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Fix Admin UI configuration and navigation #4

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Merged
magdasmat merged 1 commit into from
Jul 27, 2026
Merged

Fix Admin UI configuration and navigation #4

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51 changes: 22 additions & 29 deletions adminui/adminbackend/forms/entry_types.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,9 +74,7 @@ def __init__(self, *args, **kwargs):
if analysis_endpoint_name != '':
entry_types.append('analysis')
endpoint_names.append(analysis_endpoint_name)
self.initial['Analysis'] = True
else:
self.initial['Analysis'] = None
self.initial['Analysis'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['AnalysisNonFiltered'] = None
else:
Expand All @@ -93,9 +91,7 @@ def __init__(self, *args, **kwargs):
if biosample_endpoint_name != '':
entry_types.append('biosample')
endpoint_names.append(biosample_endpoint_name)
self.initial['Biosample'] = True
else:
self.initial['Biosample'] = None
self.initial['Biosample'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['BiosampleNonFiltered'] = None
else:
Expand All @@ -112,9 +108,7 @@ def __init__(self, *args, **kwargs):
if cohort_endpoint_name != '':
entry_types.append('cohort')
endpoint_names.append(cohort_endpoint_name)
self.initial['Cohort'] = True
else:
self.initial['Cohort'] = None
self.initial['Cohort'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['CohortNonFiltered'] = None
else:
Expand All @@ -131,9 +125,7 @@ def __init__(self, *args, **kwargs):
if dataset_endpoint_name != '':
entry_types.append('dataset')
endpoint_names.append(dataset_endpoint_name)
self.initial['Dataset'] = True
else:
self.initial['Dataset'] = None
self.initial['Dataset'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['DatasetNonFiltered'] = None
else:
Expand All @@ -150,9 +142,7 @@ def __init__(self, *args, **kwargs):
if genomicVariant_endpoint_name != '':
entry_types.append('genomicVariant')
endpoint_names.append(genomicVariant_endpoint_name)
self.initial['GenomicVariant'] = True
else:
self.initial['GenomicVariant'] = None
self.initial['GenomicVariant'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['GenomicVariantNonFiltered'] = None
else:
Expand All @@ -169,9 +159,7 @@ def __init__(self, *args, **kwargs):
if individual_endpoint_name != '':
entry_types.append('individual')
endpoint_names.append(individual_endpoint_name)
self.initial['Individual'] = True
else:
self.initial['Individual'] = None
self.initial['Individual'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['IndividualNonFiltered'] = None
else:
Expand All @@ -188,9 +176,7 @@ def __init__(self, *args, **kwargs):
if run_endpoint_name != '':
entry_types.append('run')
endpoint_names.append(run_endpoint_name)
self.initial['Run'] = True
else:
self.initial['Run'] = None
self.initial['Run'] = conf['entry_type_enabled']
if conf['allow_queries_without_filters'] == False:
self.initial['RunNonFiltered'] = None
else:
Expand Down Expand Up @@ -281,7 +267,8 @@ def clean(self):
analysis_choices=generate_endpoints(analysis_choices, analysis_endpoint_name, analysis_endpoint_name, analysis_entry_type, analysis_lookups)
AnalysisEndpoints = forms.MultipleChoiceField(
choices=analysis_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
analysis_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -301,7 +288,8 @@ def clean(self):
biosample_choices=generate_endpoints(biosample_choices, biosample_endpoint_name, biosample_endpoint_name, biosample_entry_type, biosample_lookups)
BiosampleEndpoints = forms.MultipleChoiceField(
choices=biosample_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
biosample_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -321,7 +309,8 @@ def clean(self):
cohort_choices=generate_endpoints(cohort_choices, cohort_endpoint_name, cohort_endpoint_name, cohort_entry_type, cohort_lookups)
CohortEndpoints = forms.MultipleChoiceField(
choices=cohort_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
cohort_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -341,7 +330,8 @@ def clean(self):
dataset_choices=generate_endpoints(dataset_choices, dataset_endpoint_name, dataset_endpoint_name, dataset_entry_type, dataset_lookups)
DatasetEndpoints = forms.MultipleChoiceField(
choices=dataset_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
dataset_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -361,7 +351,8 @@ def clean(self):
genomicVariant_choices=generate_endpoints(genomicVariant_choices, genomicVariant_endpoint_name, genomicVariant_endpoint_name, genomicVariant_entry_type, genomicVariant_lookups)
GenomicVariantEndpoints = forms.MultipleChoiceField(
choices=genomicVariant_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
genomicVariation_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -381,7 +372,8 @@ def clean(self):
individual_choices=generate_endpoints(individual_choices, individual_endpoint_name, individual_endpoint_name, individual_entry_type, individual_lookups)
IndividualEndpoints = forms.MultipleChoiceField(
choices=individual_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
individual_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
Expand All @@ -401,10 +393,11 @@ def clean(self):
run_choices=generate_endpoints(run_choices, run_endpoint_name, run_endpoint_name, run_entry_type, run_lookups)
RunEndpoints = forms.MultipleChoiceField(
choices=run_choices,
widget=forms.CheckboxSelectMultiple
widget=forms.CheckboxSelectMultiple,
required=False,
)
run_granularity= forms.ChoiceField(
widget=forms.RadioSelect,
choices=granularity_choices,
)
run_engine= forms.ChoiceField(choices=database_choices, help_text="Database Engine")
run_engine= forms.ChoiceField(choices=database_choices, help_text="Database Engine")
46 changes: 26 additions & 20 deletions adminui/adminclient/views/datasets.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
from django.urls import resolve
from beacon.connections.mongo.__init__ import client
from adminbackend.forms.datasets import DatasetsForm
import yaml
from django.contrib.auth.decorators import login_required, permission_required

import logging
Expand All @@ -24,6 +23,7 @@
def default_view(request):
analyses=client["beacon"].analyses
datasets=client["beacon"].datasets
datasets_conf=client["beacon"].datasetsConf
biosamples=client["beacon"].biosamples
cohorts=client["beacon"].cohorts
runs=client["beacon"].runs
Expand Down Expand Up @@ -81,33 +81,38 @@ def default_view(request):
entry_types_included.append('g_variants')
dataset_dict["entry_types_included"]=entry_types_included
dataset_list.append(dataset_dict)
with open("beacon/conf/datasets/datasets_conf.yml") as f:
datasets_test=yaml.safe_load(f)
datasets_test = {
conf["_id"]: {
"isTest": conf.get("isTest", False),
"isSynthetic": conf.get("isSynthetic", False),
}
for conf in datasets_conf.find({})
}
if request.method == 'POST':
form = DatasetsForm(request.POST)
if form.is_valid():
dataID = form.cleaned_data['DatasetID']
if 'Test Mode' in request.POST:
with open("beacon/conf/datasets/datasets_conf.yml") as f:
datasets_conf=yaml.safe_load(f)
test_datasets=[]
for key2, value2 in request.POST.items():
if value2 == 'on':
try:
datasets_conf[key2]['isTest']=True
except Exception:
datasets_conf[key2]={}
datasets_conf[key2]['isTest']=True
test_datasets.append(key2)
for key, value in datasets_conf.items():
if key not in test_datasets:
try:
datasets_conf[key]['isTest']=False
except Exception:
datasets_conf[key]={}
datasets_conf[key]['isTest']=False
with open('/home/app/web/beacon/conf/datasets/datasets_conf.yml', 'w') as outfile:
yaml.dump(datasets_conf, outfile)
for dataset in datasets.find({}, {"id": 1}):
dataset_id = dataset["id"]

datasets_conf.update_one(
{"_id": dataset_id},
{
"$set": {
"isTest": dataset_id in test_datasets
},
"$setOnInsert": {
"isSynthetic": False
}
},
upsert=True
)

elif 'Delete Dataset' in request.POST:
analyses.delete_many({"datasetId": dataID})
biosamples.delete_many({"datasetId": dataID})
Expand All @@ -118,7 +123,8 @@ def default_view(request):
individuals.delete_many({"datasetId": dataID})
runs.delete_many({"datasetId": dataID})
targets.delete_many({"datasetId": dataID})
datasets_conf.delete_one({"_id": dataID})
return redirect("adminclient:datasets")
context={"datasets_found": dataset_list, "datasets_test": datasets_test}
template = "general_configuration/datasets.html"
return render(request, template, context)
return render(request, template, context)
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