Expand plugin and external.lib test coverage (#606)

plugin/build.xml

@@ -145,11 +145,7 @@
 
 			<test name="${testcase}" todir="${test_report}" if="testcase" />
 
-			<batchtest todir="${test_report}" unless="testcase">
-				<fileset dir="${test_build}">
-					<include name="**/PluginTest.class" />
-				</fileset>
-			</batchtest>
+			<test name="org.aavso.tools.vstar.external.plugin.AllTests" todir="${test_report}" unless="testcase" />
 
 			<classpath refid="test.classpath" />
 		</junit>
@@ -199,11 +195,7 @@
 
 				<jvmarg value="-ea" />
 
-				<batchtest todir="${test_report}" unless="testcase">
-					<fileset dir="${test_build}">
-						<include name="**/PluginTest.class" />
-					</fileset>
-				</batchtest>
+				<test name="org.aavso.tools.vstar.external.plugin.AllTests" todir="${test_report}" unless="testcase" />
 
 				<classpath refid="test.classpath" />
 			</junit>

plugin/src/org/aavso/tools/vstar/external/lib/FitsTestData.java

@@ -0,0 +1,83 @@
+/**
+ * VStar: a statistical analysis tool for variable star data.
+ * Copyright (C) 2009  AAVSO (http://www.aavso.org/)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package org.aavso.tools.vstar.external.lib;
+
+import java.io.ByteArrayOutputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
+
+import nom.tam.fits.BinaryTableHDU;
+import nom.tam.fits.Fits;
+import nom.tam.fits.FitsException;
+import nom.tam.fits.ImageHDU;
+
+/**
+ * Builds minimal in-memory FITS files for plugin self-tests.
+ */
+public final class FitsTestData {
+
+    private FitsTestData() {
+    }
+
+    /**
+     * Lightkurve-style FITS with Kepler telescope metadata and one valid row.
+     */
+    public static byte[] createLightKurveKeplerFits() throws FitsException, IOException {
+        return createFits("Kepler", new String[] { "TIME", "FLUX", "FLUX_ERR" },
+                new Object[] { new double[] { 0.5 }, new float[] { 1000f }, new float[] { 10f } },
+                null, null);
+    }
+
+    /**
+     * Kepler/TESS archive-style FITS with PDCSAP columns (corrected flux).
+     */
+    public static byte[] createKeplerArchiveFits() throws FitsException, IOException {
+        String[] names = { "TIME", "COL1", "COL2", "SAP_FLUX", "SAP_FLUX_ERR", "COL5", "COL6",
+                "PDCSAP_FLUX", "PDCSAP_FLUX_ERR", "QUALITY" };
+        Object[] cols = { new double[] { 0.5 }, new float[] { 0f }, new float[] { 0f },
+                new float[] { 1000f }, new float[] { 10f }, new float[] { 0f }, new float[] { 0f },
+                new float[] { 1000f }, new float[] { 10f }, new int[] { 0 } };
+        return createFits("Kepler", names, cols, 2454833, 0.0);
+    }
+
+    private static byte[] createFits(String telescope, String[] columnNames, Object[] columns,
+            Integer bjdRefInt, Double bjdRefFrac) throws FitsException, IOException {
+        Fits fits = new Fits();
+
+        nom.tam.fits.Data imageData = ImageHDU.encapsulate(new double[1][1]);
+        ImageHDU image = new ImageHDU(ImageHDU.manufactureHeader(imageData), imageData);
+        image.getHeader().addValue("TELESCOP", telescope, "");
+        image.getHeader().addValue("OBJECT", "TEST", "");
+        fits.addHDU(image);
+
+        nom.tam.fits.Data tableData = BinaryTableHDU.encapsulate(columns);
+        BinaryTableHDU table = new BinaryTableHDU(BinaryTableHDU.manufactureHeader(tableData), tableData);
+        for (int i = 0; i < columnNames.length; i++) {
+            table.setColumnName(i, columnNames[i], "");
+        }
+        if (bjdRefInt != null && bjdRefFrac != null) {
+            table.getHeader().addValue("BJDREFI", bjdRefInt.longValue(), "");
+            table.getHeader().addValue("BJDREFF", bjdRefFrac.doubleValue(), "");
+        }
+        fits.addHDU(table);
+
+        ByteArrayOutputStream out = new ByteArrayOutputStream();
+        fits.write(new DataOutputStream(out));
+        return out.toByteArray();
+    }
+}

plugin/src/org/aavso/tools/vstar/external/lib/GaiaObSourceBase.java

@@ -34,7 +34,9 @@
 
 import java.awt.Color;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -56,6 +58,7 @@
 import org.aavso.tools.vstar.exception.ObservationValidationError;
 import org.aavso.tools.vstar.input.AbstractObservationRetriever;
 import org.aavso.tools.vstar.plugin.ObservationSourcePluginBase;
+import org.aavso.tools.vstar.util.Tolerance;
 
 public abstract class GaiaObSourceBase extends ObservationSourcePluginBase {
 
@@ -782,4 +785,75 @@ public String getSourceType() {
 		}
 	}
 
+	@Override
+	public Boolean test() {
+		setTestMode(true);
+		paramIgnoreFlags = true;
+		paramGaiaRelease = GaiaRelease.DR2;
+
+		boolean success = true;
+		try {
+			success &= runGaiaFileTest(false);
+			success &= runGaiaFileTest(true);
+		} catch (Exception e) {
+			success = false;
+		} finally {
+			setTestMode(false);
+		}
+		return success;
+	}
+
+	private boolean runGaiaFileTest(boolean transform) throws Exception {
+		paramTransform = transform;
+
+		String header = "source_id,transit_id,band,time,mag,flux,flux_error,flux_over_error,rejected_by_photometry,rejected_by_variability,other_flags,solution_id\n";
+		String[] lines;
+		if (transform) {
+			lines = new String[] {
+					header,
+					"1951343009975999744,1,BP,1000.0,11.0,1000.0,10.0,,FALSE,FALSE,0,1\n",
+					"1951343009975999744,1,G,1000.0,10.0,1000.0,10.0,,FALSE,FALSE,0,1\n",
+					"1951343009975999744,1,RP,1000.0,12.0,1000.0,10.0,,FALSE,FALSE,0,1\n" };
+		} else {
+			lines = new String[] {
+					header,
+					"1951343009975999744,1,G,1000.0,10.0,1000.0,10.0,,FALSE,FALSE,0,1\n" };
+		}
+
+		StringBuffer content = new StringBuffer();
+		for (String line : lines) {
+			content.append(line);
+		}
+		InputStream in = new ByteArrayInputStream(content.toString().getBytes());
+		List<InputStream> streams = new ArrayList<InputStream>();
+		streams.add(in);
+		setInputInfo(streams, "Gaia test");
+
+		GAIADR2FormatRetriever retriever = new GAIADR2FormatRetriever(transform, true, GaiaRelease.DR2);
+		retriever.getNumberOfRecords();
+		retriever.retrieveObservations();
+
+		List<ValidObservation> gaiaObs = retriever.getValidObservations();
+		if (!transform) {
+			boolean success = 1 == gaiaObs.size();
+			ValidObservation ob = gaiaObs.get(0);
+			success &= gaiaGseries == ob.getBand();
+			success &= Tolerance.areClose(2456197.5, ob.getJD(), 1e-6, true);
+			success &= Tolerance.areClose(10.0, ob.getMag(), 1e-6, true);
+			success &= "GaiaDR2 1951343009975999744".equals(ob.getName());
+			success &= JDflavour.BJD == ob.getJDflavour();
+			return success;
+		}
+
+		boolean success = 3 == gaiaObs.size();
+		success &= SeriesType.Johnson_V == gaiaObs.get(0).getBand();
+		success &= SeriesType.Cousins_R == gaiaObs.get(1).getBand();
+		success &= SeriesType.Cousins_I == gaiaObs.get(2).getBand();
+		for (ValidObservation ob : gaiaObs) {
+			success &= ob.isTransformed();
+			success &= Tolerance.areClose(2456197.5, ob.getJD(), 1e-6, true);
+		}
+		return success;
+	}
+
 }

plugin/src/org/aavso/tools/vstar/external/lib/ZTFObSourceBase.java

@@ -19,8 +19,11 @@
 
 import java.awt.Color;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.util.Locale;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -42,6 +45,7 @@
 import org.aavso.tools.vstar.exception.ObservationValidationError;
 import org.aavso.tools.vstar.input.AbstractObservationRetriever;
 import org.aavso.tools.vstar.plugin.ObservationSourcePluginBase;
+import org.aavso.tools.vstar.util.Tolerance;
 
 /**
  * 
@@ -321,4 +325,49 @@ public String getSourceType() {
 		}
 	}
 
+	@Override
+	public Boolean test() {
+		setTestMode(true);
+
+		String[] lines = {
+				"oid\thjd\tmag\tmagerr\tcatflags\tfiltercode\texptime\tairmass\n",
+				"12345\t2458000.5\t12.5\t0.01\t0\tzg\t30\t1.2\n" };
+
+		boolean success = true;
+
+		try {
+			StringBuffer content = new StringBuffer();
+			for (String line : lines) {
+				content.append(line);
+			}
+			InputStream in = new ByteArrayInputStream(content.toString().getBytes());
+			List<InputStream> streams = new ArrayList<InputStream>();
+			streams.add(in);
+			setInputInfo(streams, "ZTF test");
+
+			ZTFFormatRetriever retriever = new ZTFFormatRetriever();
+			retriever.getNumberOfRecords();
+			retriever.retrieveObservations();
+
+			List<ValidObservation> ztfObs = retriever.getValidObservations();
+			success &= 1 == ztfObs.size();
+
+			ValidObservation ob = ztfObs.get(0);
+			success &= "12345".equals(ob.getName());
+			success &= Tolerance.areClose(2458000.5, ob.getJD(), 1e-6, true);
+			success &= Tolerance.areClose(12.5, ob.getMag(), 1e-6, true);
+			success &= Tolerance.areClose(0.01, ob.getMagnitude().getUncertainty(), 1e-6, true);
+			success &= ztfgSeries == ob.getBand();
+			success &= JDflavour.HJD == ob.getJDflavour();
+			success &= String.format(Locale.ENGLISH, "ZTF object %s", "12345")
+					.equals(retriever.getSourceName());
+		} catch (Exception e) {
+			success = false;
+		} finally {
+			setTestMode(false);
+		}
+
+		return success;
+	}
+
 }

plugin/src/org/aavso/tools/vstar/external/plugin/FlexibleTextFileFormatObservationSource.java

@@ -884,4 +884,42 @@ private boolean isNullOrEmpty(String s) {
 		}
 
 	}
+
+	@Override
+	public Boolean test() {
+		setTestMode(true);
+		String[] lines = {
+				"#FIELDS=time,mag,magerr\n",
+				"#DELIM=comma\n",
+				"#DATE=JD\n",
+				"2450000,5.0,0.01\n" };
+
+		boolean success = true;
+		try {
+			StringBuffer content = new StringBuffer();
+			for (String line : lines) {
+				content.append(line);
+			}
+			java.io.InputStream in = new java.io.ByteArrayInputStream(content.toString().getBytes());
+			java.util.List<java.io.InputStream> streams = new java.util.ArrayList<java.io.InputStream>();
+			streams.add(in);
+			setInputInfo(streams, "flex test");
+
+			AbstractObservationRetriever retriever = getObservationRetriever();
+			retriever.getNumberOfRecords();
+			retriever.retrieveObservations();
+
+			success &= 1 == retriever.getValidObservations().size();
+			ValidObservation ob = retriever.getValidObservations().get(0);
+			success &= 2450000 == ob.getJD();
+			success &= 5.0 == ob.getMag();
+			success &= 0.01 == ob.getMagnitude().getUncertainty();
+			success &= JDflavour.JD == ob.getJDflavour();
+		} catch (Exception e) {
+			success = false;
+		} finally {
+			setTestMode(false);
+		}
+		return success;
+	}
 }

plugin/src/org/aavso/tools/vstar/external/plugin/HipparcosObservationSource.java

@@ -30,6 +30,7 @@
 import org.aavso.tools.vstar.input.AbstractObservationRetriever;
 import org.aavso.tools.vstar.plugin.InputType;
 import org.aavso.tools.vstar.plugin.ObservationSourcePluginBase;
+import org.aavso.tools.vstar.util.Tolerance;
 //12/02/2018 C. Kotnik added name to observations so they can be
 //saved and reloaded from a file.
 /**
@@ -209,4 +210,24 @@ private String getNextLine(BufferedReader reader, int lineNum) {
 			return line;
 		}
 	}
+
+	@Override
+	public Boolean test() {
+		setTestMode(true);
+		try {
+			String[] lines = { "JD\n", "10000|10.0|0|0\n" };
+			AbstractObservationRetriever retriever = getTestRetriever(lines, "HIP test");
+			if (retriever.getValidObservations().size() != 1) {
+				return false;
+			}
+			ValidObservation ob = retriever.getValidObservations().get(0);
+			// Epoch field is HT1-style offset: sample 10000 -> BJD 2450000 with this reader
+			return Tolerance.areClose(2450000.0, ob.getJD(), 1e-6, true)
+					&& Tolerance.areClose(10.0, ob.getMag(), 1e-6, true);
+		} catch (Exception e) {
+			return false;
+		} finally {
+			setTestMode(false);
+		}
+	}
 }

plugin/src/org/aavso/tools/vstar/external/plugin/JulianDateObservationsFilter.java

@@ -17,8 +17,11 @@
  */
 package org.aavso.tools.vstar.external.plugin;
 
+import java.util.ArrayList;
+import java.util.LinkedHashSet;
 import java.util.List;
 
+import org.aavso.tools.vstar.data.Magnitude;
 import org.aavso.tools.vstar.data.ValidObservation;
 import org.aavso.tools.vstar.data.ValidObservation.JDflavour;
 import org.aavso.tools.vstar.plugin.CustomFilterPluginBase;
@@ -55,4 +58,34 @@ public String getDocName() {
 		return "https://github.com/AAVSO/VStar/wiki/Custom-Filter-Plug%E2%80%90ins#julian-date-observations-filter";
 	}
 
+	@Override
+	public Boolean test() {
+		setTestMode(true);
+
+		List<ValidObservation> obs = new ArrayList<ValidObservation>();
+
+		ValidObservation jdOb = new ValidObservation();
+		jdOb.setJD(2450000);
+		jdOb.setMagnitude(new Magnitude(5, 0));
+		jdOb.setJDflavour(JDflavour.JD);
+		obs.add(jdOb);
+
+		ValidObservation bjdOb = new ValidObservation();
+		bjdOb.setJD(2450001);
+		bjdOb.setMagnitude(new Magnitude(6, 0));
+		bjdOb.setJDflavour(JDflavour.BJD);
+		obs.add(bjdOb);
+
+		filteredObs = new LinkedHashSet<ValidObservation>();
+		Pair<String, String> idPair = filter(obs);
+
+		boolean success = filteredObs.size() == 1;
+		success &= filteredObs.contains(jdOb);
+		success &= "Julian Date Observations".equals(idPair.first);
+		success &= "Julian Date Observations".equals(idPair.second);
+
+		setTestMode(false);
+		return success;
+	}
+
 }