing values: {missing}"]}
errors = {}
aliases = [s.strip() for s in jsondata["aliases"].split(",")]
if method == "PUT":
for name in [jsondata["name"]] + aliases:
try:
Species.objects.get({"$or": [{"name": name}, {"alias": name}]})
except DoesNotExist:
pass
else:
errors["name"] = [
f"Name/alias {name} already exists in the database as name or alias"
]
elif method == "POST":
s_name = jsondata["name"]
try:
found_species = Species.objects.get({"name": s_name})
except DoesNotExist:
errors["not_found"] = [f"Species {s_name} not found"]
for name in [s_name] + aliases:
try:
Species.objects.get({
"$and": [{
"$or": [{
"name": name
}, {
"alias": name
}]
}, {
"name": {
"$ne": s_name
}
}]
})
except DoesNotExist:
pass
else:
errors["name"] = [
f"Name/alias {name} already exists in the database as name or alias"
]
for key, value in jsondata.items():
if key not in ["name", "aliases", "editRow"]:
if len(key.split(".")) != 4:
errors[f"invalid_field_{key}"] = [
f"Field {key} was unexpected. Contact Admin."
]
if len(value) == 0:
errors[f"empty_value_{key}"] = [
f"Field {key} contains an empty value {value}"
]
return errors
def validate_step_start(step_name, json_data):
# It should also validate if all the samples are ready to start it.
errors = {}
missing = expect(json_data, ["sample_barcodes", "workflow_batch"])
if len(missing):
errors["missing_parameters"] = "Missing parameters {}".format(",".join(missing))
return errors
# Check missing step
step = None
try:
step = m_step.Step.objects.get({"name":step_name})
except pymodm.errors.DoesNotExist:
errors["step_name"] = "Step doesn't exist"
# Check missing samples
samples = []
if len(json_data.get("sample_barcodes",[])) == 0:
errors["sample_barcodes"] = "No samples provided"
else:
missing_samples = []
for s_b in json_data["sample_barcodes"]:
sample = None
try:
sample_o = m_sample.Sample.objects.get({"barcode": s_b})
samples.append(sample_o)
except pymodm.errors.DoesNotExist:
missing_samples.append(s_b)
if len(missing_samples) > 0:
e_b = "Missing samples: {}".format(",".join(missing_samples))
errors["sample_barcodes"] = e_b
# Check if there are samples that have started this step already
# (and haven't finished)
started_is = step.get_started()
potential_samples = set(json_data["sample_barcodes"])
for started_i in started_is:
started_samples = set([s.barcode for s in started_i.samples])
intersection = potential_samples.intersection(started_samples)
if len(intersection) > 0:
errors["already_running"] = "Samples {} are already running this step. Go to that currently running step or cancel it.".format(", ".join(intersection))
# Check if step is correct.
workflow_name, batch_name = json_data["workflow_batch"].split(": ")
if step is not None:
next_step = step.category
invalid_step = []
for sample in samples:
if not sample.valid_next_step(next_step, batch_name):
invalid_step.append(sample.barcode)
if len(invalid_step) > 0:
e_b = "Invalid next step for samples: {}".format(",".join(invalid_step))
errors["invalid_step"] = e_b
return errors
def validate_species_delete(jsondata):
missing = expect(jsondata, ["name"])
if len(missing):
return {"missing values": [f"Missing values: {missing}"]}
s_name = jsondata["name"]
try:
found_species = Species.objects.get({"name": s_name})
except DoesNotExist:
return {"not_found": [f"Species {s_name} not found"]}
return {}
def validate_and_add(jsonbody):
errors = {}
missing = expect(jsonbody, ["value"])
if missing:
errors["missing_property"] = f"Missing properties: {missing}"
if len(errors):
return errors
#Cleaning other fields
tag_data = {k: v for k, v in jsonbody.items() if k in ["value", "style", "description"]}
Tag(**tag_data).save()
return errors
def validate_results_report(jsondata):
errors = {}
missing = expect(jsondata, ["sample_barcodes", "workflow_batch"])
if len(missing):
errors["missing_parameters"] = "Missing parameters {}".format(",".join(missing))
return errors
missing_barcodes = []
for s_b in jsondata["sample_barcodes"]:
try:
sample = m_sample.Sample.objects.get({"barcode": s_b})
except pymodm.errors.DoesNotExist:
missing_barcodes.append(s_b)
if len(missing_barcodes):
errors["sample_barcodes"] = "Missing samples: ({})".format(", ".join(missing_barcodes))
if not ": " in jsondata["workflow_batch"]:
errors["workflow_batch"] = "Invalid workflow_batch"
return errors
def validate_and_remove_from_sample(tagvalue, jsonbody):
errors = {}
missing = expect(jsonbody, ["sample_barcodes"])
if missing:
errors["missing_property"] = f"Missing properties: {missing}"
try:
tag = Tag.objects.get({"_id": tagvalue})
except pymodm.errors.DoesNotExist:
errors["tag_not_found"] = [f"Tag {tagvalue} not found."]
samples = list(Sample.objects.raw({"barcode": {"$in": jsonbody["sample_barcodes"]}}))
if len(samples) == 0:
errors["no_valid_samples"] = ["No valid samples found with the provided barcodes."]
if len(errors):
return errors
for sample in samples:
sample.unassign_tag(tag)
return errors
def validate_assign(jsonbody):
"""
Expects dictionary with fields
workflow, sample_barcodes, batch_name
"""
errors = expect(jsonbody, ["plate_type", "workflow", "sample_barcodes", "batch_name"])
if len(errors):
return {"missing argument": errors}
errors = {}
try:
workflow_name = jsonbody["workflow"]
workflow = m_workflow.Workflow.objects.get({"name": workflow_name})
except pymodm.errors.DoesNotExist:
errors["workflow"] = "Workflow doesn't exist"
return errors
allowed_as_first_step = False
if "step_name" in jsonbody:
workflow_step_names = [s["name"] for s in workflow.steps_denormalized]
try:
i = workflow_step_names.index(jsonbody["step_name"])
if i == 0:
prev_step = "root"
else:
prev_step = workflow.steps[i - 1].category
if workflow.steps[i].requirements.get("allow_as_first_step", False):
allowed_as_first_step = True
except ValueError:
errors["step_name"] = "Invalid step {} for workflow {}".format(jsonbody["step_name"], jsonbody["workflow"])
if len(jsonbody["sample_barcodes"]) == 0:
errors["sample_barcodes"] = "No samples provided"
else:
wrong_samples = []
already_assigned = []
errors_step = []
for s_b in jsonbody["sample_barcodes"]:
if s_b != "None":
try:
sample = m_sample.Sample.objects.get({"barcode": s_b})
except pymodm.errors.DoesNotExist:
wrong_samples.append(s_b)
continue
for batch in sample.get_batches(workflow_name):
if not(jsonbody.get("reorganizing", False) or batch.archived):
already_assigned.append(s_b)
if "step_name" in jsonbody:
if (prev_step != "root" and
prev_step not in sample.workflows.get(jsonbody["workflow"], []) and
not allowed_as_first_step):
errors_step.append(s_b)
if len(wrong_samples) > 0:
e_b = "Missing samples: {}".format(",".join(wrong_samples))
errors["sample_barcodes"] = e_b
if len(already_assigned) > 0:
errors["already_assigned"] = "Some samples were already assigned to workflow. ({})".format(",".join(already_assigned))
if len(errors_step) > 0:
errors["step"] = "Invalid step for some samples. ({})".format(",".join(errors_step))
if not m_sample.Sample.validate_field("batch_name", jsonbody["batch_name"]):
errors["batch_name"] = "Invalid batch name. Name should only have letters, dash (-) or underscore(_)"
if len(jsonbody["sample_barcodes"]) > m_sample.Sample.plate_size(jsonbody["plate_type"]):
errors["sample_barcodes_amount"] = "Too many samples for plate size."
return errors