DM-7162: adding first skeleton and test for lightcurve handler

src/firefly/java/edu/caltech/ipac/firefly/server/query/lc/IrsaLightCurveHandler.java

@@ -0,0 +1,144 @@
+/*
+ * License information at https://github.com/Caltech-IPAC/firefly/blob/master/License.txt
+ */
+package edu.caltech.ipac.firefly.server.query.lc;
+
+import edu.caltech.ipac.astro.IpacTableWriter;
+import edu.caltech.ipac.firefly.server.ServerContext;
+import edu.caltech.ipac.util.DataGroup;
+import edu.caltech.ipac.util.VoTableUtil;
+import edu.caltech.ipac.util.download.FailedRequestException;
+import edu.caltech.ipac.util.download.URLDownload;
+import org.apache.commons.lang.NotImplementedException;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+
+
+/**
+ * .
+ * Should handle the LC transformations to get files out of the API result VOtable xml
+ *
+ * @author ejoliet
+ * @see PeriodogramAPIRequest
+ */
+public class IrsaLightCurveHandler implements LightCurveHandler {
+
+
+    /**
+     * TODO Update with correct API root url
+     */
+    public final String rootApiUrl = "http://irsa.ipac.caltech.edu/periodogram";
+
+    public File getPeriodogramTable(PeriodogramAPIRequest request) {
+
+        return ipacTableFromAPI(request, RESULT_TABLES_IDX.PERIODOGRAM);
+
+    }
+
+
+    /**
+     * @return peaks table (default: 50 rows)
+     */
+    public File getPeaksTable(PeriodogramAPIRequest request) {
+
+        return ipacTableFromAPI(request, RESULT_TABLES_IDX.PEAKS);
+    }
+
+    /**
+     * Return a phase folded curve form original light-curve
+     *
+     * @param tbl    orginal lc table
+     * @param period period for phase folding the lc curve
+     * @return phase folded curve (x2 original input table 0,2 phase)
+     */
+    public File toPhaseFoldedTable(File tbl, float period) {
+        //get raw lcTable and phase fold on time/period
+        //for now, return same table.
+        //TODO change it with the implementation DM-7165
+        return tbl;
+    }
+
+    /**
+     * Return the API URL to be called to get VOTable from Nexsci, which will contain 2 tables: periodogram and peaks tables.
+     * <p>
+     * TODO need to be implemented
+     *
+     * @param request object to contain the required paramter to make the API call
+     * @return the URL object
+     * @throws MalformedURLException
+     * @see LightCurveProcessor#computePeriodogram(PeriodogramAPIRequest, java.lang.String)
+     * @see IrsaLightCurveHandler#buildUrl(PeriodogramAPIRequest)
+     */
+    protected URL buildUrl(PeriodogramAPIRequest request) throws MalformedURLException {
+        //loop other request and append to rootApiUrl
+        throw new NotImplementedException("Not yet implemented");
+    }
+
+    protected File extractTblFrom(File votableResult, RESULT_TABLES_IDX resultTable) {
+        File resultTblFile = null;
+        try {
+            resultTblFile = makeResultTempFile(resultTable);
+            DataGroup[] dataGroups = VoTableUtil.voToDataGroups(votableResult.getAbsolutePath());
+
+            IpacTableWriter.save(resultTblFile, dataGroups[resultTable.ordinal()]);
+            return resultTblFile;
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+        return resultTblFile;
+    }
+
+    protected File ipacTableFromAPI(PeriodogramAPIRequest request, RESULT_TABLES_IDX resultTable) {
+        File tempFile = null;
+        try {
+            /**
+             * @see LightCurveProcessor#computePeriodogram(PeriodogramAPIRequest, java.lang.String)
+             */
+            URL url = buildUrl(request);
+
+            File apiResult = apiDownlaod(url);
+
+            tempFile = extractTblFrom(apiResult, resultTable);
+
+        } catch (IOException e) {
+            e.printStackTrace();
+        } catch (FailedRequestException e) {
+            e.printStackTrace();
+        }
+        return tempFile;
+    }
+
+    protected File apiDownlaod(URL url) throws IOException, FailedRequestException {
+
+        File apiResultTempFile = makeApiResultTempFile();
+
+        URLConnection aconn = URLDownload.makeConnection(url);
+        aconn.setRequestProperty("Accept", "*/*");
+        URLDownload.getDataToFile(aconn, apiResultTempFile); //TODO Get from cache
+
+        return apiResultTempFile;
+    }
+
+
+    protected File makeResultTempFile(RESULT_TABLES_IDX resultTable) throws IOException {
+        String prefix = "error";
+        switch (resultTable) {
+            case PERIODOGRAM:
+                prefix = "periodogram-";
+                break;
+            case PEAKS:
+                prefix = "peaks-";
+                break;
+        }
+
+        return File.createTempFile(prefix, ".tbl", ServerContext.getTempWorkDir());
+    }
+
+    protected File makeApiResultTempFile() throws IOException {
+        return File.createTempFile("lc-api-result-", ".xml", ServerContext.getTempWorkDir());
+    }
+}

src/firefly/java/edu/caltech/ipac/firefly/server/query/lc/LightCurveHandler.java

@@ -0,0 +1,45 @@
+/*
+ * License information at https://github.com/Caltech-IPAC/firefly/blob/master/License.txt
+ */
+package edu.caltech.ipac.firefly.server.query.lc;
+
+import java.io.File;
+
+/**
+ * Class should handle the input user parameter to
+ * call an API to
+ * get at least the periodogram and peaks table
+ * out of a raw time changin flux curve
+ *
+ * @author ejoliet
+ * @see PeriodogramAPIRequest
+ */
+public interface LightCurveHandler {
+    /**
+     * TODO check ordinals when API call is implemented
+     * Represent the tables in votable result from API: 0 for periodogram, 1 for peaks
+     */
+    enum RESULT_TABLES_IDX {
+        PERIODOGRAM, PEAKS
+    }
+
+
+    /**
+     * return a periodogram table from a request
+     *
+     * @return periodogram (power vs period) file
+     */
+    public File getPeriodogramTable(PeriodogramAPIRequest request);
+
+    /**
+     * Return the table which contains N peaks, N integer from request object
+     *
+     * @return peaks table
+     * @see PeriodogramAPIRequest#getNumberPeaks()
+     */
+    public File getPeaksTable(PeriodogramAPIRequest request);
+
+    /**
+     * TODO add extra output parameters getter that might be interesting
+     */
+}

src/firefly/java/edu/caltech/ipac/firefly/server/query/lc/LightCurveProcessor.java

@@ -0,0 +1,155 @@
+/*
+ * License information at https://github.com/Caltech-IPAC/firefly/blob/master/License.txt
+ */
+package edu.caltech.ipac.firefly.server.query.lc;
+
+import edu.caltech.ipac.firefly.core.EndUserException;
+import edu.caltech.ipac.firefly.data.TableServerRequest;
+import edu.caltech.ipac.firefly.server.ServerContext;
+import edu.caltech.ipac.firefly.server.query.DataAccessException;
+import edu.caltech.ipac.firefly.server.query.IpacTablePartProcessor;
+import edu.caltech.ipac.firefly.server.query.SearchProcessorImpl;
+import edu.caltech.ipac.firefly.server.util.Logger;
+import edu.caltech.ipac.firefly.server.util.QueryUtil;
+import edu.caltech.ipac.util.AppProperties;
+import edu.caltech.ipac.util.StringUtils;
+import edu.caltech.ipac.util.download.FailedRequestException;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+/**
+ * This class takes care of the LC api call and return result IpacTable Data.
+ */
+
+@SearchProcessorImpl(id = "LightCurveProcessor")
+
+public class LightCurveProcessor extends IpacTablePartProcessor {
+
+    private static final String PERIODOGRAM_API_URL = AppProperties.getProperty("periodogram.host", "default_periodogram_host_url");
+
+    private static final Logger.LoggerImpl _log = Logger.getLogger();
+
+    // API will return votable, depending on the request, return either peaks or periodogram table, which names are predefined here:
+    private static final String PERIODOGRAM_TABLE_NAME = "periodogram_table.tbl";
+    private static final String PEAKS_TABLE_NAME = "peaks_table.tbl";
+
+    /**
+     * Class handling the API call and returning LC result table
+     */
+    public LightCurveProcessor() {
+
+        // TODO enable the nadler in constructor when the NexsciHandler is ready
+        //        LightCurveHandler h = new IrsaLightCurveHandler() {
+    }
+
+    /**
+     * This method is defined as an abstract in the IpacTablePartProcessor and it is implemented here.
+     * The TableServerRequest is passed here and processed.  Only when the "searchRequest" is set, the request
+     * is processed.
+     *
+     * @return File with statistics on a table
+     * @throws IOException
+     * @throws DataAccessException
+     */
+    protected File loadDataFile(TableServerRequest request) throws IOException, DataAccessException {
+
+        PeriodogramAPIRequest req = QueryUtil.assureType(PeriodogramAPIRequest.class, request);
+        String tblType = req.getParam(PeriodogramAPIRequest.TABLE_NAME);
+        String tblName = (tblType != null && tblType.equalsIgnoreCase(PeriodogramAPIRequest.RESULT_TABLE))
+                ? PERIODOGRAM_TABLE_NAME : PEAKS_TABLE_NAME;
+
+        //In order to get any of those tables, computing the periodogram need to happen:
+        // Result is a Votable containing 2 tables:periodogram and peaks
+        File resTable = null;
+        try {
+            resTable = computePeriodogram(req, tblName);
+        } catch (FailedRequestException e) {
+            e.printStackTrace();
+        }
+
+//        if (tblType.equalsIgnoreCase(PeriodogramAPIRequest.PEAKS_TABLE)) {
+//
+//        }
+
+        return resTable;
+    }
+
+    /**
+     * From the request, get the file and the algorithm to compute the peridogram by calling external API
+     *
+     * @param req     request
+     * @param tblName table name to distinguish them
+     * @return table file result either peaks por periodogram
+     * @throws FailedRequestException
+     */
+    public File computePeriodogram(PeriodogramAPIRequest req, String tblName) throws FailedRequestException {
+
+        //Fake call API, parse VOTable result. See for example QueryMOS
+        try {
+            Thread.sleep(5000);
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        }
+
+        //TODO this is used with overwritten method. Once API known, remove and use the handler directly
+        LightCurveHandler h = new IrsaLightCurveHandler() {
+
+            /**
+             * For testing purposes returned periodogram from here:
+             * PeriodogramAPIRequest.RESULT_TABLE = "http://web.ipac.caltech.edu/staff/ejoliet/demo/vo-nexsci-result-sample.xml"
+             * TODO remove after implementing NexsciHandler
+             * @param req
+             * @return url api
+             * @throws MalformedURLException
+             */
+            @Override
+            protected URL buildUrl(PeriodogramAPIRequest req) throws MalformedURLException {
+                /**
+                 * For now just download the file from the url from req.getResultTable()
+                 * and stream it out
+                 */
+                String SAMPLE_URL = req.getResultTable();
+                return new URL(SAMPLE_URL);
+            }
+        };
+
+//        LightCurveHandler h = new IrsaLightCurveHandler();
+        if (tblName.equalsIgnoreCase(PERIODOGRAM_TABLE_NAME)) {
+            return h.getPeriodogramTable(req);
+        } else if (tblName.equalsIgnoreCase(PEAKS_TABLE_NAME)) {
+            return h.getPeaksTable(req);
+        } else {
+            throw new FailedRequestException("Unable to deal with the request table name " + tblName);
+        }
+    }
+
+    private static File makeFileName(PeriodogramAPIRequest req) throws IOException {
+        return File.createTempFile("lc-result", ".xml", ServerContext.getPermWorkDir());
+    }
+
+    private URL createURL(PeriodogramAPIRequest req) throws EndUserException, IOException {
+        PeriodogramAPIRequest request = (PeriodogramAPIRequest) req.cloneRequest();
+        String url = req.getUrl();
+        if (url == null || url.length() < 5) {
+            url = PERIODOGRAM_API_URL;
+        }
+        String paramStr = buildParamFrom(request);
+        if (paramStr.startsWith("&")) {
+            paramStr = paramStr.substring(1);
+        }
+        url += "?" + paramStr;
+
+        return new URL(url);
+    }
+
+    private String buildParamFrom(PeriodogramAPIRequest request) {
+        String outputMode = request.getParam(PeriodogramAPIRequest.OUTPUT_MODE);
+        if (StringUtils.isEmpty(outputMode)) {
+            outputMode = "VOTable";
+        }
+        return "min_period=0&n_peaks=50";
+    }
+}