public void TestMeSHHeadingReport()
{
// 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);
// Write the MeSH Heading report
StreamWriter writer = new StreamWriter(AppDomain.CurrentDomain.BaseDirectory + "\\MeSHHeadingReport.csv");
Reports.ReportStatus StatusCallback = delegate(int number, int total, Person person, bool ProgressBarOnly)
{
//
};
Reports.ReportMessage MessageCallback = delegate(string Message)
{
//
};
reports.MeSHHeadingReport(writer, StatusCallback, MessageCallback);
writer.Close();
// Verify that the MeSH headings were written properly
// Read the rows back from the file
string ConnectionString =
"Driver={Microsoft Text Driver (*.txt; *.csv)};Dbq="
+ AppDomain.CurrentDomain.BaseDirectory + ";";
OdbcConnection Connection = new OdbcConnection(ConnectionString);
OdbcDataAdapter DataAdapter = new OdbcDataAdapter
("SELECT * FROM [MeSHHeadingReport.csv]", Connection);
DataTable Results = new DataTable();
int Rows = DataAdapter.Fill(Results);
Connection.Close();
int numChecked = 0;
// Check a few selected results
foreach (DataRow Row in Results.Rows)
{
string Setnb = Row[0].ToString();
int Year = Convert.ToInt32(Row[1]);
string Heading = Row[2].ToString();
int Count = Convert.ToInt32(Row[3]);
switch (Setnb)
{
case "A6009400": // Van Eys
if ((Year == 1998) && (Heading == "Humans"))
{
Assert.IsTrue(Count == 2);
numChecked++;
}
if ((Year == 1998) && (Heading == "Child"))
{
Assert.IsTrue(Count == 1);
numChecked++;
}
if ((Year == 2001) && (Heading == "Humans"))
{
Assert.IsTrue(Count == 1);
numChecked++;
}
break;
case "A5702471": // Guillemin
if ((Year == 2005) && (Heading == "Hypothalamic Hormones/*physiology"))
{
Assert.IsTrue(Count == 1);
numChecked++;
}
break;
}
}
Assert.IsTrue(numChecked == 4);
File.Delete(AppDomain.CurrentDomain.BaseDirectory + "\\MeSHHeadingReport.csv");
}
public void TestSkipSetnbs()
{
// 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);
Reports.ReportStatus StatusCallback = delegate(int number, int total, Person person, bool ProgressBarOnly)
{
//
};
Reports.ReportMessage MessageCallback = delegate(string Message)
{
//
};
// Set up the Setnbs to skip
ArrayList SetnbsToSkip = new ArrayList();
SetnbsToSkip.Add("A5401532");
SetnbsToSkip.Add("A6009400");
// Verify that the people report skips the setnbs
StreamWriter writer = new StreamWriter(AppDomain.CurrentDomain.BaseDirectory + "\\TestSkipSetnbs.csv");
reports.PeopleReport(SetnbsToSkip, writer, StatusCallback, MessageCallback);
writer.Close();
StreamReader reader = new StreamReader(AppDomain.CurrentDomain.BaseDirectory + "\\TestSkipSetnbs.csv");
string Line = reader.ReadLine(); // skip the header row
while ((Line = reader.ReadLine()) != null)
{
Assert.IsFalse(Line.StartsWith("A5401532"));
Assert.IsFalse(Line.StartsWith("A6009400"));
}
reader.Close();
// Verify that the people report skips the setnbs
writer = new StreamWriter(AppDomain.CurrentDomain.BaseDirectory + "\\TestSkipSetnbs.csv", false);
reports.PubsReport(SetnbsToSkip, writer, StatusCallback, MessageCallback);
writer.Close();
reader = new StreamReader(AppDomain.CurrentDomain.BaseDirectory + "\\TestSkipSetnbs.csv");
Line = reader.ReadLine(); // skip the header row
while ((Line = reader.ReadLine()) != null)
{
Assert.IsFalse(Line.StartsWith("A5401532"));
Assert.IsFalse(Line.StartsWith("A6009400"));
}
reader.Close();
File.Delete(AppDomain.CurrentDomain.BaseDirectory + "\\TestSkipSetnbs.csv");
}
/// <summary>
/// Write the People or Publications report
/// </summary>
private void PeopleOrPublicationsReport(WhichReport whichReport, bool ContinuePreviousReport, Reports reports)
{
ArrayList SetnbsToSkip = null;
string Filename = Folder.Text + "\\";
if (whichReport == WhichReport.People)
{
Filename += People.Text;
}
else
{
Filename += Publications.Text;
}
// If we're continuing the previous report, rename it to a backup filename,
// then copy every person in it to the file to append -- except for the
// last person, which we'll restart.
if (ContinuePreviousReport && File.Exists(Filename))
{
try
{
SetnbsToSkip = Reports.BackupReportAndGetSetnbs(Filename);
}
catch (Exception ex)
{
AddLogEntry("An error occurred while creating the report '" + Filename + "': " + ex.Message);
return;
}
}
// Make an anonymous callback function that keeps track of the callback data
Reports.ReportStatus StatusCallback = delegate(int number, int total, Person person, bool StatusBarOnly)
{
toolStripProgressBar1.Minimum = 0;
toolStripProgressBar1.Maximum = total;
toolStripProgressBar1.Value = number;
if (!StatusBarOnly)
{
AddLogEntry("Writing " + person.Last + " " + person.Setnb + " (" + number.ToString() + " of " + total.ToString() + ")");
}
Application.DoEvents();
};
// Make an anonymous callback function to receive message
Reports.ReportMessage MessageCallback = delegate(string Message)
{
AddLogEntry(Message);
Application.DoEvents();
};
// Write the Stars report
StreamWriter writer;
try
{
// Open the writer to append the file only if continuing from a previous report
writer = new StreamWriter(Filename, ContinuePreviousReport);
}
catch (Exception ex)
{
AddLogEntry("An error occurred while creating the report '" + Filename + "': " + ex.Message);
return;
}
try
{
if (whichReport == WhichReport.People)
{
reports.PeopleReport(SetnbsToSkip, writer, StatusCallback, MessageCallback);
}
else
{
reports.PubsReport(SetnbsToSkip, writer, StatusCallback, MessageCallback);
}
}
catch (Exception ex)
{
AddLogEntry("An error occurred while creating the report '" + Filename + "': " + ex.Message);
}
finally
{
writer.Close();
}
}
public void TestEntireReport()
{
string Setnb = "";
// 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);
// Write the report
StreamWriter writer = new StreamWriter(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv");
Reports.ReportStatus StatusCallback = delegate(int number, int total, Person person, bool ProgressBarOnly) {
//
};
Reports.ReportMessage MessageCallback = delegate(string Message)
{
//
};
reports.PeopleReport(null, writer, StatusCallback, MessageCallback);
writer.Close();
// Read the report into an array
var lines = File.ReadAllLines($"{AppDomain.CurrentDomain.BaseDirectory}\\TestEntireReport.csv")
.Select(line => line.Split(new char[] { ',' }));
var header = lines.First();
var data = lines.Skip(1).ToList();
Assert.AreEqual(85, data.Count);
string ReportData(string setnb, string year, string column)
{
var index = Array.IndexOf(header, column);
var row = data.Where(line => line[0] == setnb && line[1] == year);
Assert.AreEqual(1, row.Count(), $"Unable to find setnb={setnb} year={year} in TestEntireReport.csv");
return(row.First()[index]);
}
var q = ReportData("A5401532", "1997", "wghtd_pubcount_pos1");
// Read the report file that was generated by hand (TestEntireReport_Data.xls)
// and check each value against the report that was generated by Reports()
string[] Columns =
{
"setnb", "year", "pubcount", "wghtd_pubcount", "pubcount_pos1",
"wghtd_pubcount_pos1", "pubcount_posN", "wghtd_pubcount_posN",
"pubcount_posM", "wghtd_pubcount_posM", "pubcount_posNTL",
"wghtd_pubcount_posNTL", "pubcount_pos2", "wghtd_pubcount_pos2",
"123pubcount", "wghtd_123pubcount", "123pubcount_pos1",
"wghtd_123pubcount_pos1", "123pubcount_posN", "wghtd_123pubcount_posN",
"123pubcount_posM", "wghtd_123pubcount_posM", "123pubcount_posNTL",
"wghtd_123pubcount_posNTL", "123pubcount_pos2", "wghtd_123pubcount_pos2",
"1pubcount", "wghtd_1pubcount", "1pubcount_pos1", "wghtd_1pubcount_pos1",
"1pubcount_posN", "wghtd_1pubcount_posN", "1pubcount_posM",
"wghtd_1pubcount_posM", "1pubcount_posNTL", "wghtd_1pubcount_posNTL",
"1pubcount_pos2", "wghtd_1pubcount_pos2", "2pubcount", "wghtd_2pubcount",
"2pubcount_pos1", "wghtd_2pubcount_pos1", "2pubcount_posN",
"wghtd_2pubcount_posN", "2pubcount_posM", "wghtd_2pubcount_posM",
"2pubcount_posNTL", "wghtd_2pubcount_posNTL", "2pubcount_pos2",
"wghtd_2pubcount_pos2", "3pubcount", "wghtd_3pubcount", "3pubcount_pos1",
"wghtd_3pubcount_pos1", "3pubcount_posN", //"wghtd_3pubcount_posN",
"3pubcount_posM", "wghtd_3pubcount_posM", "3pubcount_posNTL",
"wghtd_3pubcount_posNTL", "3pubcount_pos2", "wghtd_3pubcount_pos2",
"4pubcount", "wghtd_4pubcount", "4pubcount_pos1", "wghtd_4pubcount_pos1",
"4pubcount_posN", "wghtd_4pubcount_posN", "4pubcount_posM",
"wghtd_4pubcount_posM", "4pubcount_posNTL", "wghtd_4pubcount_posNTL",
"4pubcount_pos2", "wghtd_4pubcount_pos2"
};
DataTable HandGeneratedData = NpoiHelper.ReadExcelFileToDataTable(AppDomain.CurrentDomain.BaseDirectory +
"\\Unit Tests\\TestReports", "TestEntireReport_Data.xls");
Assert.AreEqual(HandGeneratedData.Rows.Count, 85);
var valuesChecked = 0;
for (int RowNum = 0; RowNum < HandGeneratedData.Rows.Count; RowNum++)
{
// Find the rows in the hand-generated data and the report
DataRow HandGeneratedRow = HandGeneratedData.Rows[RowNum];
Setnb = HandGeneratedRow[0].ToString();
int Year = Convert.ToInt32(HandGeneratedRow[1]);
for (int i = 2; i < Columns.Length; i++)
{
valuesChecked++;
String columnName = Columns[i];
var actualValue = ReportData(Setnb, Year.ToString(), columnName);
string expectedValue = HandGeneratedRow[columnName].ToString();
Assert.AreEqual(expectedValue, actualValue, Setnb + "/" + Year.ToString() + "/" + columnName + " -- hand generated has " + expectedValue + ", report has" + actualValue);
}
}
Assert.AreEqual((HandGeneratedData.Rows.Count) * (Columns.Length - 2), valuesChecked);
// Use BackupReportAndGetSetnbs to back up the report -- check that it
// returns the correct list of Setnbs and removes the last one from
// the file. The last Setnb should still be in Setnb.
ArrayList Setnbs = Reports.BackupReportAndGetSetnbs(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv");
// Read the backup file that was created, make sure that the last setnb in the
// file isn't contained and the others are
StreamReader reader = new StreamReader(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv.bak");
string Line = reader.ReadLine(); //skip the header row
while ((Line = reader.ReadLine()) != null) // Find the last setnb in the original file
{
Setnb = Line.Substring(0, 8);
}
string RemovedSetnb = Setnb;
Assert.IsFalse(Setnbs.Contains(RemovedSetnb));
reader.Close();
// Verify that the new file contains only the other setnbs
Assert.IsTrue(Setnbs.Count == 3);
Assert.IsFalse(Setnbs.Contains(RemovedSetnb));
reader = new StreamReader(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv");
Line = reader.ReadLine(); //skip the header row
while ((Line = reader.ReadLine()) != null)
{
Setnb = Line.Substring(0, 8);
Assert.IsTrue(Setnbs.Contains(Setnb));
Assert.IsFalse(Setnb == RemovedSetnb);
}
reader.Close();
// Delete the temporary files
File.Delete(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv");
File.Delete(AppDomain.CurrentDomain.BaseDirectory + "\\TestEntireReport.csv.bak");
}
/// <summary>
/// Generate the reports
/// </summary>
private void GenerateReports_Click(object sender, EventArgs e)
{
// Make an anonymous callback function that keeps track of the callback data
// and one that reports messages
Reports.ReportStatus StatusCallback = delegate(int number, int total, Person person, bool StatusBarOnly)
{
toolStripProgressBar1.Minimum = 0;
toolStripProgressBar1.Maximum = total;
toolStripProgressBar1.Value = number;
if (!StatusBarOnly)
{
AddLogEntry("Writing " + person.Last + " " + person.Setnb + " (" + number.ToString() + " of " + total.ToString() + ")");
}
Application.DoEvents();
};
Reports.ReportMessage MessageCallback = delegate(string Message)
{
AddLogEntry(Message);
Application.DoEvents();
};
if ((JournalWeights.Text == "") || (!File.Exists(JournalWeights.Text)))
{
MessageBox.Show("Please specify a valid Journal Weights file.", "Unable to Generate Reports", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
AddLogEntry("Generating reports");
this.Enabled = false;
Reports reports = new Reports(DB, JournalWeights.Text);
StreamWriter writer = null;
int NumReports = 0;
if (DoPeople.Checked)
{
NumReports++;
toolStripStatusLabel1.Text = "People";
// Set the people report sections based on the listbox
string[] ReportSections = new string[peopleReportSections.Items.Count];
for (int i = 0; i < peopleReportSections.Items.Count; i++)
{
ReportSections[i] = peopleReportSections.Items[i].ToString();
}
reports.PeopleReportSections = ReportSections;
PeopleOrPublicationsReport(WhichReport.People, ContinuePeople.Checked, reports);
}
if (DoPublications.Checked)
{
NumReports++;
toolStripStatusLabel1.Text = "Publications";
PeopleOrPublicationsReport(WhichReport.Publications, ContinuePeople.Checked, reports);
}
if (DoMeSHHeadings.Checked)
{
writer = null;
try
{
NumReports++;
toolStripStatusLabel1.Text = "MeSHHeadings";
AddLogEntry("Writing MeSH Headings report");
toolStripProgressBar1.Value = 0;
writer = new StreamWriter(Folder.Text + "\\" + MeSHHeadings.Text, false);
reports.MeSHHeadingReport(writer, StatusCallback, MessageCallback);
}
catch (Exception ex)
{
AddLogEntry("An error occurred while writing the MeSH Headings report: " + ex.Message);
}
finally
{
if (writer != null)
{
writer.Close();
}
}
}
if (DoGrantIDs.Checked)
{
writer = null;
try
{
NumReports++;
toolStripStatusLabel1.Text = "Grants";
AddLogEntry("Writing Grants report");
toolStripProgressBar1.Value = 0;
writer = new StreamWriter(Folder.Text + "\\" + GrantIDs.Text, false);
reports.GrantsReport(writer);
}
catch (Exception ex)
{
AddLogEntry("An error occurred while writing the Grants report: " + ex.Message);
}
finally
{
if (writer != null)
{
writer.Close();
}
}
}
toolStripStatusLabel1.Text = "Done";
AddLogEntry(NumReports.ToString() + " reports written");
// Refresh the radio buttons
this.Enabled = true;
CheckForExistingFiles();
}
