private void Persist(string dbConn, Dictionary<string, OntologyEntry> entries, int paneId)
{
OntologyEntry rootEntry = new OntologyEntry("<!-- ROOT -->", "<!-- ROOT -->", "<!-- ROOT -->");
foreach (OntologyEntry entry in entries.Values)
{
int p = 0;
foreach (string parentID in entry.Parents)
{
OntologyEntry parent;
if (!entries.TryGetValue(parentID, out parent))
continue;
p++;
parent.Children.Add(entry);
}
if (p == 0)
{
rootEntry.Children.Add(entry);
continue;
}
}
int left, right;
int nest = 1;
int depth = 0;
left = nest++;
NestIt(rootEntry, ref nest, depth+1);
right = nest;
rootEntry.LeftRights.Add(new int[] { left, right, depth });
try
{
if(Settings.SSHEnabled)
OpenSSH();
using (MySqlConnection conn = new MySqlConnection(dbConn))
{
conn.Open();
string query;
// Clear the ontology
query = "DELETE FROM OntologyEntries WHERE Pane = {0};";
query += "DELETE FROM OntologyRelations WHERE Pane = {0};";
query += "DELETE FROM OntologySynonyms WHERE Pane = {0};";
query = string.Format(query, paneId);
using (MySqlCommand cmd = new MySqlCommand())
{
cmd.Connection = conn;
cmd.CommandText = query;
cmd.CommandType = CommandType.Text;
cmd.ExecuteNonQuery();
}
// Input the ontology
foreach (OntologyEntry entry in entries.Values)
{
DoEntry(conn, paneId, entry);
}
}
}
finally
{
CloseSSH();
}
}
private void NestIt(OntologyEntry entry, ref int nest, int depth)
{
foreach (OntologyEntry child in entry.Children)
{
int left, right;
left = nest++;
NestIt(child, ref nest, depth+1);
right = nest++;
child.LeftRights.Add(new int[] { left, right, depth });
}
}
private void DoEntry(MySqlConnection conn, int paneId, OntologyEntry entry)
{
string query = string.Empty;
string id = entry.ID.Replace("'", "''");
int parentCount = entry.Parents.Count;
foreach (int[] lr in entry.LeftRights)
{
if (lr[2] == 1 && parentCount > 0)// If depth is top then no parents
parentCount--;
query += string.Format("INSERT INTO OntologyRelations VALUES ({0}, '{1}',{2},{3},{4});", paneId, id, lr[0].ToString(), lr[1].ToString(), lr[2].ToString());
}
query += string.Format("INSERT INTO OntologyEntries VALUES ({0}, '{1}','{2}','{3}','{4}',{5},{6});", paneId, id, entry.AltID.Replace("'", "''"), entry.Label.Replace("'", "''"), entry.Definition.Replace("'", "''"), parentCount, entry.Children.Count);
query += string.Format("INSERT INTO OntologySynonyms VALUES ({0}, '{1}','{2}');", paneId, id, entry.Label.Replace("'", "''"));
foreach (string synonym in entry.Synonyms)
{
query += string.Format("INSERT INTO OntologySynonyms VALUES ({0}, '{1}','{2}');", paneId, id, synonym.Replace("'", "''"));
}
using (MySqlCommand cmd = new MySqlCommand())
{
cmd.Connection = conn;
cmd.CommandText = query;
cmd.CommandType = CommandType.Text;
cmd.ExecuteNonQuery();
}
}
private void ImportOntology(string dbConn, string filename, int paneId)
{
Dictionary<string, OntologyEntry> entries = new Dictionary<string, OntologyEntry>();
string idKey = null;
bool headerDone = false;
XmlDocument doc = new XmlDocument();
doc.Load(filename);
foreach (XmlNode n in doc.DocumentElement.ChildNodes)
{
if (!(n is XmlElement))
continue;
XmlElement el = (XmlElement)n;
if (!headerDone && el.Name == "owl:DatatypeProperty")
{
XmlAttribute a = el.Attributes["rdf:ID"];
if (a != null)
{
idKey = a.InnerText;
headerDone = true;
}
}
if (el.Name != "owl:Class")
continue;
else
headerDone = true;
XmlAttribute idXml = el.Attributes["rdf:about"];
if (idXml == null)
idXml = el.Attributes["rdf:ID"];
if (idXml == null)
idXml = el.Attributes["rdf:resource"];
if (idXml == null)
continue;
string id = idXml.InnerText;
string altID = id;
if (idKey != null)
{
XmlElement idKeyXml = el[idKey];
if (idKeyXml == null)
continue;
altID = idKeyXml.InnerText;
}
XmlElement l = el["rdfs:label"];
if (l == null)
continue;
string label = l.InnerText;
OntologyEntry entry = new OntologyEntry(id, label, altID);
entries.Add(id, entry);
XmlNodeList subClasses = el.GetElementsByTagName("rdfs:subClassOf");
foreach (XmlNode node in subClasses)
{
XmlNode c = node["owl:Class"];
if (c == null)
c = node;
XmlAttribute a = c.Attributes["rdf:about"];
if (a == null)
a = c.Attributes["rdf:ID"];
if (a == null)
a = c.Attributes["rdf:resource"];
if (a != null)
{
string parentID = a.InnerText;
if (parentID.StartsWith("#"))
parentID = parentID.Substring(1);
if (!entry.Parents.Contains(parentID))
entry.Parents.Add(parentID);
}
}
XmlNodeList synonyms = el.GetElementsByTagName("Synonym");
foreach (XmlNode node in synonyms)
{
entry.Synonyms.Add(node.InnerText);
}
List<XmlNodeList> oboSynonyms = new List<XmlNodeList>();
oboSynonyms.Add(el.GetElementsByTagName("oboInOwl:hasSynonym"));
oboSynonyms.Add(el.GetElementsByTagName("oboInOwl:hasExactSynonym"));
oboSynonyms.Add(el.GetElementsByTagName("oboInOwl:hasNarrowSynonym"));
oboSynonyms.Add(el.GetElementsByTagName("oboInOwl:hasBroadSynonym"));
oboSynonyms.Add(el.GetElementsByTagName("oboInOwl:hasRelatedSynonym"));
foreach (XmlNodeList oboSynonym in oboSynonyms)
{
foreach (XmlNode node in oboSynonym)
{
if (!(node is XmlElement))
continue;
XmlElement mysyn = (XmlElement)node;
foreach (XmlNode syn in mysyn.GetElementsByTagName("oboInOwl:Synonym"))
{
if (!(syn is XmlElement))
continue;
XmlElement elsyn = (XmlElement)syn;
foreach (XmlNode synlab in elsyn.GetElementsByTagName("rdfs:label"))
{
entry.Synonyms.Add(synlab.InnerText);
}
}
}
}
}
Persist(dbConn, entries, paneId);
}
private void customButton_Click(object sender, EventArgs e)
{
try
{
Dictionary<string, OntologyEntry> entries = new Dictionary<string, OntologyEntry>();
// Published Dates
OntologyEntry ent;
string top;
string child;
top = "Published Date";
OntologyEntry pubdate = new OntologyEntry(top, top, top);
entries.Add(top, pubdate);
int yearStart = 1900, yearEnd = 2100;
for (int i = yearStart; i <= yearEnd; i++)
{
string yrid = i.ToString("0000");
OntologyEntry yrentry = new OntologyEntry(yrid, yrid, yrid);
yrentry.Parents.Add(top);
entries.Add(yrid, yrentry);
for (int j = 1; j <= 12; j++)
{
string mnid = j.ToString("00") + '/' + yrid;
DateTime d = DateTime.ParseExact("01/" + mnid, "dd/MM/yyyy", null);
OntologyEntry mnentry = new OntologyEntry(mnid, mnid, mnid);
mnentry.Parents.Add(yrid);
mnentry.Synonyms.Add(d.ToString("MMM"));
mnentry.Synonyms.Add(d.ToString("MMMM"));
entries.Add(mnid, mnentry);
}
}
// Phase
top = "Phase";
ent = new OntologyEntry(top, top, top);
entries.Add(top, ent);
child = "Phase I";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Phase 1");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Phase II";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Phase 2");
ent.Synonyms.Add("Phase IIa");
ent.Synonyms.Add("Phase IIb");
ent.Synonyms.Add("Phase 2/3");
ent.Synonyms.Add("Phase II/III");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Phase II/III";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Phase 2");
ent.Synonyms.Add("Phase IIa");
ent.Synonyms.Add("Phase IIb");
ent.Synonyms.Add("Phase 2/3");
ent.Synonyms.Add("Phase 3");
ent.Synonyms.Add("Phase 2/Phase 3");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Phase III";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Phase 3");
ent.Synonyms.Add("Phase 2/3");
ent.Synonyms.Add("Phase II/III");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Phase IV";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Phase 4");
ent.Parents.Add(top);
entries.Add(child, ent);
// Blinding
top = "Blinding";
ent = new OntologyEntry(top, top, top);
entries.Add(top, ent);
child = "Open";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Open label");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Blind";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Blinded");
ent.Synonyms.Add("Single-blind");
ent.Synonyms.Add("Single blind");
ent.Synonyms.Add("Single-blinded");
ent.Synonyms.Add("Single blinded");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Double-blind";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Double-blinded");
ent.Synonyms.Add("Double blind");
ent.Synonyms.Add("Double blinded");
ent.Parents.Add(top);
entries.Add(child, ent);
child = "Triple-blind";
ent = new OntologyEntry(child, child, child);
ent.Synonyms.Add("Triple-blinded");
ent.Synonyms.Add("Triple blind");
ent.Synonyms.Add("Triple blinded");
ent.Parents.Add(top);
entries.Add(child, ent);
// Randomisation
top = "Randomization";
ent = new OntologyEntry(top, top, top);
ent.Synonyms.Add("Randomized");
ent.Synonyms.Add("Randomised");
ent.Synonyms.Add("Random");
ent.Synonyms.Add("Randomisation");
entries.Add(top, ent);
Persist(dbConnBox.Text, entries, 4);
MessageBox.Show("Successful.");
}
catch (Exception ex)
{
MessageBox.Show(string.Format("Unsuccessful.\n{0}", ex));
}
}
