public void ArchivePreventsValidation()
{
const string annotation = "ASXL1 gene mutations are associated with...";
const string annType = "case";
const string description = "Presence of mutation in ASXL1";
const string name = "ASXL1 Positive";
const string panel = "yale/amlmds";
const string query = "WHERE GENE = 'ASXL1'";
var valid = new AnnotationRule()
{
Annotation = annotation,
AnnotationType = annType,
Description = description,
Name = name,
Panel = panel,
Query = query
};
var created = _rules.Create(valid);
Assert.IsFalse(created.IsValidated);
Assert.IsFalse(created.IsArchived);
_rules.ArchiveRule(created.Id);
Assert.Throws(typeof(Exception), delegate { _rules.ValidateRule(created.Id); });
var verify = _rules.Find(created.Id);
Assert.IsFalse(verify.IsValidated);
Assert.IsTrue(created.IsArchived);
}
public void ArchivedTestCannotBeListed()
{
const string annotation = "ASXL1 gene mutations are associated with...";
const string annType = "case";
const string description = "Presence of mutation in ASXL1";
const string name = "ASXL1 Positive";
const string panel = "yale/amlmds";
const string query = "WHERE GENE = 'ASXL1'";
var valid = new AnnotationRule()
{
Annotation = annotation,
AnnotationType = annType,
Description = description,
Name = name,
Panel = panel,
Query = query
};
var created = _rules.Create(valid);
_rules.ValidateRule(created.Id);
var rules = _rules.FindByPanel("yale/amlmds");
var count = rules.Count;
Assert.IsTrue(rules.Any(r => r.Id == created.Id));
_rules.ArchiveRule(created.Id);
rules = _rules.FindByPanel("yale/amlmds");
Assert.AreEqual(count-1, rules.Count);
Assert.IsFalse(rules.Any(r => r.Id == created.Id));
}
public AnnotationRule Create(AnnotationRule rule)
{
if (string.IsNullOrEmpty(rule.Panel) || string.IsNullOrEmpty(rule.Annotation) ||
string.IsNullOrEmpty(rule.AnnotationType) || string.IsNullOrEmpty(rule.Name) ||
string.IsNullOrEmpty(rule.Query))
throw new Exception("Create rule failed: must include panel, annotation, annotation type, rule name, and query.");
var newRule = new AnnotationRule()
{
Annotation = rule.Annotation,
AnnotationType = rule.AnnotationType,
CreatedUtc = DateTime.UtcNow,
Description = rule.Description,
Name = rule.Name,
Panel = rule.Panel.ToLower(),
Query = rule.Query,
IsValidated = false,
IsArchived = false
};
_db.AnnotationRules.Add(newRule);
_db.SaveChanges();
return newRule;
}
public ActionResult Create(CreateRule model)
{
var rule = new AnnotationRule()
{
Annotation = model.Annotation,
AnnotationType = model.SelectedAnnotationType,
Description = model.Description,
Name = model.Name,
Panel = model.Panel,
Query = model.Query
};
_rules.Create(rule);
return RedirectToAction("Index");
}
public void RequireFieldsForRuleCreation()
{
var count = _rules.Count();
Assert.AreEqual(_db.AnnotationRules.Count(), count);
var noAnnotation = new AnnotationRule()
{
AnnotationType = "case",
Name = "ASXL1 Positive",
Panel = "yale/amlmds",
Query = "WHERE GENE = 'ASXL1'"
};
Assert.Throws(typeof (Exception), delegate { _rules.Create(noAnnotation); });
Assert.AreEqual(count, _rules.Count());
var noAnnType = new AnnotationRule()
{
Annotation = "ASXL1 gene mutations are associated with...",
Name = "ASXL1 Positive",
Panel = "yale/amlmds",
Query = "WHERE GENE = 'ASXL1'"
};
Assert.Throws(typeof (Exception), delegate { _rules.Create(noAnnType); });
Assert.AreEqual(count, _rules.Count());
var noName = new AnnotationRule()
{
Annotation = "ASXL1 gene mutations are associated with...",
AnnotationType = "case",
Panel = "yale/amlmds",
Query = "WHERE GENE = 'ASXL1'"
};
Assert.Throws(typeof (Exception), delegate { _rules.Create(noName); });
Assert.AreEqual(count, _rules.Count());
var noPanel = new AnnotationRule()
{
Annotation = "ASXL1 gene mutations are associated with...",
AnnotationType = "case",
Name = "ASXL1 Positive",
Query = "WHERE GENE = 'ASXL1'"
};
Assert.Throws(typeof (Exception), delegate { _rules.Create(noPanel); });
Assert.AreEqual(count, _rules.Count());
var noQuery = new AnnotationRule()
{
Annotation = "ASXL1 gene mutations are associated with...",
AnnotationType = "case",
Name = "ASXL1 Positive",
Panel = "aml/mds"
};
Assert.Throws(typeof (Exception), delegate { _rules.Create(noQuery); });
Assert.AreEqual(count, _rules.Count());
var valid = new AnnotationRule()
{
Annotation = "ASXL1 gene mutations are associated with...",
AnnotationType = "case",
Name = "ASXL1 Positive",
Panel = "aml/mds",
Query = "WHERE GENE = 'ASXL1'"
};
AnnotationRule created = null;
Assert.DoesNotThrow(delegate { created = _rules.Create(valid); });
Assert.AreEqual(count + 1, _rules.Count());
Assert.IsNotNull(created);
}
public void FindAllLocatesAllRules()
{
const string annotation = "ASXL1 gene mutations are associated with...";
const string annType = "case";
const string description = "Presence of mutation in ASXL1";
const string name = "ASXL1 Positive";
const string panel = "yale/amlmds";
const string query = "WHERE GENE = 'ASXL1'";
var valid = new AnnotationRule()
{
Annotation = annotation,
AnnotationType = annType,
Description = description,
Name = name,
Panel = panel,
Query = query
};
var rules = _rules.FindAll();
var initialCount = rules.Count();
var created = _rules.Create(valid);
_rules.ValidateRule(created.Id);
rules = _rules.FindAll();
var countAdded = rules.Count();
Assert.IsTrue(rules.Any(r => r.Id == created.Id));
Assert.AreEqual(initialCount+1, countAdded);
_rules.ArchiveRule(created.Id);
rules = _rules.FindAll();
Assert.AreEqual(initialCount+1, rules.Count());
Assert.IsTrue(rules.Any(r => r.Id == created.Id));
}
public void CreateRule()
{
var count = _rules.Count();
Assert.AreEqual(_db.AnnotationRules.Count(), count);
var createdUtc = DateTime.UtcNow.AddDays(-1);
const string annotation = "ASXL1 gene mutations are associated with...";
const string annType = "case";
const string description = "Presence of mutation in ASXL1";
const string name = "ASXL1 Positive";
const string panel = "yale/amlmds";
const string query = "WHERE GENE = 'ASXL1'";
// Create new rule, set validated=true to verify that create method sets to false (can only validate through Validate())
// Created date should also be set by method, not calling function, so verify that date differs
var valid = new AnnotationRule()
{
Annotation = annotation,
AnnotationType = annType,
CreatedUtc = createdUtc,
Description = description,
Name = name,
Panel = panel,
Query = query,
IsValidated = true
};
var created = _rules.Create(valid);
Assert.AreNotEqual(0, created.Id);
Assert.AreEqual(count + 1, _rules.Count());
Assert.AreEqual(annotation, created.Annotation);
Assert.AreEqual(annType, created.AnnotationType);
Assert.AreEqual(description, created.Description);
Assert.AreEqual(name, created.Name);
Assert.AreEqual(panel, created.Panel);
Assert.AreEqual(query, created.Query);
Assert.IsFalse(created.IsValidated);
Assert.AreNotEqual(valid.CreatedUtc, created.CreatedUtc);
}
public void CanUpdateRule()
{
const string annotation = "ASXL1 gene mutations are associated with...";
const string annType = "case";
const string description = "Presence of mutation in ASXL1";
const string name = "ASXL1 Positive";
const string panel = "yale/amlmds";
const string query = "WHERE GENE = 'ASXL1'";
var valid = new AnnotationRule()
{
Annotation = annotation,
AnnotationType = annType,
Description = description,
Name = name,
Panel = panel,
Query = query
};
var created = _rules.Create(valid);
const string uAnn = "ASXL1 gene variants are assocaited with";
const string uQuery = "WHERE GENE = 'ASXL1' AND AF > 5";
const string uDesc = "ASXL1 variant >5% AF";
Assert.Throws(typeof (Exception), delegate { _rules.UpdateRule(created.Id + 1, null, null, null); });
_rules.UpdateRule(created.Id, uAnn, uQuery, uDesc);
var updated = _rules.Find(created.Id);
Assert.AreEqual(uAnn, updated.Annotation);
Assert.AreEqual(uQuery, updated.Query);
Assert.AreEqual(uDesc, updated.Description);
_rules.UpdateRule(created.Id, null, null, null);
var nullUpdate = _rules.Find(created.Id);
Assert.AreEqual(uAnn, nullUpdate.Annotation);
Assert.AreEqual(uQuery, nullUpdate.Query);
Assert.AreEqual(uDesc, nullUpdate.Description);
}
