| @@ -5,6 +5,7 @@ |
| */ |
| package oms.utils; |
| |
| +import csip.Config; |
| import csip.api.server.Executable; |
| import csip.api.server.PayloadParameter; |
| import csip.api.server.ServiceException; |
| @@ -47,6 +48,11 @@ |
| |
| public static final String FILE_PARAMETER_REGEX_PATTERN = "\\A([^/]+)/([^/]+)/([^/]+)(?:/([^/;]+(?:;[^/;]+)*))?\\Z"; |
| |
| + public static final String LOCATION_MNT_DATA |
| + = Config.getString("oms.data.path", "/mnt/csip-oms"); |
| + |
| + public static final String PROJECT = "project"; |
| + |
| /** |
| * |
| */ |
| @@ -93,7 +99,7 @@ |
| double avg = 0.0; |
| for (int i = 0; i < sim.length; i++) { |
| if (sim[i] >= 0.0 && obs[i] >= 0.0) { |
| - // summing up |
| + // summing up |
| avg += Math.log1p(obs[i]); |
| valid++; |
| } |
| @@ -103,7 +109,7 @@ |
| return Double.NEGATIVE_INFINITY; |
| } |
| |
| - // calculating mean |
| + // calculating mean |
| avg /= valid; |
| |
| // calculating mean pow deviations |
| @@ -501,7 +507,66 @@ |
| dsl, // the dsl file to run |
| jvmOptions, // jvm options |
| ws, // workspace dir |
| - Arrays.asList(res.getFile(ID_AGES_JAR)), // the ages jar file |
| + Arrays.asList(res.getFile(ID_AGES_JAR)), // the ages jar file |
| + param.getString(KEY_LOGLEVEL, "INFO"), // The log level |
| + LOG); // This session logger |
| + } |
| + |
| + /** |
| + * Run Ages |
| + * |
| + * @param dsl |
| + * @throws Exception |
| + */ |
| + public static void runAgesNew(File dsl, File ws, PayloadParameter param, |
| + ServiceResources res, SessionLogger LOG) throws Exception { |
| + |
| + // Create/execute a Ages. |
| + Executable p = createProcessNew(dsl, ws, param, res, LOG); |
| + int result = p.exec(); |
| + if (result > 0) { |
| +// File f = p.stderr(); |
| +// if (f.exists() && f.length() > 10) { |
| +// String err = FileUtils.readFileToString(f, "UTF-8"); |
| +// LOG.info("Ages execution error. " + f + ":\n" + err); |
| +// throw new ServiceException("Ages execution error. " + f + ":\n" + err); |
| +// } |
| + throw new ServiceException("Ages execution error." + result); |
| + } |
| + } |
| + |
| + /** |
| + * Create the external Ages process. |
| + * |
| + * @param dsl |
| + * @param ws |
| + * @param param |
| + * @param res |
| + * @param LOG |
| + * @return |
| + * @throws java.lang.Exception |
| + */ |
| + public static Executable createProcessNew(File dsl, File ws, |
| + PayloadParameter param, ServiceResources res, SessionLogger LOG) throws Exception { |
| + |
| + Map<String, String> sysprops = new HashMap(); |
| + sysprops.put("oms_prj", ws.toString()); |
| + //System.out.println(" !!!! ws: " + ws.toString()); |
| + sysprops.put("csip_ages", LOCATION_MNT_DATA + "/ages_projects/ages_1_0/" + param.getString(PROJECT, "SFIR3")); |
| + //System.out.println(" csip_ages: " + LOCATION_MNT_DATA + "/ages_projects/ages_1_0/" + param.getString(PROJECT, "SFIR3")); |
| + |
| + String[] jvmOptions = Binaries.asSysProps(sysprops); |
| + String options = param.getString(KEY_OPTIONS, ""); |
| + if (options != null && !options.isEmpty()) { |
| + jvmOptions = (String[]) ArrayUtils.addAll(jvmOptions, options.split("\\s+")); |
| + } |
| + |
| + // java -Doms_prj=. -cp "dist/AgES.jar" oms3.CLI -l OFF -r "projects/sfir30/simulation/sfir30.sim" |
| + return Binaries.getResourceOMSDSL( |
| + dsl, // the dsl file to run |
| + jvmOptions, // jvm options |
| + ws, // workspace dir |
| + Arrays.asList(res.getFile(ID_AGES_JAR)), // the ages jar file |
| param.getString(KEY_LOGLEVEL, "INFO"), // The log level |
| LOG); // This session logger |
| } |
| @@ -545,7 +610,7 @@ |
| |
| // static void d() throws IOException { |
| // CSProperties pr = DataIO.properties(new File("/od/projects/csip-all/csip-oms/tmp/data/main_params.csv"), "Parameter"); |
| -// List<String> l = new ArrayList<>(pr.keySet()) ; |
| +// List<String> l = new ArrayList<>(pr.keySet()) ; |
| // Collections.sort(l); |
| // for (String string : l) { |
| // System.out.println("\"" + string + "\","); |