public Server(int port)
{
Version = 1;
Methods = new Methods();
Subscriptions = new Subscriptions();
Publications = new Publications();
new PublicationMethods(this).AttachMethods();
var messageMethods = new MessageMethods(this).GetMethods();
var messageProcessor = new MessageProcessor(messageMethods);
_messageQueue = new ResultQueue<KeyValuePair<IWebSocketConnection, string>>(messageProcessor);
_connector = new Connector(this, "127.0.0.1", port);
}
public async Task <IActionResult> Create([Bind("Id,Books_Copies,Publisher_detailId,Books_detailId")] Publications publications)
{
if (ModelState.IsValid)
{
_context.Add(publications);
await _context.SaveChangesAsync();
return(RedirectToAction(nameof(Index)));
}
ViewData["Books_detailId"] = new SelectList(_context.Books, "Id", "Tittle", publications.Books_detailId);
ViewData["Publisher_detailId"] = new SelectList(_context.Publisher, "Id", "Publisher_Name", publications.Publisher_detailId);
return(View(publications));
}
public void UpdateRatingForPublication(int publicationId)
{
var publication = Publications.Include(pub => pub.Reviews).Where(p => p.Id == publicationId).FirstOrDefault();
if (publication.Reviews.Count > 0)
{
publication.Rating = publication.Reviews.Average(rev => rev.Rating);
}
else
{
publication.Rating = 0;
}
Publications.Update(publication);
}
private void ListBook_Load(object sender, EventArgs e)
{
inpu = new List <Input>();
Books books = new Books();
inpu = books.selected();
int currentX = 20, currentY = 5;
// MessageBox.Show(inpu.Count()+"");
for (int i = 0; i <= inpu.Count() - 1; i++)
{
ListOfData lsd = new ListOfData();
lsd.namee = inpu[i].Title;
Authors authors = new Authors();
// MessageBox.Show(inpu[i].Isbn + "");
authorsId = authors.selectedAuthorId(inpu[i].Isbn);
if (authorsId.Count() != 0)
{
for (int c = 0; c <= authorsId.Count() - 1; c++)
{
authorsName.Add(authors.selectedAuthorName(authorsId[c]));
//MessageBox.Show("m " + authorsId[c] + " authorsId[c] " + authorsName[c]+" authorsName[c]");
inpu[i].Name = inpu[i].Name + "|" + authorsName[c];
}
lsd.family = "..." + authorsName[0];
}
// MessageBox.Show(inpu[i].Name + "");
Publications publications = new Publications();
publicId = publications.selectedpublicationsId(inpu[i].Isbn);
inpu[i].Family = publications.selectedpublicationName(publicId);
lsd.code = inpu[i].Family;
lsd.number = inpu[i].Isbn;
lsd.btnTagDelete = inpu[i].Isbn + "*";
lsd.btnTagDetails = i;
authorsName.Clear();
if (i % 2 == 0)
{
lsd.colour = "#EDF0FC";
}
else
{
lsd.colour = "#ffffff";
}
lsd.Location = new Point(currentX, currentY);
this.panel5.Controls.Add(lsd);
currentY = currentY + 50;
}
}
// GET: Publications/Details/5
public ActionResult Details(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
Publications publications = db.Publications.Find(id);
if (publications == null)
{
return(HttpNotFound());
}
return(View(publications));
}
public async Task <JsonResult> OnPostGetPDF([FromBody] Publications publication)
{
var token = HttpContext.Session.GetString("token");
var id = User.Claims.Where(x => x.Type == "Id").Select(x => x.Value).SingleOrDefault();
var l = await this._aS.RefreshToken(id, CultureInfo.CurrentCulture.Name, "SUPPLIER", token);
if (l.Error == null)
{
HttpContext.Session.SetString("token", l.Token);
}
var refreshToken = "Token refreshed";
return(new JsonResult(refreshToken));
}
public async Task <ActionResult <Users> > AddPublication()
{
try
{
using (var reader = new StreamReader(Request.Body))
{
var body = reader.ReadToEnd();
dynamic data = JsonConvert.DeserializeObject(body);
Publications publication = new Publications();
publication.Date = data["date"];
publication.Description = data["description"];
publication.Userid = data["userId"];
_context.Publications.Add(publication);
await _context.SaveChangesAsync();
var files = data["files"];
foreach (var file in files)
{
Contents content = new Contents();
content.Format = file["format"];
content.Src = file["src"];
_context.Contents.Add(content);
await _context.SaveChangesAsync();
var contentId = content.Id;
PublicationContents publicationContent = new PublicationContents();
publicationContent.Contentid = contentId;
publicationContent.Pubid = publication.Id;
_context.PublicationContents.Add(publicationContent);
await _context.SaveChangesAsync();
}
return(Json(new { success = true, pubId = publication.Id }));
}
}
catch (System.Exception e)
{
System.Diagnostics.Debug.Write(e);
return(Json(new
{
success = false,
message = "Could not add user to the Data Base"
}));
}
}
public Publications LoadPublications(string fileName)
{
Publications publications = null;
using (TextReader textReader = new StreamReader(fileName))
{
using (XmlTextReader reader = new XmlTextReader(textReader))
{
reader.Namespaces = false;
XmlSerializer serializer = new XmlSerializer(typeof(Publications));
publications = (Publications)serializer.Deserialize(reader);
}
}
return(publications);
}
public void TestLongGrantID()
{
Publication p = new Publication();
Assert.IsNull(p.Grants);
Publications.ProcessMedlineTag(ref p, "GR - GM 28356/GM/NIGMS", pubTypes);
Publications.ProcessMedlineTag(ref p, "GR - AM18811/AM/NIADDK", pubTypes);
Publications.ProcessMedlineTag(ref p, "GR - HD09690/HD/NICHD", pubTypes);
Publications.ProcessMedlineTag(ref p, "GR - AG11624/AG/NIA", pubTypes);
Publications.ProcessMedlineTag(ref p, "GR - AG20557/AG/NIA", pubTypes);
Assert.IsTrue(p.Grants.Count == 5);
foreach (string Grant in new string[] { "GM 28356/GM/NIGMS", "AM18811/AM/NIADDK",
"HD09690/HD/NICHD", "AG11624/AG/NIA", "AG20557/AG/NIA" })
{
Assert.IsTrue(p.Grants.Contains(Grant));
}
}
public override int GetHashCode()
{
unchecked
{
var hashCode = (Basics != null ? Basics.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Work != null ? Work.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Volunteer != null ? Volunteer.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Education != null ? Education.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Awards != null ? Awards.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Publications != null ? Publications.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Skills != null ? Skills.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Languages != null ? Languages.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Interests != null ? Interests.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (References != null ? References.GetHashCode() : 0);
return(hashCode);
}
}
private void UpdatePublications(List <Publication> newList, bool isOffline = false)
{
bool isDataChanged = false;
if (Publications != null)
{
if (newList == null)
{
Publications = null;
isDataChanged = true;
}
else
{
var newCollection = new List <PublicationViewModel>();
foreach (var publication in newList)
{
var currrentPublicaton = Publications.FirstOrDefault(x => x.BookId == publication.BookId);
if (currrentPublicaton != null)
{
if (currrentPublicaton.Version != publication.CurrentVersion.ToString() || isOffline)
{
currrentPublicaton.UpdateData(publication);
isDataChanged = true;
}
newCollection.Add(currrentPublicaton);
}
else
{
newCollection.Add(new PublicationViewModel(publication));
isDataChanged = true;
}
}
Publications = newCollection;
}
}
else
{
Publications = newList == null ? null : newList.Select(x => new PublicationViewModel(x)).ToList();
isDataChanged = true;
}
if (isDataChanged)
{
FilterData();
SessionService.SessionState[ALL_PUBLICATIONS_SESSION_KEY] = Publications;
}
}
public void EmptyPublicationList()
{
string emptySearchResults = @"<?xml version=""1.0"" encoding=""UTF-8""?>
<eFetchResult>
<ERROR>Empty result - nothing to do</ERROR>
</eFetchResult>";
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
Publications mpr = new Publications(emptySearchResults, ptc);
Assert.IsNull(mpr.PublicationList);
}
// GET: Publications/Edit/5
public ActionResult Edit(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
Publications publications = db.Publications.Find(id);
Student student = publications.Student;
if (publications == null)
{
return(HttpNotFound());
}
ViewBag.PubMonthId = new SelectList(db.CommonFields.Where(o => o.Category == "Months"), "ID", "Name", publications.PubMonthId);
ViewBag.Student = student;
ViewBag.StudentID = student.Id;
return(View(publications));
}
// GET: Publications/Delete/5
public ActionResult Delete(int?id)
{
if (id == null)
{
TempData["msg"] = "<script>alert('Sorry! No record found to delete.')</script>";
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
Publications publications = db.Publications.Find(id);
if (publications == null)
{
TempData["msg"] = "<script>alert('Sorry! No record found to delete.')</script>";
return(HttpNotFound());
}
int sendId = (int)id;
return(DeleteConfirmed(sendId));
}
public async Task <IActionResult> Create([Bind("PublicationId,GameId,PublisherId")] Publications publications)
{
bool duplicate = await _context.Publications.AnyAsync(l => l.GameId.Equals(publications.GameId) && l.PublisherId.Equals(publications.PublisherId));
if (duplicate)
{
ModelState.AddModelError("", "Така публікація вже додана");
}
if (ModelState.IsValid)
{
_context.Add(publications);
await _context.SaveChangesAsync();
return(RedirectToAction(nameof(Index)));
}
ViewData["GameId"] = new SelectList(_context.Games, "GameId", "Name", publications.GameId);
ViewData["PublisherId"] = new SelectList(_context.Publishers, "PublisherId", "Name", publications.PublisherId);
return(View(publications));
}
private void button4_Click(object sender, EventArgs e)
{
if (n_e == false)
{
string name = txtName.Text;
string family = txtFamily.Text;
Authors authores = new Authors();
authores.name = txtName.Text;
authores.family = txtFamily.Text;
authores.insert();
fill_datagridview_nevisande_select();
}
else
{
Publications publications = new Publications();
publications.name = txtName.Text;
publications.insert();
fill_datagridview_entesharat_select();
}
}
public void TestCreateFromDatabase()
{
// Add a publication to the database
Database DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
Publication write = CreateTestPublication();
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
Publications.WriteToDB(write, DB, ptc, new string[] { "eng" });
// Read it back
Publication read;
Assert.IsTrue(Publications.GetPublication(DB, 15904469, out read, false));
TestCreatedPublication(read);
}
private void button1_Click(object sender, EventArgs e)
{
Calender cl = new Calender();
DateTime d1 = DateTime.Now;
string dateShamse = cl.MilliTimeStamp(d1);
if (txtTitle.Text != "" && txtYear.Text != "" && txtNumber.Text != "" && txtIsbn.Text != "" && txtPublication.Text != "" && txtC.Text != "" && panel10.Enabled)
{
Books books = new Books();
books.isbn = txtIsbn.Text;
books.title = txtTitle.Text;
books.yearPublication = Convert.ToInt16(txtYear.Text);
books.numberBook = Convert.ToInt16(txtNumber.Text);
books.picture = pic.Tag.ToString();
books.date = dateShamse;
int i = books.insert();
for (int c = 0; c < A_id.Count(); c++)
{
Authors authors = new Authors();
authors.insertToBook_Writtenby(A_id[c], txtIsbn.Text);
}
A_id.Clear();
Publications publications = new Publications();
publications.insertToBooks_published(P_id, txtIsbn.Text);
if (i == 1)
{
MessageBox.Show("با موفقیت ثبت شد ");
//each(2);
}
else
{
MessageBox.Show(" خطا در ثبت ");
}
}
else
{
MessageBox.Show("لطفا اطلاعات را کامل وارد کنید ", "هشدار");
}
}
private void FilterData()
{
readyForReorder = false;
FiltedPublications.Clear();
if (Publications != null)
{
switch (SelectedFilter)
{
case FILTER_VALUE_ALL:
Publications.ForEach(x => FiltedPublications.Add(x));
break;
case FILTER_VALUE_LOAN:
Publications.ForEach(x =>
{
if (x.IsLoan)
{
FiltedPublications.Add(x);
}
});
break;
case FILTER_VALUE_SUBSCRIPTION:
Publications.ForEach(x =>
{
if (!x.IsLoan)
{
FiltedPublications.Add(x);
}
});
break;
}
}
PublicationCount = FiltedPublications.Count();
readyForReorder = true;
}
public async Task <Task> Publicar([FromBody] Offert oferta)
{
Publications resultado = new Publications()
{
Error = new Exception("Invalid offert")
};
resultado = await this._aS.OfferPublication(oferta, oferta.Token);
if (resultado.Errors != null)
{
return(Clients.Caller.SendAsync("Publications", resultado));
}
if (resultado.Error != null)
{
return(Clients.Caller.SendAsync("Publications", resultado));
}
resultado.Bids = new List <Bids>()
{
new Bids()
{
Factor = new People()
{
Id = oferta.Factor_id
}
}
};
if (oferta.Factor_id == resultado.Bids[0].Factor_id)
{
resultado.isOffered = true;
}
return(Clients.Group(resultado.Invoice.Country.Value + "").SendAsync("Publications", resultado));
}
public static void Main()
{
Contanct[] contacts = new Contanct[6];
contacts[0] = new Contact(
"Dick", "Traci",
"123 Main St., Spokane, WA 99037",
"123-123-1234"
);
//...
// 클래스는 지원되는 인터페이스로 암시적 변환된다.
catacts.List(Contact.Headers);
Console.WriteLine();
Publication[] publications = new Publication[3] {
new Publication("Celebration of Discipline", "Richard Foster", 1978),
new Publication("Orthodoxy", "G.K. Chesterton", 1908),
new Publication("The Hitchhiker's Guide to thr Galaxy", "Douglas Adams", 1979)
};
Publications.List(Publication.Headers);
}
async Task ExecuteLoadGivesCommand()
{
IsBusy = true;
try
{
Publications.Clear();
var publications = await DataStoreGive.GetItemsAsync(true);
foreach (var publication in publications)
{
Publications.Add(publication);
}
}
catch (Exception ex)
{
Debug.WriteLine(ex);
}
finally
{
IsBusy = false;
}
}
public async Task <JsonResult> OnPostOfertar([FromBody] Offert oferta)
{
var token = HttpContext.Session.GetString("token");
Publications data = new Publications();
oferta.Factor_id = this._signInManager.UserManager.GetUserId(User);
data = await this._aS.OfferPublication(oferta, token);
if (data.Error == null)
{
var id = User.Claims.Where(x => x.Type == "Id").Select(x => x.Value).SingleOrDefault();
var l = await this._authS.RefreshToken(id, CultureInfo.CurrentCulture.Name, "FACTOR", token);
if (l.Error == null)
{
HttpContext.Session.SetString("token", l.Token);
}
}
return(new JsonResult(data));
}
public async Task <IActionResult> Edit(int id, [Bind("PublicationId,GameId,PublisherId")] Publications publications)
{
bool duplicate = await _context.Publications.AnyAsync(l => l.GameId.Equals(publications.GameId) && l.PublisherId.Equals(publications.PublisherId) && !l.PublicationId.Equals(publications.PublicationId));
if (duplicate)
{
ModelState.AddModelError("", "Така публікація вже додана");
}
if (id != publications.PublicationId)
{
return(NotFound());
}
if (ModelState.IsValid)
{
try
{
_context.Update(publications);
await _context.SaveChangesAsync();
}
catch (DbUpdateConcurrencyException)
{
if (!PublicationsExists(publications.PublicationId))
{
return(NotFound());
}
else
{
throw;
}
}
return(RedirectToAction(nameof(Index)));
}
ViewData["GameId"] = new SelectList(_context.Games, "GameId", "Name", publications.GameId);
ViewData["PublisherId"] = new SelectList(_context.Publishers, "PublisherId", "Name", publications.PublisherId);
return(View(publications));
}
public virtual IPublication Publish(IComputed computed)
{
ThrowIfDisposedOrDisposing();
var spinWait = new SpinWait();
while (true)
{
var p = Publications.GetOrAddChecked(
computed.Input,
(key, arg) => {
var(this1, computed1) = arg;
var id = this1.PublicationIdGenerator.Next();
var p1 = this1.PublicationFactory.Create(this1.PublicationGeneric, this1, computed1, id, Clock);
this1.PublicationsById[id] = p1;
p1.RunAsync();
return(p1);
}, (this, computed));
if (p.Touch())
{
return(p);
}
spinWait.SpinOnce();
}
}
private async Task ReorderPublications()
{
if (SelectedFilter == FILTER_VALUE_ALL)
{
for (int i = 0; i < FiltedPublications.Count; i++)
{
Publications[i] = FiltedPublications[i];
}
}
else
{
int j = 0;
foreach (var p in FiltedPublications)
{
while (Publications[j].IsLoan != p.IsLoan)
{
j++;
}
Publications[j] = p;
j++;
}
}
await PublicationUtil.Instance.OrganiseDlsOrder(Publications.Select(x => x.BookId).ToList());
}
static void Run1()
{
Console.Write("hello \n");
string authorstxt = @"C:\Users\jakub\Documents\Visual Studio 2017\dblp-reducer\data\Authors_short.txt";
string authorsxml = @"C:\dblp_result\636733187090414687\Authors.xml";
string publicationsxml = @"C:\dblp_result\636733187090414687\Publications.xml";
// TODO: load list of restricted authors
List <string> AuthorsName = Loader.TextListLoader.LoadAuthors(authorstxt);
// TODO: load authors.xml
Loader.XmlLoader XmlParser = new Loader.XmlLoader();
Authors parsedData = XmlParser.LoadAuthors(authorsxml);
// TODO: Find authors from restricted list in xml file and return list of ids
List <Author> AuthorsList = parsedData.AuthorsList;
int TotalCount = AuthorsName.Count;
HashSet <Author> FoundAuthorsList = new HashSet <Author>();
Dictionary <string, string> FoundNames = new Dictionary <string, string>();
foreach (string queryName in AuthorsName)
{
var item = AuthorsList.Where(x => Compare(x.Name, queryName)).FirstOrDefault();
if (item != null && !FoundNames.ContainsKey(queryName))
{
FoundNames.Add(queryName, item.Name);
FoundAuthorsList.Add(item);
}
}
bool Compare(string nameA, string nameB)
{
if (nameA == nameB)
{
return(true);
}
else
{
int LastSpaceIndexA = nameA.LastIndexOf(' ');
int LastSpaceIndexB = nameB.LastIndexOf(' ');
if (LastSpaceIndexA > 0 && LastSpaceIndexB > 0)
{
string nameALastName = nameA.Substring(LastSpaceIndexA, (nameA.Length - LastSpaceIndexA));
string nameBLastName = nameB.Substring(LastSpaceIndexB, (nameB.Length - LastSpaceIndexB));
if (nameALastName == nameBLastName)
{
if (nameA.Substring(0, (nameA.IndexOf(' '))) == nameB.Substring(0, (nameB.IndexOf(' '))))
{
return(true);
}
}
}
}
return(false);
}
// TODO: Print stats
Console.WriteLine("Count of found = " + FoundAuthorsList.Count + " of " + TotalCount);
foreach (KeyValuePair <string, string> kvp in FoundNames)
{
Console.WriteLine(kvp.Key + " - " + kvp.Value);
}
Console.WriteLine("-------------------");
foreach (string name in AuthorsName)
{
if (!FoundNames.ContainsKey(name))
{
Console.WriteLine(name);
}
}
// TODO: Load publications.xml
Publications publications = XmlParser.LoadPublications(publicationsxml);
// TODO: Walkthrou publications and find coauthors.
bool first = true;
Dictionary <int, List <int> > CooperationNetwork = new Dictionary <int, List <int> >();
foreach (Publication publication in publications.PublicationsList)
{
first = true;
foreach (Author author in publication.AuthorsList)
{
if (FoundAuthorsList.Contains(author))
{
if (first)
{
CooperationNetwork.Add(publication.Id, new List <int>());
CooperationNetwork[publication.Id].Add(author.Id);
first = false;
}
else
{
CooperationNetwork[publication.Id].Add(author.Id);
}
}
}
}
Dictionary <int, List <int> > AnotherDic = new Dictionary <int, List <int> >();
Dictionary <int, int> NodeToIndexDict = new Dictionary <int, int>();
Dictionary <int, int> IndexToNodeDict = new Dictionary <int, int>();
int index = 0;
foreach (KeyValuePair <int, List <int> > item in CooperationNetwork)
{
if (item.Value.Count >= 2)
{
AnotherDic.Add(item.Key, item.Value);
foreach (int author in item.Value)
{
if (!NodeToIndexDict.ContainsKey(author))
{
NodeToIndexDict.Add(author, index);
IndexToNodeDict.Add(index, author);
index++;
}
}
}
}
int[,] WeightedAdjacencyMatrix = new int[NodeToIndexDict.Count, NodeToIndexDict.Count];
foreach (KeyValuePair <int, List <int> > item in CooperationNetwork)
{
for (int i = 0; i < item.Value.Count - 1; i++)
{
WeightedAdjacencyMatrix[NodeToIndexDict[item.Value[i]], NodeToIndexDict[item.Value[i + 1]]]++;
}
}
// TODO: Export network of coauthors to file
GmlExporter exporter = new GmlExporter();
exporter.Export("stanford.gml", FoundAuthorsList.ToList(), WeightedAdjacencyMatrix, IndexToNodeDict);
Console.WriteLine("DONE");
}
public void TestPubsReportRow()
{
// Set up the database with test publications (and don't forget to add the
// publication types!)
DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
PublicationTypes PubTypes = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
PubTypes.WriteToDB(DB);
reports = new Reports(DB, AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestReports\\pubmed_jifs.xls");
Assert.IsTrue(reports.Weights.Count == 10);
TestHarvester.GetPublicationsFromInput1XLS_Using_MockNCBI(false, new string[] { "eng" }, 22);
people = new People(DB);
foreach (Person person in people.PersonList)
{
Publications pubs = new Publications(DB, person, false);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
DataRow Row = WriteAndReadBackCSVRow(reports.PubsReportRow(person, pub));
switch (pub.PMID)
{
case 15249795:
// 0. setnb
Assert.IsTrue(Row.ItemArray[0].ToString() == "A5401532");
// 1. pmid
Assert.IsTrue(Row.ItemArray[1].ToString() == "15249795");
// 2. journal_name
Assert.IsTrue(Row.ItemArray[2].ToString() == "J Clin Hypertens (Greenwich)");
// 3. year
Assert.IsTrue(Row.ItemArray[3].ToString() == "2004");
// 4. Month
Assert.IsTrue(Row.ItemArray[4].ToString() == "Jul");
// 5. day
Assert.IsTrue(Row.ItemArray[5].ToString() == "");
// 6. title
Assert.IsTrue(Row.ItemArray[6].ToString() == "Interview with Louis Tobian, MD. Interview by Marvin Moser.");
// 7. Volume
Assert.IsTrue(Row.ItemArray[7].ToString() == "6");
// 8. issue
Assert.IsTrue(Row.ItemArray[8].ToString() == "7");
// 9. position
Assert.IsTrue(Row.ItemArray[9].ToString() == "1");
// 10. nbauthors
Assert.IsTrue(Row.ItemArray[10].ToString() == "1");
// 11. Bin
Assert.IsTrue(Row.ItemArray[11].ToString() == "0");
// 12. Pages
Assert.IsTrue(Row.ItemArray[12].ToString() == "391-2");
// 13. Publication_type
Assert.IsTrue(Row.ItemArray[13].ToString() == "Historical Article");
break;
}
}
}
}
}
public void TestPeopleReportRows()
{
// Set up the database with test publications (and don't forget to add the
// publication types!)
DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
PublicationTypes PubTypes = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
PubTypes.WriteToDB(DB);
reports = new Reports(DB, AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestReports\\pubmed_jifs.xls");
Assert.IsTrue(reports.Weights.Count == 10);
TestHarvester.GetPublicationsFromInput1XLS_Using_MockNCBI(false, new string[] { "eng" }, 22);
people = new People(DB);
foreach (Person person in people.PersonList)
{
Publications pubs = new Publications(DB, person, false);
switch (person.Setnb)
{
case "A6009400":
// Van Eys has two publications in 1998, both have zero weight
DataRow Row = WriteAndReadBackCSVRow(reports.ReportRow(person, pubs, 1998));
Assert.IsTrue(Row.ItemArray.Length == 74);
Assert.IsTrue(Row.ItemArray[0].ToString() == "A6009400");
Assert.IsTrue(Row.ItemArray[1].ToString() == "1998");
// Verify that all values are zero, except for pubcount (#3),
// pubcount_pos1 (#5), 123pubcount (#15), 123pubcount_pos1 (#17),
// 3pubcount (#51), 3pubcount_pos1 (#53)
for (int i = 2; i <= 73; i++)
{
if ((i == 2) || (i == 4) || (i == 14) || (i == 16) ||
(i == 50) || (i == 52))
{
Assert.IsTrue(Row.ItemArray[i].ToString() == "2", "Failed at i == " + i.ToString());
}
else
{
Assert.IsTrue(Row.ItemArray[i].ToString() == "0", "Failed at i == " + i.ToString());
}
}
break;
case "A5401532":
// Tobian has two publications in 1997 of type 3 with a
// combined weight of 4.602
Row = WriteAndReadBackCSVRow(reports.ReportRow(person, pubs, 1997));
Assert.IsTrue(Row.ItemArray.Length == 74);
Assert.IsTrue(Row.ItemArray[0].ToString() == "A5401532");
Assert.IsTrue(Row.ItemArray[1].ToString() == "1997");
// Verify that all values are zero, except for pubcount (#3),
// pubcount_pos1 (#5), 123pubcount (#15), 123pubcount_pos1 (#17),
// 3pubcount (#51), 3pubcount_pos1 (#53), which should be 2
//
// and wghtd_pubcount (#4), wghtd_pubcount_pos1 (#6),
// wghtd_123pubcount (#16), wghtd_123pubcount_pos1 (#18),
// wghtd_3pubcount (#52), wghtd_3pubcount_pos1 (#54),
// which should be 4.602
for (int i = 2; i <= 73; i++)
{
if ((i == 2) || (i == 4) || (i == 14) || (i == 16) ||
(i == 50) || (i == 52))
{
Assert.IsTrue(Row.ItemArray[i].ToString() == "2", "Failed at i == " + i.ToString());
}
else if ((i == 3) || (i == 5) || (i == 15) || (i == 17) ||
(i == 51) || (i == 53))
{
Assert.IsTrue(Row.ItemArray[i].ToString() == "4.602", "Failed at i == " + i.ToString());
}
else
{
Assert.IsTrue(Row.ItemArray[i].ToString() == "0", "Failed at i == " + i.ToString());
}
}
break;
}
}
}
private Tool ExtractPublications(Tool info)
{
if (info == null)
{
return(null);
}
foreach (var filename in info.XMLFiles)
{
Logger.LogDebug(
$"Extracting publication info from XML file " +
$"`{Path.GetFileNameWithoutExtension(filename)}` " +
$"of tool `{info.Name}`.");
try
{
XElement toolDoc = XElement.Load(filename);
foreach (var item in toolDoc.Elements("citations").Descendants())
{
if (item.Attribute("type") != null)
{
switch (item.Attribute("type").Value.Trim().ToUpperInvariant())
{
case "DOI":
if (!Publications.ContainsKey(info.ID))
{
Publications.TryAdd(info.ID, new List <Publication>());
}
Publications[info.ID].Add(new Publication()
{
DOI = item.Value
});
/// Some tools have one BibItem that contains only DOI, and
/// another BibItem that contains publication info. There should
/// be only one BibItem per publication contains both DOI and
/// publication info. Therefore, for tools with two bibitems,
/// we consider only the one containing DOI.
continue;
case "BIBTEX":
try
{
if (TryParseBibitem(item.Value, out Publication pub))
{
if (!Publications.ContainsKey(info.ID))
{
Publications.TryAdd(info.ID, new List <Publication>());
}
Publications[info.ID].Add(pub);
}
}
catch (ArgumentException e)
{
Logger.LogDebug(
$"Error extracting publication from XML file of tool " +
$"`{info.Name}`:{e.Message}");
}
break;
}
}
}
Logger.LogDebug(
$"Successfully extract publication info from XML file " +
$"`{Path.GetFileNameWithoutExtension(filename)}` " +
$"of tool `{info.Name}`.");
}
catch (System.Xml.XmlException e)
{
/// This exception may happen if the XML
/// file has multiple roots.
Logger.LogDebug(
$"Failed extracting publication info from XML file " +
$"`{Path.GetFileNameWithoutExtension(filename)}`" +
$" of tool `{info.Name}`: {e.Message}");
return(null);
}
}
return(info);
}
/// <summary>
/// Add five extra articles to the database for Tobian and Bunn
/// </summary>
public static void CreateExtraArticlesForTobianAndBunn(Database DB, PublicationTypes PubTypes, string[] Languages)
{
// Create people objects for Tobian and Bunn
Person Tobian = new Person("A5401532", "Louis", "", "Tobian", true,
new String[] { "tobian l", "tobian l jr", "tobian lj" },
"(\"tobian l\"[au] OR \"tobian l jr\"[au] OR \"tobian lj\"[au])");
Person Bunn = new Person("A4800524", "PAUL", "A.", "BUNN", true,
new String[] { "bunn p jr", "bunn pa jr", "bunn pa", "bunn p" },
"((\"bunn pa jr\"[au] or \"bunn p jr\"[au]) or ((\"bunn p\"[au] or \"bunn pa\"[au]) and (lymphoma or cancer)) and 1970:2005[dp])");
// First, add a few more publications to the colleague.
Publication pub = new Publication();
string[] Authors = new String[] { "TOBIAN L", "BUNN P" };
pub.Year = 1993;
pub.Journal = "Fake Journal";
pub.Authors = Authors;
pub.PMID = 22222222;
pub.Title = "Fake article #1";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "BUNN P", "TOBIAN L" };
pub.Year = 1996;
pub.Journal = "Xenotransplantation";
pub.Authors = Authors;
pub.PMID = 12345678;
pub.Title = "Fake article #2";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "TOBIAN L", "BUNN P" };
pub.Year = 1996;
pub.Journal = "Fake Journal";
pub.Authors = Authors;
pub.PMID = 98765432;
pub.Title = "Fake article #3";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "TOBIAN L", "BUNN P", "SCHMOE J" };
pub.Year = 2001;
pub.Journal = "Nature";
pub.Authors = Authors;
pub.PMID = 55555555;
pub.Title = "Fake article #4";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
}
