public static void DoUpgrade(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
int sel = doc.Application.Selection.Range.Start;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
try
{
string extension = doc.FullName.Split('.').Last();
string guid = Guid.NewGuid().ToString("N");
string timestamp = DateTime.Now.ToString("yyyyMMdd-HHmmss", CultureInfo.InvariantCulture);
string destination = Path.Combine(Globals.Chem4WordV3.AddInInfo.ProductAppDataPath, "Backups", $"Chem4Word-{timestamp}-{guid}.{extension}");
File.Copy(doc.FullName, destination);
}
catch (Exception ex)
{
// Nothing much we can do here :-(
Debug.WriteLine(ex.Message);
}
List <UpgradeTarget> targets = CollectData(doc);
int upgradedCCs = 0;
int upgradedXml = 0;
foreach (var target in targets)
{
if (target.ContentControls.Count > 0)
{
upgradedXml++;
upgradedCCs += target.ContentControls.Count;
}
foreach (var cci in target.ContentControls)
{
foreach (Word.ContentControl cc in doc.ContentControls)
{
if (cc.ID.Equals(cci.Id))
{
if (cci.Type.Equals("2D"))
{
cc.LockContents = false;
cc.Title = Constants.ContentControlTitle;
cc.Tag = target.Model.CustomXmlPartGuid;
cc.LockContents = true;
}
else
{
cc.LockContents = false;
cc.Range.Delete();
int start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
bool isFormula = false;
string source;
string text = CustomRibbon.GetInlineText(target.Model, cci.Type, ref isFormula, out source);
Word.ContentControl ccn = CustomRibbon.Insert1D(doc.Application, doc, text, isFormula, $"{cci.Type}:{target.Model.CustomXmlPartGuid}");
ccn.LockContents = true;
}
}
}
}
CMLConverter converter = new CMLConverter();
CustomXMLPart cxml = doc.CustomXMLParts.SelectByID(target.CxmlPartId);
cxml.Delete();
doc.CustomXMLParts.Add(converter.Export(target.Model));
}
EraseChemistryZones(doc);
Globals.Chem4WordV3.EnableDocumentEvents(doc);
doc.Application.Selection.SetRange(sel, sel);
if (upgradedCCs + upgradedXml > 0)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
UserInteractions.AlertUser($"Upgrade Completed{Environment.NewLine}{Environment.NewLine}Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
}
}
public static void DoUpgrade(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
int sel = doc.Application.Selection.Range.Start;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
try
{
string extension = doc.FullName.Split('.').Last();
string guid = Guid.NewGuid().ToString("N");
string timestamp = DateTime.Now.ToString("yyyyMMdd-HHmmss", CultureInfo.InvariantCulture);
string destination = Path.Combine(Globals.Chem4WordV3.AddInInfo.ProductAppDataPath, "Backups", $"Chem4Word-{timestamp}-{guid}.{extension}");
File.Copy(doc.FullName, destination);
}
catch (Exception ex)
{
// Nothing much we can do here :-(
Debug.WriteLine(ex.Message);
}
Dictionary <string, CustomXMLPart> customXmlParts = new Dictionary <string, CustomXMLPart>();
List <UpgradeTarget> targets = CollectData(doc);
int upgradedCCs = 0;
int upgradedXml = 0;
foreach (var target in targets)
{
if (target.ContentControls.Count > 0)
{
upgradedXml++;
upgradedCCs += target.ContentControls.Count;
}
foreach (var cci in target.ContentControls)
{
foreach (Word.ContentControl cc in doc.ContentControls)
{
if (cc.ID.Equals(cci.Id))
{
int start;
bool isFormula;
string source;
string text;
switch (cci.Type)
{
case "2D":
cc.LockContents = false;
cc.Title = Constants.ContentControlTitle;
cc.Tag = target.Model.CustomXmlPartGuid;
cc.LockContents = true;
// ToDo: Regenerate converted 2D structures
break;
case "new":
cc.LockContents = false;
cc.Range.Delete();
start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
var model = new Model.Model();
var molecule = new Molecule();
molecule.ChemicalNames.Add(new ChemicalName {
Id = "m1.n1", Name = cci.Text, DictRef = Constants.Chem4WordUserSynonym
});
model.Molecules.Add(molecule);
model.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
var cmlConvertor = new CMLConverter();
doc.CustomXMLParts.Add(cmlConvertor.Export(model));
Word.ContentControl ccn = doc.ContentControls.Add(Word.WdContentControlType.wdContentControlRichText, ref _missing);
ChemistryHelper.Insert1D(ccn, cci.Text, false, $"m1.n1:{model.CustomXmlPartGuid}");
ccn.LockContents = true;
break;
default:
cc.LockContents = false;
cc.Range.Delete();
start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
isFormula = false;
text = ChemistryHelper.GetInlineText(target.Model, cci.Type, ref isFormula, out source);
Word.ContentControl ccr = doc.ContentControls.Add(Word.WdContentControlType.wdContentControlRichText, ref _missing);
ChemistryHelper.Insert1D(ccr, text, isFormula, $"{cci.Type}:{target.Model.CustomXmlPartGuid}");
ccr.LockContents = true;
break;
}
}
}
}
CMLConverter converter = new CMLConverter();
CustomXMLPart cxml = doc.CustomXMLParts.SelectByID(target.CxmlPartId);
if (customXmlParts.ContainsKey(cxml.Id))
{
customXmlParts.Add(cxml.Id, cxml);
}
doc.CustomXMLParts.Add(converter.Export(target.Model));
}
EraseChemistryZones(doc);
foreach (var kvp in customXmlParts.ToList())
{
kvp.Value.Delete();
}
Globals.Chem4WordV3.EnableDocumentEvents(doc);
doc.Application.Selection.SetRange(sel, sel);
if (upgradedCCs + upgradedXml > 0)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
UserInteractions.AlertUser($"Upgrade Completed{Environment.NewLine}{Environment.NewLine}Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
}
}
private string FetchStructure()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
string result = lastSelected;
ImportButton.Enabled = false;
ListView.SelectedListViewItemCollection selected = Results.SelectedItems;
if (selected.Count > 0)
{
ListViewItem item = selected[0];
string pubchemId = item.Text;
PubChemId = pubchemId;
if (!pubchemId.Equals(lastSelected))
{
Cursor = Cursors.WaitCursor;
// https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/record/SDF
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
try
{
var request = (HttpWebRequest)WebRequest.Create(
string.Format(CultureInfo.InvariantCulture, "{0}rest/pug/compound/cid/{1}/record/SDF",
UserOptions.PubChemRestApiUri, pubchemId));
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
HttpWebResponse response;
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
// we will read data via the response stream
using (var resStream = response.GetResponseStream())
{
lastMolfile = new StreamReader(resStream).ReadToEnd();
SdFileConverter sdFileConverter = new SdFileConverter();
Model.Model model = sdFileConverter.Import(lastMolfile);
if (model.MeanBondLength < Core.Helpers.Constants.MinimumBondLength - Core.Helpers.Constants.BondLengthTolerance ||
model.MeanBondLength > Core.Helpers.Constants.MaximumBondLength + Core.Helpers.Constants.BondLengthTolerance)
{
model.ScaleToAverageBondLength(Core.Helpers.Constants.StandardBondLength);
}
this.display1.Chemistry = model;
if (model.AllWarnings.Count > 0 || model.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", lastMolfile);
List <string> lines = new List <string>();
if (model.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllErrors));
lines.Add("Errors(s)");
lines.AddRange(model.AllErrors);
}
if (model.AllWarnings.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllWarnings));
lines.Add("Warnings(s)");
lines.AddRange(model.AllWarnings);
}
ErrorsAndWarnings.Text = string.Join(Environment.NewLine, lines);
}
else
{
CMLConverter cmlConverter = new CMLConverter();
Cml = cmlConverter.Export(model);
ImportButton.Enabled = true;
}
}
result = pubchemId;
}
else
{
result = string.Empty;
lastMolfile = string.Empty;
StringBuilder sb = new StringBuilder();
sb.AppendLine($"Bad request. Status code: {response.StatusCode}");
UserInteractions.AlertUser(sb.ToString());
}
}
catch (Exception ex)
{
if (ex.Message.Equals("The operation has timed out"))
{
ErrorsAndWarnings.Text = "Please try again later - the service has timed out";
}
else
{
ErrorsAndWarnings.Text = ex.Message;
Telemetry.Write(module, "Exception", ex.Message);
Telemetry.Write(module, "Exception", ex.StackTrace);
}
}
finally
{
ServicePointManager.SecurityProtocol = securityProtocol;
Cursor = Cursors.Default;
}
}
}
return(result);
}
private void GetData(string idlist)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
var request = (HttpWebRequest)
WebRequest.Create(
string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esummary.fcgi?db=pccompound&id={1}&retmode=xml",
UserOptions.PubChemWebServiceUri, idlist));
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
HttpWebResponse response;
try
{
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
Results.Enabled = true;
// we will read data via the response stream
using (var resStream = response.GetResponseStream())
{
var resultDocument = XDocument.Load(new StreamReader(resStream));
var compounds = resultDocument.XPathSelectElements("//DocSum");
if (compounds.Any())
{
foreach (var compound in compounds)
{
var id = compound.XPathSelectElement("./Id");
var name = compound.XPathSelectElement("./Item[@Name='IUPACName']");
//var smiles = compound.XPathSelectElement("./Item[@Name='CanonicalSmile']")
var formula = compound.XPathSelectElement("./Item[@Name='MolecularFormula']");
ListViewItem lvi = new ListViewItem(id.Value);
lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, name.Value));
//lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, smiles.ToString()))
lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, formula.Value));
Results.Items.Add(lvi);
// Add to a list view ...
}
}
else
{
Debug.WriteLine("Something went wrong");
}
}
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"Bad request. Status code: {response.StatusCode}");
UserInteractions.AlertUser(sb.ToString());
}
}
catch (Exception ex)
{
if (ex.Message.Equals("The operation has timed out"))
{
ErrorsAndWarnings.Text = "Please try again later - the service has timed out";
}
else
{
ErrorsAndWarnings.Text = ex.Message;
Telemetry.Write(module, "Exception", ex.Message);
Telemetry.Write(module, "Exception", ex.StackTrace);
}
}
finally
{
ServicePointManager.SecurityProtocol = securityProtocol;
}
}
private void ExecuteSearch(int direction)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (!string.IsNullOrEmpty(SearchFor.Text))
{
Cursor = Cursors.WaitCursor;
string webCall;
if (direction == 0)
{
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall);
}
else
{
if (direction == 1)
{
int startFrom = firstResult + numResults;
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}&WebEnv={3}&RetStart={4}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall, webEnv, startFrom);
}
else
{
int startFrom = firstResult - numResults;
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}&WebEnv={3}&RetStart={4}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall, webEnv, startFrom);
}
}
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
var request = (HttpWebRequest)WebRequest.Create(webCall);
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
HttpWebResponse response;
try
{
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
using (var resStream = response.GetResponseStream())
{
var resultDocument = XDocument.Load(new StreamReader(resStream));
// Get the count of results
resultsCount = int.Parse(resultDocument.XPathSelectElement("//Count").Value);
// Current position
firstResult = int.Parse(resultDocument.XPathSelectElement("//RetStart").Value);
int fetched = int.Parse(resultDocument.XPathSelectElement("//RetMax").Value);
lastResult = firstResult + fetched;
// WebEnv for history
webEnv = resultDocument.XPathSelectElement("//WebEnv").Value;
// Set flags for More/Prev buttons
if (lastResult > numResults)
{
PreviousButton.Enabled = true;
}
else
{
PreviousButton.Enabled = false;
}
if (lastResult < resultsCount)
{
NextButton.Enabled = true;
}
else
{
NextButton.Enabled = false;
}
var ids = resultDocument.XPathSelectElements("//Id");
var count = ids.Count();
Results.Items.Clear();
if (count > 0)
{
// Set form title
Text = $"Search PubChem - Showing {firstResult + 1} to {lastResult} [of {resultsCount}]";
Refresh();
var sb = new StringBuilder();
for (var i = 0; i < count; i++)
{
var id = ids.ElementAt(i);
if (i > 0)
{
sb.Append(",");
}
sb.Append(id.Value);
}
GetData(sb.ToString());
}
else
{
// Set error box
ErrorsAndWarnings.Text = "Sorry, no results were found.";
}
}
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"Status code {response.StatusCode} was returned by the server");
Telemetry.Write(module, "Warning", sb.ToString());
UserInteractions.AlertUser(sb.ToString());
}
}
catch (Exception ex)
{
if (ex.Message.Equals("The operation has timed out"))
{
ErrorsAndWarnings.Text = "Please try again later - the service has timed out";
}
else
{
ErrorsAndWarnings.Text = ex.Message;
Telemetry.Write(module, "Exception", ex.Message);
Telemetry.Write(module, "Exception", ex.StackTrace);
}
}
finally
{
ServicePointManager.SecurityProtocol = securityProtocol;
Cursor = Cursors.Default;
}
}
}
public static void DoUpgrade(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
int sel = doc.Application.Selection.Range.Start;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
List <UpgradeTarget> targets = CollectData(doc);
int upgradedCCs = 0;
int upgradedXml = 0;
foreach (var target in targets)
{
if (target.ContentControls.Count > 0)
{
upgradedXml++;
upgradedCCs += target.ContentControls.Count;
}
foreach (var cci in target.ContentControls)
{
foreach (Word.ContentControl cc in doc.ContentControls)
{
if (cc.ID.Equals(cci.Id))
{
if (cci.Type.Equals("2D"))
{
cc.LockContents = false;
cc.Title = Constants.ContentControlTitle;
cc.Tag = target.Model.CustomXmlPartGuid;
cc.LockContents = true;
}
else
{
cc.LockContents = false;
cc.Range.Delete();
int start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
bool isFormula = false;
string source;
string text = CustomRibbon.GetInlineText(target.Model, cci.Type, ref isFormula, out source);
Word.ContentControl ccn = CustomRibbon.Insert1D(doc.Application, doc, text, isFormula, $"{cci.Type}:{target.Model.CustomXmlPartGuid}");
ccn.LockContents = true;
}
}
}
}
CMLConverter converter = new CMLConverter();
CustomXMLPart cxml = doc.CustomXMLParts.SelectByID(target.CxmlPartId);
cxml.Delete();
doc.CustomXMLParts.Add(converter.Export(target.Model));
}
EraseChemistryZones(doc);
Globals.Chem4WordV3.EnableDocumentEvents(doc);
doc.Application.Selection.SetRange(sel, sel);
if (upgradedCCs + upgradedXml > 0)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
UserInteractions.AlertUser($"Upgrade Completed{Environment.NewLine}{Environment.NewLine}Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
}
}
