Adding healthchecks

dspace-api/src/main/java/org/dspace/health/AdditionalInfoCheck.java

@@ -0,0 +1,31 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.health;
+
+import org.dspace.health.additionalUtilities.Info;
+
+public class AdditionalInfoCheck extends Check {
+
+    @Override
+    protected String run(ReportInfo ri) {
+        String output = "";
+
+        output += String.format(
+                "Server uptime: %s\n", Info.get_proc_uptime());
+        output += String.format(
+                "JVM uptime: %s\n", Info.get_jvm_uptime());
+        output += String.format(
+                "Testing build time: %s\n", Info.get_build_time());
+
+        output += "\n\n";
+
+        output += "Example url 1:       https://dev-5.pc:8443/repository/home\n";
+        output += "Example url 2:       https://dev-5.pc:85/repository/home\n";
+        return output;
+    }
+}

dspace-api/src/main/java/org/dspace/health/OAIPMHCheck.java

@@ -0,0 +1,35 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.health;
+
+import org.dspace.health.additionalUtilities.IOUtils;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
+
+import java.io.File;
+
+public class OAIPMHCheck extends Check {
+    protected static final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
+
+    @Override
+    protected String run(ReportInfo ri) {
+        String output = "";
+        String dspace_dir = configurationService.getProperty("dspace.dir");
+        String dspace_url = configurationService.getProperty("dspace.server.url");
+        String oaiurl = dspace_url + "/oai/request";
+        output += String.format("Trying [%s]\n", oaiurl);
+
+        File scriptDir = new File(
+        "C:\\WorkSpace\\DSpace\\dspace-api\\src\\main\\java\\org\\dspace\\health\\additionalUtilities\\");
+
+        output += IOUtils.runScript(scriptDir, new String[]{
+                "python", "validate.py", oaiurl});
+        return output;
+    }
+}

dspace-api/src/main/java/org/dspace/health/ShibbolethCheck.java

@@ -0,0 +1,127 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.health;
+
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.InputStreamReader;
+import java.io.StringWriter;
+import java.net.URL;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+public class ShibbolethCheck extends Check {
+
+    protected static final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
+
+    @Override
+    protected String run(ReportInfo ri) {
+//        StringBuilder ret = new StringBuilder();
+//        final String input_dir = configurationService.getProperty("lr",
+//                "lr.shibboleth.log.path");
+//        final String default_log = configurationService.getProperty("lr",
+//                "lr.shibboleth.log.defaultName");
+//
+//        String input_file = new File(input_dir, default_log).toString();
+//
+//        ret.append(String.format("Parsing %s:\n", input_file));
+//        BufferedReader safe_reader = null;
+//        try {
+//            safe_reader = IOUtils.safe_reader(input_file);
+//            // output warnings
+//            ShibUserLogins user_logins = new ShibUserLogins(safe_reader);
+//            if (0 < user_logins.warnings().size()) {
+//                for (String warning : user_logins.warnings()) {
+//                    ret.append(warning + "\n");
+//                }
+//            } else {
+//                ret.append("No shibboleth warnings have been found.\n");
+//            }
+//        } catch (Exception e) {
+//            error(e, String.format("Problematic file [%s]", default_log));
+//            return ret.toString();
+//        }
+//
+//        // > WARN from shibd_warn in the last week
+//        ret.append("\nParsing shibd_warn.*:\n");
+//        File dir = new File(input_dir);
+//        String[] files = dir.list(new java.io.FilenameFilter() {
+//            @Override
+//            public boolean accept(File dir, String name) {
+//                return name.contains("shibd_warn");
+//            }
+//        });
+//        Long nowMillis = System.currentTimeMillis();
+//        String weekAgo = new SimpleDateFormat("yyyy-MM-dd").format(new Date(
+//                nowMillis - 604800000));
+//        String[] cmd = new String[] { "awk", "-v", "from=" + weekAgo,
+//                "BEGIN{FS=\" \"} {if($1>=from) print $0}" };
+//        String[] cmdWithFiles = new String[cmd.length + files.length];
+//        System.arraycopy(cmd, 0, cmdWithFiles, 0, cmd.length);
+//        System.arraycopy(files, 0, cmdWithFiles, cmd.length, files.length);
+//        try {
+//            Process child = Runtime.getRuntime().exec(cmdWithFiles, null, dir);
+//            BufferedReader[] outputs = new BufferedReader[] {
+//                    new BufferedReader(new InputStreamReader(
+//                            child.getInputStream())),
+//                    new BufferedReader(new InputStreamReader(
+//                            child.getErrorStream())) };
+//            for (BufferedReader out : outputs) {
+//                String s = null;
+//                while ((s = out.readLine()) != null) {
+//                    ret.append(s);
+//                    ret.append("\n");
+//                }
+//            }
+//        } catch (java.io.IOException e) {
+//            error(e);
+//        }
+//
+//
+//        try {
+//            String feedsConfig = configurationService.getProperty("discojuice", "feeds");
+//            ret.append(String.format( "Using these static discojuice feeds [%s] as source.\n",
+//                    feedsConfig ));
+//            // Try to download our feeds file, so the proper action is triggered
+//            StringWriter writer = new StringWriter();
+//            org.apache.commons.io.IOUtils.copy(
+//                    new URL(configurationService.getProperty("dspace.url")
+//                            + "/discojuice/feeds").openStream(), writer);
+//            String json = writer.toString();
+//            // end download
+//            Set<String> entities = new HashSet<String>();
+//            JSONParser parser = new JSONParser();
+//            JSONArray entityArray = (JSONArray) parser.parse(json);
+//            Iterator<JSONObject> i = entityArray.iterator();
+//            int counter = 0;
+//            while (i.hasNext()) {
+//                counter++;
+//                JSONObject entity = i.next();
+//                String entityID = (String) entity.get("entityID");
+//                entities.add(entityID);
+//            }
+//            int idCount = entities.size();
+//            ret.append(String.format(
+//                    "Our feeds file contains %d entities out of which %d are unique.\n"
+//                            + "This number should be around 1200?? (20.11.2014).",
+//                    counter, idCount)
+//            );
+//        } catch (Exception e) {
+//            error(e);
+//        }
+//
+//        return ret.toString();
+        return "Space for shibboleth output.";
+    }
+}

dspace-api/src/main/java/org/dspace/health/additionalUtilities/IOUtils.java

@@ -0,0 +1,89 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.health.additionalUtilities;
+
+import org.apache.logging.log4j.Logger;
+
+import java.io.BufferedReader;
+import java.io.EOFException;
+import java.io.File;
+import java.io.InputStreamReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+public class IOUtils {
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IOUtils.class);
+
+    public static String runScript(File where, String[] cmd) {
+        String message = null;
+        try {
+            ProcessBuilder pb = new ProcessBuilder(cmd);
+            pb.directory( where );
+            Process p = pb.start();
+            BufferedReader std_out = new BufferedReader(new InputStreamReader(p.getInputStream()) );
+            BufferedReader std_err = new BufferedReader(new InputStreamReader(p.getErrorStream()) );
+
+            String s = null;
+            message = "Returned stdout:\n";
+            while ((s = std_out.readLine()) != null) {
+                message += s + "\n  ";
+            }
+            message += "Returned stderr:\n";
+            while ((s = std_err.readLine()) != null) {
+                message += s + "\n  ";
+            }
+
+            //Wait to get exit value
+            int exitValue = p.waitFor();
+            message += "Exit code: [" + String.valueOf( exitValue ) + "]\n";
+
+        } catch (Exception e) {
+            message += "\nException:" + e.toString();
+            log.error( e );
+        }
+        return message;
+    }
+
+    /**
+     *
+     * @param input_file
+     * @return
+     * @throws InstantiationException
+     */
+    static public BufferedReader safe_reader( String input_file )
+            throws EOFException, InstantiationException
+    {
+
+        File file = new File(input_file);
+        String file_id = file.getPath();
+
+        if( !file.exists() ) {
+            throw new InstantiationException( file_id + " does not exist!" );
+        }
+        if( file.exists() && 0 == file.length() ) {
+            throw new EOFException( file_id + " is empty!" );
+        }
+
+        BufferedReader reader = null;
+        try {
+            reader = new BufferedReader(
+                    new InputStreamReader(new FileInputStream(file), Charset.forName("UTF8")) );
+        } catch( IOException e ) {
+            throw new InstantiationException( file_id + " exception while reading: " + e.toString() );
+        }
+
+        return reader;
+    }
+
+    static public String today_string() {
+        return new SimpleDateFormat("yyyy-MM-dd").format(new Date());
+    }
+}

dspace-api/src/main/java/org/dspace/health/additionalUtilities/Info.java

@@ -0,0 +1,66 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.health.additionalUtilities;
+
+import java.io.FileInputStream;
+import java.lang.management.ManagementFactory;
+import java.lang.management.RuntimeMXBean;
+import java.util.Scanner;
+
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
+//import src.main.java.org.dspace.xoai.services.impl.config.DSpaceConfigurationService;
+
+public class Info {
+
+    protected static final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
+
+    final static public String get_proc_uptime() {
+        String uptime = "unknown";
+        try {
+            //works only on linux
+            uptime = new Scanner(new FileInputStream("/proc/uptime")).next();
+            System.out.println("\nUPTIME " + uptime);
+            float fuptime = Float.parseFloat( uptime );
+            int seconds = (int) (fuptime % 60);
+            int minutes = (int) ((fuptime / 60) % 60);
+            int hours   = (int) ((fuptime / (60 * 60)) % 24);
+            int days   = (int) ((fuptime / (60 * 60 * 24)) );
+            return Integer.toString( days ) + "d " +
+                    Integer.toString( hours ) + "h:" +
+                    Integer.toString( minutes ) + "m." +
+                    Integer.toString( seconds );
+        } catch (Exception e) {
+            return uptime;
+        }
+    }
+
+    final static public String get_jvm_uptime() {
+        RuntimeMXBean mxBean = ManagementFactory.getRuntimeMXBean();
+        long milliseconds = mxBean.getUptime();
+        int seconds = (int) (milliseconds / 1000) % 60 ;
+        int minutes = (int) ((milliseconds / (1000 * 60)) % 60);
+        int hours   = (int) ((milliseconds / (1000 * 60 * 60)) % 24);
+        int days   = (int) ((milliseconds / (1000 * 60 * 60 * 24)));
+
+        return Integer.toString( days ) + "d " +
+                Integer.toString( hours ) + "h:" +
+                Integer.toString( minutes ) + "m." +
+                Integer.toString( seconds );
+    }
+
+    final static public String get_build_time() {
+        //springacka do nespring triedy, chceme autowired, component
+        String buildTime = configurationService.getProperty("testing-config");
+        if (buildTime != null && !buildTime.equals("")) {
+            return buildTime;
+        }
+        return "unknown";
+    }
+}

dspace-api/src/main/java/org/dspace/health/additionalUtilities/oval/__init__.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+"""
+    oval
+    ~~~~
+
+    BASE OAI-PMH Validity Checker
+
+    :copyright: Copyright 2011 Mathias Loesch.
+"""
+
+import os
+import oval
+
+this_dir, this_filename = os.path.split(__file__)
+
+DATA_PATH = os.path.join(this_dir, "data")
+__version__ = '0.2.0'
+OAI_PMH_VERSION = '2.0'
+
+
+def compress(_list):
+    _list.remove(_list[0])
+    return [item for item in _list if item != '']
+
+
+iso_639_file = open(
+    os.path.join(DATA_PATH, 'iso-639-3.tab'), 'r', encoding='utf-8'
+)
+ISO_639_3_CODES = compress([line.split('\t')[0] for line in iso_639_file])
+iso_639_file.seek(0)
+ISO_639_2B_CODES = compress([line.split('\t')[1] for line in iso_639_file])
+iso_639_file.seek(0)
+ISO_639_2T_CODES = compress([line.split('\t')[2] for line in iso_639_file])
+iso_639_file.seek(0)
+ISO_639_1_CODES = compress([line.split('\t')[3] for line in iso_639_file])