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Added only recorded in optional type of samples and save opt values a…
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…s names
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@luissian
luissian committed Jul 28, 2023
1 parent d8390e7 commit 35d1ee6
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Showing 7 changed files with 69 additions and 59 deletions.
5 changes: 5 additions & 0 deletions conf/0002_core_migration_v2.3.1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -767,6 +767,11 @@ class Migration(migrations.Migration):
verbose_name="Species",
),
),
migrations.AlterField(
model_name="sampletype",
name="optional_fields",
field=models.CharField(blank=True, max_length=300, null=True),
),
migrations.AlterModelTable(
name="commercialkits",
table="core_commercial_kits",
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5 changes: 3 additions & 2 deletions core/core_config.py
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Expand Up @@ -20,6 +20,7 @@
"Date sample reception",
"Collection Sample Date",
"Sample Storage Location",
"Only recorded",
]

HEADING_FOR_DISPLAY_RECORDED_SAMPLES = [
Expand Down Expand Up @@ -288,9 +289,9 @@
SUCCESSFUL_JSON_SCHEMA = ["Json schema was loaded successfully"]
# #################### ERROR MESSAGES #####################
ERROR_TYPE_OF_SAMPLE_EXISTS = ["Type of sample is already recorded"]
ERROR_TYPE_OF_SAMPLE_ID_DOES_NOT_EXISTS = [
ERROR_TYPE_OF_SAMPLE_ID_DOES_NOT_EXISTS = (
"The type of sample that you request does not exist"
]
)
ERROR_MOLECULE_USE_FOR_EXISTS = ["Molecule use has been already recorded"]

ERROR_SPECIES_ALREADY_DEFINED = ["Species name is already defined"]
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4 changes: 2 additions & 2 deletions core/models.py
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Expand Up @@ -396,7 +396,7 @@ def create_sample_type(self, sample_type_data):
class SampleType(models.Model):
sample_type = models.CharField(max_length=50)
apps_name = models.CharField(max_length=50)
optional_fields = models.CharField(max_length=50, null=True, blank=True)
optional_fields = models.CharField(max_length=300, null=True, blank=True)
generated_at = models.DateTimeField(auto_now_add=True, null=True)

class Meta:
Expand All @@ -415,7 +415,7 @@ def get_optional_values(self):
if self.optional_fields == "" or self.optional_fields is None:
return []
else:
return list(map(int, self.optional_fields.split(",")))
return self.optional_fields.split(",")

objects = SampleTypeManager()

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30 changes: 10 additions & 20 deletions core/utils/samples.py
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Expand Up @@ -1469,15 +1469,11 @@ def get_type_of_sample_information(sample_type_id):
sample_type_obj = core.models.SampleType.objects.get(pk__exact=sample_type_id)
opt_list = sample_type_obj.get_optional_values()
sample_type_data["sample_type_name"] = sample_type_obj.get_name()
for i in range(len(core.core_config.HEADING_FOR_RECORD_SAMPLES)):
if i in opt_list:
sample_type_data["optional_data"].append(
[core.core_config.HEADING_FOR_RECORD_SAMPLES[i], "Not Required"]
)
for field in core.core_config.HEADING_FOR_RECORD_SAMPLES:
if field in opt_list:
sample_type_data["optional_data"].append([field, "Not Required"])
else:
sample_type_data["optional_data"].append(
[core.core_config.HEADING_FOR_RECORD_SAMPLES[i], "Mandatory"]
)
sample_type_data["optional_data"].append([field, "Mandatory"])
else:
sample_type_data[
"ERROR"
Expand Down Expand Up @@ -1909,27 +1905,21 @@ def save_type_of_sample(form_data, app_name):
save_s_type
"""
save_s_type = {}
optional_index_field_list = []
optional_fields = []
if core.models.SampleType.objects.filter(
sample_type__exact=form_data["sampleTypeName"], apps_name__exact=app_name
).exists():
save_s_type["ERROR"] = core.core_config.ERROR_TYPE_OF_SAMPLE_EXISTS
return save_s_type
# select the optional fields and get the indexes
for field in core.core_config.HEADING_FOR_RECORD_SAMPLES:
if (
field not in form_data
and field in core.core_config.HEADING_FOR_OPTIONAL_FIELD_SAMPLES
):
optional_index_field_list.append(
str(core.core_config.HEADING_FOR_RECORD_SAMPLES.index(field))
)
# add only recorded as always optional
optional_index_field_list.append("9")
for field in core.core_config.HEADING_FOR_OPTIONAL_FIELD_SAMPLES:
if field not in form_data:
optional_fields.append(field)

data = {}
data["sampleType"] = form_data["sampleTypeName"]
data["apps_name"] = app_name
data["optional_fields"] = ",".join(optional_index_field_list)
data["optional_fields"] = ",".join(optional_fields)
# Store in database
sample_type_obj = core.models.SampleType.objects.create_sample_type(data)
save_s_type = {}
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2 changes: 1 addition & 1 deletion wetlab/templates/wetlab/define_type_of_samples.html
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Expand Up @@ -59,7 +59,7 @@
</div>
{% endfor %}
</div>
<p class="mt-2"> Fields marked with <FONT COLOR="Red">*</FONT> are mandatory</p>
<p class="mt-2"> Fields marked in <FONT COLOR="Red">Red</FONT> are mandatory</p>
<input class="btn float-end btn-outline-primary mb-2 me-2" type="submit" value="Submit" id="btnSubmit">
</form>
</div>
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76 changes: 42 additions & 34 deletions wetlab/templates/wetlab/display_type_of_sample.html
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Expand Up @@ -4,41 +4,49 @@
{% include "wetlab/menu.html" %}
{% include 'registration/login_inline.html' %}
<section class="iskylims">
{% if sample_types.error_message %}
<div class="row my-2">
<div class="col-sm-6 offset-2" >
<div class="card border-danger mb-3">
<div class="card-header text-danger"><h3>Unable to display your Sample Type</h3> </div>
<div class="card-body">
<p>
{% for value in sample_types.ERROR %}
{{ value }} <br>
{% endfor %}
</p>
</div>
<div class="container-md">
{% if error_message %}
<div class="row my-2">
<div class="col-sm-6 offset-2" >
<div class="card border-danger mb-3">
<div class="card-header text-danger"><h3>Unable to display your Sample Type</h3> </div>
<div class="card-body">
<p> {{ error_message }}</p>
</div>
</div>
</div>
</div>
{% else %}
<div class="row my-2 justify-content-center">
<div class="col-md-6">
<div class="card ">
<div class="card-header text-center"><h3>Type of Sample : {{type_of_sample_data.sample_type_name}}</h3> </div>
<div class="card-body">
<p>Information below describes which fields are set to mandatory when recording samples</p>
<div class="row mt-3">
<div class="col-md-6">
<h5 class="text-center">Field name</h5>
</div>
<div class="col-md-6">
<h5 class="float-end">Mandatory</h5>
</div>
</div>

{% for field, requested in type_of_sample_data.optional_data %}
<div class="form-check form-switch col mb-2">
<label class="form-check-label form-label" for="{{field}}">{{field}}</label>
{% if requested == 'Mandatory' %}
<input class="form-check-input float-end" type="checkbox" checked disabled>
{% else %}
<input class="form-check-input float-end" type="checkbox" disabled>
{% endif %}
</div>
{% endfor %}
</div>
</div>
</div>
</div>
</div>
{% endif %}
<div class="row my-2">
<div class="col-sm-4 offset-4" >
<div class="card ">
<div class="card-header"><h3 style="text-align:center">Type of Sample : {{type_of_sample_data.sample_type_name}}</h3> </div>
<div class="card-body">
<p>Information below describes which fields are mandatory or optional when recording new sample</p>
{% for field, requested in type_of_sample_data.optional_data %}
<div class="form-check form-switch col mb-2">
<label class="form-check-label form-label" for="{{field}}">{{field}}</label>
{% if requested == 'Mandatory' %}
<input class="form-check-input float-end" type="checkbox" checked disabled>
{% else %}
<input class="form-check-input float-end" type="checkbox" disabled>
{% endif %}
</div>
{% endfor %}
</div>
</div>
</div>
</div>
{% endif %}
</div>
</section>
{% endblock %}
6 changes: 6 additions & 0 deletions wetlab/views.py
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Expand Up @@ -2644,6 +2644,12 @@ def display_type_of_sample(request, sample_type_id):
type_of_sample_data = core.utils.samples.get_type_of_sample_information(
sample_type_id
)
if "ERROR" in type_of_sample_data:
return render(
request,
"wetlab/display_type_of_sample.html",
{"error_message": type_of_sample_data["ERROR"]},
)
return render(
request,
"wetlab/display_type_of_sample.html",
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