forked from enviPath/enviPy
[Feature] Basic logging of Jobs, Model Evaluation (#169)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#169
This commit is contained in:
163
epdb/views.py
163
epdb/views.py
@ -47,6 +47,7 @@ from .models import (
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ExternalDatabase,
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ExternalIdentifier,
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EnzymeLink,
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JobLog,
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)
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logger = logging.getLogger(__name__)
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@ -754,8 +755,8 @@ def package_models(request, package_uuid):
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context["unreviewed_objects"] = unreviewed_model_qs
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context["model_types"] = {
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"ML Relative Reasoning": "ml-relative-reasoning",
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"Rule Based Relative Reasoning": "rule-based-relative-reasoning",
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"ML Relative Reasoning": "mlrr",
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"Rule Based Relative Reasoning": "rbrr",
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}
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if s.FLAGS.get("ENVIFORMER", False):
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@ -775,69 +776,67 @@ def package_models(request, package_uuid):
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model_type = request.POST.get("model-type")
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# Generic fields for ML and Rule Based
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rule_packages = request.POST.getlist("model-rule-packages")
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data_packages = request.POST.getlist("model-data-packages")
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# Generic params
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params = {
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"package": current_package,
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"name": name,
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"description": description,
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"data_packages": [
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PackageManager.get_package_by_url(current_user, p) for p in data_packages
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],
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}
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if model_type == "enviformer":
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threshold = float(request.POST.get(f"{model_type}-threshold", 0.5))
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threshold = float(request.POST.get("model-threshold", 0.5))
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params["threshold"] = threshold
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mod = EnviFormer.create(current_package, name, description, threshold)
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mod = EnviFormer.create(**params)
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elif model_type == "mlrr":
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# ML Specific
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threshold = float(request.POST.get("model-threshold", 0.5))
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# TODO handle additional fingerprinter
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# fingerprinter = request.POST.get("model-fingerprinter")
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elif model_type == "ml-relative-reasoning" or model_type == "rule-based-relative-reasoning":
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# Generic fields for ML and Rule Based
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rule_packages = request.POST.getlist("package-based-relative-reasoning-rule-packages")
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data_packages = request.POST.getlist("package-based-relative-reasoning-data-packages")
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eval_packages = request.POST.getlist(
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"package-based-relative-reasoning-evaluation-packages", []
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)
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params["rule_packages"] = [
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PackageManager.get_package_by_url(current_user, p) for p in rule_packages
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]
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# Generic params
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params = {
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"package": current_package,
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"name": name,
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"description": description,
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"rule_packages": [
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PackageManager.get_package_by_url(current_user, p) for p in rule_packages
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],
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"data_packages": [
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PackageManager.get_package_by_url(current_user, p) for p in data_packages
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],
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"eval_packages": [
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PackageManager.get_package_by_url(current_user, p) for p in eval_packages
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],
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}
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# App Domain related parameters
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build_ad = request.POST.get("build-app-domain", False) == "on"
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num_neighbors = request.POST.get("num-neighbors", 5)
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reliability_threshold = request.POST.get("reliability-threshold", 0.5)
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local_compatibility_threshold = request.POST.get("local-compatibility-threshold", 0.5)
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if model_type == "ml-relative-reasoning":
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# ML Specific
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threshold = float(request.POST.get(f"{model_type}-threshold", 0.5))
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# TODO handle additional fingerprinter
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# fingerprinter = request.POST.get(f"{model_type}-fingerprinter")
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params["threshold"] = threshold
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# params['fingerprinter'] = fingerprinter
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params["build_app_domain"] = build_ad
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params["app_domain_num_neighbours"] = num_neighbors
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params["app_domain_reliability_threshold"] = reliability_threshold
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params["app_domain_local_compatibility_threshold"] = local_compatibility_threshold
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# App Domain related parameters
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build_ad = request.POST.get("build-app-domain", False) == "on"
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num_neighbors = request.POST.get("num-neighbors", 5)
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reliability_threshold = request.POST.get("reliability-threshold", 0.5)
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local_compatibility_threshold = request.POST.get(
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"local-compatibility-threshold", 0.5
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)
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mod = MLRelativeReasoning.create(**params)
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elif model_type == "rbrr":
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params["rule_packages"] = [
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PackageManager.get_package_by_url(current_user, p) for p in rule_packages
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]
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params["threshold"] = threshold
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# params['fingerprinter'] = fingerprinter
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params["build_app_domain"] = build_ad
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params["app_domain_num_neighbours"] = num_neighbors
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params["app_domain_reliability_threshold"] = reliability_threshold
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params["app_domain_local_compatibility_threshold"] = local_compatibility_threshold
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mod = MLRelativeReasoning.create(**params)
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else:
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mod = RuleBasedRelativeReasoning.create(**params)
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from .tasks import build_model
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build_model.delay(mod.pk)
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mod = RuleBasedRelativeReasoning.create(**params)
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elif s.FLAGS.get("PLUGINS", False) and model_type in s.CLASSIFIER_PLUGINS.values():
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pass
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else:
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return error(
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request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
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)
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return redirect(mod.url)
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from .tasks import dispatch, build_model
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dispatch(current_user, build_model, mod.pk)
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return redirect(mod.url)
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else:
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return HttpResponseNotAllowed(["GET", "POST"])
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@ -865,6 +864,10 @@ def package_model(request, package_uuid, model_uuid):
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return JsonResponse({"error": f'"{smiles}" is not a valid SMILES'}, status=400)
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if classify:
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from epdb.tasks import dispatch_eager, predict_simple
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res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
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pred_res = current_model.predict(stand_smiles)
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res = []
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@ -909,9 +912,25 @@ def package_model(request, package_uuid, model_uuid):
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current_model.delete()
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return redirect(current_package.url + "/model")
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elif hidden == "evaluate":
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from .tasks import evaluate_model
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from .tasks import dispatch, evaluate_model
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eval_type = request.POST.get("model-evaluation-type")
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if eval_type not in ["sg", "mg"]:
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return error(
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request,
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"Invalid evaluation type",
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f'Evaluation type "{eval_type}" is not supported. Only "sg" and "mg" are supported.',
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)
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multigen = eval_type == "mg"
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eval_packages = request.POST.getlist("model-evaluation-packages")
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eval_package_ids = [
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PackageManager.get_package_by_url(current_user, p).id for p in eval_packages
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]
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dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
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evaluate_model.delay(current_model.pk)
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return redirect(current_model.url)
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else:
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return HttpResponseBadRequest()
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@ -1809,9 +1828,9 @@ def package_pathways(request, package_uuid):
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pw.setting = prediction_setting
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pw.save()
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from .tasks import predict
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from .tasks import dispatch, predict
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predict.delay(pw.pk, prediction_setting.pk, limit=limit)
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dispatch(current_user, predict, pw.pk, prediction_setting.pk, limit=limit)
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return redirect(pw.url)
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@ -1930,10 +1949,16 @@ def package_pathway(request, package_uuid, pathway_uuid):
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if node_url:
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n = current_pathway.get_node(node_url)
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from .tasks import predict
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from .tasks import dispatch, predict
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dispatch(
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current_user,
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predict,
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current_pathway.pk,
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current_pathway.prediction_setting.pk,
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node_pk=n.pk,
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)
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# Dont delay?
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predict(current_pathway.pk, current_pathway.setting.pk, node_pk=n.pk)
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return JsonResponse({"success": current_pathway.url})
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return HttpResponseBadRequest()
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@ -2705,6 +2730,24 @@ def setting(request, setting_uuid):
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pass
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def jobs(request):
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current_user = _anonymous_or_real(request)
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context = get_base_context(request)
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if request.method == "GET":
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context["object_type"] = "joblog"
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context["breadcrumbs"] = [
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{"Home": s.SERVER_URL},
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{"Jobs": s.SERVER_URL + "/jobs"},
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]
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if current_user.is_superuser:
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context["jobs"] = JobLog.objects.all().order_by("-created")
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else:
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context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
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return render(request, "collections/joblog.html", context)
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###########
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# KETCHER #
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###########
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