public string GetIdentifier(MerritQueryData queryData, RepositoryModel repositoryModel)
{
throw new NotImplementedException();
}
private void WriteEML(MerritQueryData request, string filePath, DM.File file, DM.Repository repositoryData, IEnumerable<DM.FileColumnType> fileColumnTypes = null, IEnumerable<DM.FileColumnUnit> fileColumnUnits = null)
{
// XmlDocument metadataDocument = new XmlDocument();
XmlDocument emlDocument = new XmlDocument();
// metadataDocument.LoadXml(request.MetaDataDetail.MetadataMappingXML);
emlDocument.LoadXml(request.MetadataXML);
XmlNamespaceManager nsmgr = new XmlNamespaceManager(emlDocument.NameTable);
nsmgr.AddNamespace("eml", MerritConstants.EmlNamespace);
var repositoryMetadata = repositoryData.RepositoryMetadata.FirstOrDefault();
if (repositoryMetadata != null)
{
ReplaceMetadata(file, emlDocument, nsmgr, repositoryMetadata);
}
// Write Parameter Metadata properties.
if (file.FileColumns != null && file.FileColumns.Count > 0)
{
WriteParamMetadata(request, emlDocument, file, fileColumnTypes, fileColumnUnits);
}
////Added this following conditions outside the above for loop to avoid the following conditions not to repeat every time
////If contact element is not there, then insert the value from creator/surname
ManageContactElement(emlDocument);
////If no project title element ,then add the project title element value
ManageProjectTitleElement(emlDocument);
////If datatable has no entityname ,then add the entity name
ManageEntityNameElement(emlDocument);
////If datatable has no attributeList, then add attributeList node
ManageAttributeListElement(emlDocument);
////set the coordinate value for geographical location
ManageGeographicLocationCoordinates(emlDocument);
////check the temporal coverage conidtions
ManageTemporalCoverage(emlDocument);
////Remove the empty elements and remove the parent node when the no child node items are present
RemoveEmptyElements(emlDocument);
emlDocument.Save(filePath);
}
private void WriteParamMetadata(MerritQueryData request, XmlDocument emlDocument, DM.File file, IEnumerable<DM.FileColumnType> fileColumnTypes = null, IEnumerable<DM.FileColumnUnit> fileColumnUnits = null)
{
XmlNamespaceManager emlNamespaceMgr = new XmlNamespaceManager(emlDocument.NameTable);
emlNamespaceMgr.AddNamespace("eml", MerritConstants.EmlNamespace);
XmlElement emlRoot = emlDocument.DocumentElement;
XmlNode dataTableRef = emlRoot.SelectSingleNode(MerritConstants.SheetTableXPath, emlNamespaceMgr);
XmlNode parentDataTable = dataTableRef.ParentNode;
StringBuilder attibuteListBuilder;
XElement scaleNode;
var fileColumnType = string.Empty;
var fileColumnUnit = string.Empty;
List<string> sheetIds = new List<string>();
//foreach (var param in request.ParameterMetadata)
foreach (var param in file.FileColumns)
{
var sheetTable = dataTableRef.Clone();
attibuteListBuilder = new StringBuilder();
if (!sheetIds.Contains(param.EntityName))
{
sheetIds.Add(param.EntityName);
foreach (var attributeParam in file.FileColumns.Where(fc => fc.EntityName == param.EntityName).ToList())
{
fileColumnType = string.Empty;
fileColumnUnit = string.Empty;
if (attributeParam.FileColumnTypeId > 0 && fileColumnTypes != null)
{
scaleNode = new XElement("measurementScale");
fileColumnType = fileColumnTypes.Where(fc => fc.FileColumnTypeId == attributeParam.FileColumnTypeId).FirstOrDefault().Name;
if (attributeParam.FileColumnUnitId > 0 && fileColumnUnits != null)
{
fileColumnUnit = fileColumnUnits.Where(fc => fc.FileColumnUnitId == attributeParam.FileColumnUnitId).FirstOrDefault().Name;
}
if (!string.IsNullOrWhiteSpace(fileColumnType))
{
switch (fileColumnType.ToUpperInvariant())
{
case "TEXT":
scaleNode = new XElement("measurementScale", new XElement("nominal", new XElement("nonNumericDomain", new XElement("textDomain", new XElement("definition", System.Security.SecurityElement.Escape(attributeParam.Description))))));
break;
case "DATETIME":
scaleNode = new XElement("measurementScale", new XElement("dateTime", new XElement("formatString", "The user has designated this column as some form of date and/or time. No standard is specified due to DataUp coding constraints.")));
break;
case "NUMERIC":
XElement unitsElement = new XElement("unit", new XElement("standardUnit", System.Security.SecurityElement.Escape(fileColumnUnit)));
if (!string.IsNullOrWhiteSpace(fileColumnUnit))
{
unitsElement = new XElement("unit", new XElement("customUnit", System.Security.SecurityElement.Escape(fileColumnUnit)));
}
scaleNode = new XElement("measurementScale", new XElement("interval", unitsElement, new XElement("numericDomain", new XElement("numberType", "real"))));
break;
}
}
var attibuteNode = new XElement("attribute", new XElement("attributeName", System.Security.SecurityElement.Escape(attributeParam.Name)), new XElement("attributeDefinition", System.Security.SecurityElement.Escape(attributeParam.Description)), scaleNode);
attibuteListBuilder.AppendLine(attibuteNode.ToString().Trim());
}
}
sheetTable.SelectSingleNode("entityName").InnerText = string.Format(CultureInfo.InvariantCulture, "{0} - {1}", System.Security.SecurityElement.Escape(currentFileName), System.Security.SecurityElement.Escape(param.EntityName));
sheetTable.SelectSingleNode("entityDescription").InnerText = System.Security.SecurityElement.Escape(param.EntityDescription);
sheetTable.SelectSingleNode("attributeList").InnerXml = attibuteListBuilder.ToString();
parentDataTable.InsertBefore(sheetTable, dataTableRef);
}
}
parentDataTable.RemoveChild(dataTableRef);
}
private string GetIdentifierRequestBody(MerritQueryData request)
{
StringBuilder body = new StringBuilder();
// Update Profile.
string mszProfile = request["Profile"].Value;
body.AppendLine("--" + MerritConstants.Boundary);
body.AppendLine("Content-disposition: form-data; name=\"profile\"");
body.AppendLine();
body.AppendLine(mszProfile);
body.AppendLine("--" + MerritConstants.Boundary);
// Update ERC
string who = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["Who"].Key, request["Who"].Value);
string what = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["What"].Key, request["What"].Value);
string when = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["When"].Key, request["When"].Value);
string mszErc = string.Format(CultureInfo.InvariantCulture, "{0}%0A{1}%0A{2}", who, what, when);
body.AppendLine("Content-disposition: form-data; name=\"erc\"");
////body.AppendLine("Content-type: text/plain");
body.AppendLine();
body.AppendLine("erc: " + mszErc);
body.AppendLine("--" + MerritConstants.Boundary + "--");
return body.ToString();
}
public string GetIdentifier(MerritQueryData queryData, RepositoryModel repositoryModel)
{
HttpWebRequest httpRequest = null;
HttpWebResponse httpResponse = null;
Stream dataStream = null;
StreamReader reader = null;
string restResponse;
string requestBody = GetIdentifierRequestBody(queryData);
if (queryData != null && repositoryModel != null)
{
IgnoreBadCertificates();
httpRequest = (HttpWebRequest)HttpWebRequest.Create(repositoryModel.RepositoryLink);
httpRequest.ContentType = "multipart/form-data; boundary=" + MerritConstants.Boundary;
httpRequest.Method = "POST";
byte[] buffer = Encoding.UTF8.GetBytes(requestBody);
httpRequest.ContentLength = buffer.Length;
httpRequest.Headers.Add("Authorization", "Basic " + repositoryModel.Authorization);
try
{
dataStream = httpRequest.GetRequestStream();
dataStream.Write(buffer, 0, buffer.Length);
httpResponse = (HttpWebResponse)httpRequest.GetResponse();
}
catch (WebException webException)
{
dataStream.Dispose();
httpResponse = (HttpWebResponse)webException.Response;
if (httpResponse.StatusCode == HttpStatusCode.Unauthorized)
{
return "false|" + "The username or password you entered is incorrect.";
}
else if (httpResponse.StatusCode == HttpStatusCode.NotFound)
{
return "false|" + "Issue with the repository configuration, Contact administrator.";
}
return "false|" + webException.Message;
}
}
if (httpResponse.StatusCode != HttpStatusCode.OK
&& httpResponse.StatusCode != HttpStatusCode.Unauthorized
&& httpResponse.StatusCode != HttpStatusCode.NotFound)
{
return "false|Network Exception";
}
dataStream = httpResponse.GetResponseStream();
reader = new StreamReader(dataStream);
restResponse = reader.ReadToEnd();
reader.Close();
httpResponse.Close();
if (!restResponse.Contains("ark:"))
{
return "false|" + "Issue with the repository configuration, Contact administrator.";
}
// Get Identifier from the response.
return string.Concat("true|", restResponse.Substring(restResponse.IndexOf("ark:", StringComparison.Ordinal)).Trim());
}
private void CreateFile(MerritConstants.FileCreationType fileCreationType, string filePath, MerritQueryData request, Encoding encoding, DM.File file, DM.Repository repository, IEnumerable<DM.FileColumnType> fileColumnTypes = null, IEnumerable<DM.FileColumnUnit> fileColumnUnits = null)
{
StringBuilder arguments = new StringBuilder();
switch (fileCreationType)
{
case MerritConstants.FileCreationType.ManiFest:
arguments.AppendLine("#%dataonem_0.1");
arguments.AppendLine("#%profile | http://uc3.cdlib.org/registry/ingest/manifest/mrt-dataone- manifest");
arguments.AppendLine("#%prefix | dom: | http://uc3.cdlib.org/ontology/dataonem#");
arguments.AppendLine("#%prefix | mrt: | http://uc3.cdlib.org/ontology/mom#");
arguments.AppendLine("#%fields | dom:scienceMetadataFile | dom:scienceMetadataFormat | dom:scienceDataFile | mrt:mimeType");
ArrayList files = ZipUtilities.GenerateFileList(Path.GetDirectoryName(filePath));
foreach (string fileName in files)
{
var tempName = System.IO.Path.GetFileName(fileName);
arguments.AppendLine(MerritConstants.MrtErcFile + " | ERC | " + tempName + " | text/plain");
arguments.AppendLine(MerritConstants.MrtEmlFile + " | eml://ecoinformatics.org/eml-2.1.1 | " + tempName + " | text/xml");
}
arguments.AppendLine("#%eof");
break;
case MerritConstants.FileCreationType.ERC:
string who = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["who"].Key, request["who"].Value);
string what = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["what"].Key, request["what"].Value);
string when = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["when"].Key, request["when"].Value);
string where = string.Format(CultureInfo.InvariantCulture, "{0}: {1}", request["where"].Key, request["where"].Value);
arguments.AppendLine("erc:");
arguments.AppendLine(who);
arguments.AppendLine(what);
arguments.AppendLine(when);
arguments.AppendLine(where);
break;
case MerritConstants.FileCreationType.EML:
WriteEML(request, filePath, file, repository, fileColumnTypes, fileColumnUnits);
break;
}
using (FileStream fileStream = new FileStream(filePath, FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
if (encoding != null)
{
fileStream.Write(encoding.GetBytes(arguments.ToString()), 0, encoding.GetByteCount(arguments.ToString()));
}
}
}
/// <summary>
/// Helper method to get the identifier from merrit.
/// </summary>
/// <param name="postFileData"></param>
/// <param name="authorization"></param>
/// <returns></returns>
protected string GetIdentifier(PublishMessage postFileData, string authorization, string identifierUrl, Citation citation)
{
Check.IsNotNull(postFileData, "postFileData");
Check.IsNotNull(authorization, "authorization");
Check.IsNotNull(identifierUrl, "identifierUrl");
var file = this.GetFileByFileId(postFileData.FileId);
MerritQueryData queryData = new MerritQueryData();
queryData.KeyValuePair = new List<DKeyValuePair<string, string>>()
{
new DKeyValuePair<string, string> { Key = "Profile", Value = "oneshare_ark_only" },
new DKeyValuePair<string, string> { Key = "Who", Value = citation.Publisher },
new DKeyValuePair<string, string> { Key = "What", Value = citation.Title},
new DKeyValuePair<string, string> { Key = "When", Value = DateTime.UtcNow.ToString(CultureInfo.InvariantCulture) }
}.ToArray();
RepositoryModel repositoryModel = new RepositoryModel()
{
Authorization = authorization,
RepositoryLink = identifierUrl,
RepositoryName = MerritConstants.OneShare
};
return this.RepositoryAdapter.GetIdentifier(queryData, repositoryModel);
}
/// <summary>
/// Helper method to get the post query data.
/// </summary>
/// <param name="identifier">Unique identifier.</param>
/// <param name="fileData">File information.</param>
/// <param name="postFileData">Post file indormation.</param>
/// <returns></returns>
protected MerritQueryData GetPostQueryData(string identifier, DM.File fileData, Citation citation, Repository repository, PublishMessage postFileData)
{
Check.IsNotNull(identifier, "identifier");
MerritQueryData queryData = new MerritQueryData();
// TODO: Currently hard coded, needs to be replaced with specific value
queryData.MetadataXML = @"<eml:eml packageId=""doi:10.5072/12345?"" system=""DCXL"" xmlns:eml=""eml://ecoinformatics.org/eml2.1.0"" xmlns:xsi=""http://www.w3.org/2001/XMLSchema-instance"" xsi:schemaLocation=""eml://ecoinformatics.org/eml-2.1.0 eml.xsd""> <dataset id=""doi:10.5072/12345""> <creator> <!-- http://knb.ecoinformatics.org/software/eml/eml-2.1.0/eml-resource.html#creator --> <!-- multiple creators allowed --> <individualName> <givenName></givenName> <surName></surName> </individualName> <address> <deliveryPoint></deliveryPoint> <city></city> <administrativeArea></administrativeArea><postalCode></postalCode><country></country></address><phone></phone><electronicMailAddress></electronicMailAddress><organizationName></organizationName></creator><title></title><pubDate></pubDate><abstract><para></para></abstract><publisher><para></para></publisher><url></url><contact><individualName><givenName></givenName><surName></surName></individualName><address><deliveryPoint></deliveryPoint><city></city><administrativeArea></administrativeArea><postalCode></postalCode><country></country></address><phone></phone><electronicMailAddress></electronicMailAddress><organizationName></organizationName></contact><keywordSet><keyword></keyword><keywordThesaurus></keywordThesaurus></keywordSet><coverage><!-- http://knb.ecoinformatics.org/software/eml/eml-2.1.0/eml-resource.html#coverage --> <geographicCoverage><geographicDescription></geographicDescription><boundingCoordinates><westBoundingCoordinate></westBoundingCoordinate><eastBoundingCoordinate></eastBoundingCoordinate><northBoundingCoordinate></northBoundingCoordinate><southBoundingCoordinate></southBoundingCoordinate></boundingCoordinates></geographicCoverage><temporalCoverage id=""tempcov""><rangeOfDates> <beginDate><calendarDate></calendarDate></beginDate><endDate><calendarDate></calendarDate></endDate></rangeOfDates></temporalCoverage></coverage><project><!-- http://knb.ecoinformatics.org/software/eml/eml-2.1.0/eml-dataset.html#project --><title></title><abstract><para></para></abstract><funding><para></para></funding></project> <intellectualRights> <para></para> </intellectualRights> <dataTable> <!-- http://knb.ecoinformatics.org/software/eml/eml-2.1.0/eml-dataTable.html#dataTable --> <!-- dataTable is equivalent to a single tab in the excel spreadsheet. One can have multiple data tables within the document. --> <entityName></entityName> <entityDescription></entityDescription> <attributeList> <!-- http://knb.ecoinformatics.org/software/eml/eml-2.1.0/eml-dataTable.html#attributeList --> <!-- attribute list is equivalent to the parameter table from the requirements document. One can have many attributes in a single table. --> <attribute> <attributeName> <!-- non-empty string --></attributeName> <attributeDefinition> <!-- non-empty string --></attributeDefinition> </attribute> </attributeList> </dataTable> </dataset> <additionalMetadata> <describes>tempcov</describes> <metadata> <description> <!-- non-empty string describing temporal coverage --> </description> </metadata> </additionalMetadata> <additionalMetadata> <metadata> <formattedCitation> <!-- non-empty string --> </formattedCitation> </metadata> </additionalMetadata></eml:eml>";
List<DKeyValuePair<string, string>> content = new List<DKeyValuePair<string, string>>();
Check.IsNotNull<DM.Repository>(repository, "selectedRepository");
var repositoryMetadata = repository.RepositoryMetadata.FirstOrDefault();
if (repositoryMetadata != null)
{
foreach (var repositoryMetaData in repositoryMetadata.RepositoryMetadataFields)
{
DKeyValuePair<string, string> metadata = new DKeyValuePair<string, string>();
metadata.Key = repositoryMetaData.Name;
var metadataField = fileData.FileMetadataFields.Where(f => f.RepositoryMetadataFieldId == repositoryMetaData.RepositoryMetadataFieldId).FirstOrDefault();
if (metadataField != null)
{
metadata.Value = fileData.FileMetadataFields.Where(f => f.RepositoryMetadataFieldId == repositoryMetaData.RepositoryMetadataFieldId).FirstOrDefault().MetadataValue;
}
content.Add(metadata);
}
}
//set the data to filemetadata fields
//postFileData.FileMetaDataFields = fileData.FileMetadataFields;
content.Add(new DKeyValuePair<string, string>() { Key = "Profile", Value = ConfigReader<string>.GetSetting("Profile_Post") });
content.Add(new DKeyValuePair<string, string>() { Key = "who", Value = citation.Publisher });
content.Add(new DKeyValuePair<string, string>() { Key = "what", Value = citation.Title });
content.Add(new DKeyValuePair<string, string>() { Key = "when", Value = DateTime.UtcNow.ToString(CultureInfo.InvariantCulture) });
content.Add(new DKeyValuePair<string, string>() { Key = "where", Value = identifier });
content.Add(new DKeyValuePair<string, string>() { Key = "ARK", Value = identifier });
queryData.KeyValuePair = content.ToArray();
return queryData;
}
