Merge pull request #4837 from mtbc/enum-autopopulate

have OMERO server populate database with missing enumeration values

components/model/src/ome/util/SqlAction.java

@@ -332,6 +332,7 @@ private boolean append(final StringBuilder sb, final boolean first,
 
     long countFormat(String name);
 
+    @Deprecated  // use ome.services.util.EnsureEnum
     int insertFormat(String name);
 
     int closeSessions(String uuid);

components/model/src/ome/util/actions/PostgresSqlAction.java

@@ -128,9 +128,11 @@ public long countFormat(String name) {
     }
 
     // Copied from data.vm
+    @Deprecated  // use ome.services.util.EnsureEnum
     public final static String insertFormatSql = PsqlStrings
             .getString("sql_action.insert_format"); //$NON-NLS-1$
 
+    @Deprecated  // use ome.services.util.EnsureEnum
     public int insertFormat(String name) {
         return _jdbc().update(insertFormatSql, name);
     }

components/server/resources/ome/services/startup.xml

@@ -41,11 +41,27 @@
      lazy-init="false">
   </bean>
 
-  <bean id="dbEnumerationCheck"
+  <bean id="dbFormatEnumerationCheck"
      class="ome.services.util.DBEnumCheck"
      init-method="start" lazy-init="false">
      <constructor-arg ref="executor"/>
      <constructor-arg ref="preferenceContext"/>
+     <constructor-arg ref="ensureEnum"/>
+  </bean>
+
+  <bean id="dbMappedEnumerationCheck"
+     class="ome.services.util.DBMappedEnumCheck"
+     init-method="start" lazy-init="false">
+     <constructor-arg ref="executor"/>
+     <constructor-arg ref="preferenceContext"/>
+     <constructor-arg ref="ensureEnum"/>
+  </bean>
+
+  <bean id="ensureEnum"
+     class="ome.services.util.EnsureEnum">
+     <constructor-arg ref="executor"/>
+     <constructor-arg ref="uuid"/>
+     <constructor-arg ref="roles"/>
   </bean>
 
   <bean id="dbUnicodeUnitsCheck" depends-on="dbPatchCheck"

components/server/src/ome/logic/TypesImpl.java

@@ -166,10 +166,11 @@ public <T extends IEnum> Map<Class<T>, List<T>> getEnumerationsWithEntries() {
     public <T extends IEnum> List<T> getOriginalEnumerations() {
         List<IEnum> original = new ArrayList<IEnum>();
         InputStream in = null;
+        JarFile jarFile = null;
         try {
             URL file = ResourceUtils.getURL("classpath:enums.properties");
             URL jar = ResourceUtils.extractJarFileURL(file);
-            JarFile jarFile = new JarFile(jar.getPath());
+            jarFile = new JarFile(jar.getPath());
             JarEntry entry = jarFile.getJarEntry("enums.properties");
             in = jarFile.getInputStream(entry);
             Properties property = new Properties();
@@ -212,7 +213,8 @@ public <T extends IEnum> List<T> getOriginalEnumerations() {
             throw new RuntimeException("No such method. " + e.getMessage());
         } finally {
             try {
-                in.close();
+                if (in != null) in.close();
+                if (jarFile != null) jarFile.close();
             } catch (IOException e) {
             }
         }

components/server/src/ome/services/util/BaseDBCheck.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2014 University of Dundee & Open Microscopy Environment.
+ * Copyright (C) 2014-2016 University of Dundee & Open Microscopy Environment.
  * All rights reserved.
  *
  * This program is free software; you can redistribute it and/or modify
@@ -41,9 +41,7 @@ abstract class BaseDBCheck {
     private final String version;
     private final int patch;
 
-    private final String configKey = "DB check " + getClass().getSimpleName();
-    private final String configValue = getCheckDone();
-    private final String configKeyValue = configKey + ": " + configValue;
+    private final String configKey, configValue, configKeyValue;
 
     /**
      * @param executor executor to use for configuration map check
@@ -52,6 +50,11 @@ protected BaseDBCheck(Executor executor, PreferenceContext preferences) {
         this.executor = executor;
         this.version = preferences.getProperty("omero.db.version");
         this.patch = Integer.parseInt(preferences.getProperty("omero.db.patch"));
+
+        /* these values may depend upon version and patch above */
+        configKey = "DB check " + getClass().getSimpleName();
+        configValue = getCheckDone();
+        configKeyValue = configKey + ": " + configValue;
     }
 
     /**
@@ -122,4 +125,11 @@ public void start() {
     protected String getCheckDone() {
         return "done";
     }
+
+    /**
+     * @return a string representing the version and patch of this server
+     */
+    protected String getOmeroVersion() {
+        return version + "__" + patch;
+    }
 }

components/server/src/ome/services/util/DBEnumCheck.java

@@ -6,20 +6,16 @@
 package ome.services.util;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
-import ome.conditions.InternalException;
+
+import ome.model.enums.Format;
 import ome.system.PreferenceContext;
-import ome.util.SqlAction;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.transaction.annotation.Transactional;
 
 /**
  * Hook run by the context to guarantee that various enumerations are up to
@@ -29,124 +25,37 @@
  * greatest without a database upgrade.
  * 
  * @author Josh Moore, josh at glencoesoftware.com
+ * @author m.t.b.carroll@dundee.ac.uk
  * @since Beta4.1.1
  */
 public class DBEnumCheck extends BaseDBCheck {
 
     public final static Logger log = LoggerFactory.getLogger(DBEnumCheck.class);
 
-    public final static Pattern readerClass = Pattern
-            .compile("^.*?[.]?([^.]+)Reader$");
-
-    /**
-     * Hard-coded list of formats missing from 4.1 which should have a
-     * "Companion/<reader>" value in the database. Temporary until bio-formats
-     * provides inspection on this information.
-     */
-    final private static List<String> companionful = Arrays.asList("Analyze",
-            "APL", "L2D", "Nifti", "TillVision", "Scanr");
-
-    /**
-     * Hard-coded list of formats missing from 4.1 which should NOT have a
-     * "Companion/<reader>" value in the database. Temporary until bio-formats
-     * provides inspection on this information.
-     */
-    final private static List<String> companionless = Arrays.asList("Zip",
-            "APNG", "PCX", "Ivision", "FEI", "NAF", "MINC", "MRW", "ARF",
-            "Cellomics", "LiFlim", "Amira");
-
-    /**
-     * Hard-coded list of formats missing from 4.1 which should NOT have a
-     * "Companion/<reader>" NOR a format at all. Temporary until bio-formats
-     * provides inspection on this information.
-     */
-    final private static List<String> omitlist = Arrays.asList("Fake");
-
-    public static List<String> getReaderNames() {
-        List<String> rv = new ArrayList<String>();
-        IFormatReader[] readers = new ImageReader().getReaders();
-        for (IFormatReader formatReader : readers) {
-
-            String name = formatReader.getClass().getSimpleName();
-            Matcher matcher = readerClass.matcher(name);
-            if (!matcher.matches()) {
-                log.warn("Reader doesn't match: " + name);
-                continue;
-            }
-
-            rv.add(matcher.group(1));
-        }
-        return rv;
-    }
-
-    public static boolean requiresCompanion(String name) {
-        return companionful.contains(name);
-    }
-
-    public static boolean shouldBeOmitted(String name) {
-        return omitlist.contains(name);
-    }
+    private final EnsureEnum ensureEnum;
 
-    public DBEnumCheck(Executor executor, PreferenceContext preferences) {
+    public DBEnumCheck(Executor executor, PreferenceContext preferences, EnsureEnum ensureEnum) {
         super(executor, preferences);
+        this.ensureEnum = ensureEnum;
     }
 
     @Override
     protected void doCheck() {
-        try {
-            executor.executeSql(new Executor.SimpleSqlWork(this,
-                    "DBEnumCheck") {
-                @Transactional(readOnly = false)
-                public Object doWork(SqlAction sql) {
-                    for (String name : getReaderNames()) {
-                        addFormat(sql, name);
-                        if (requiresCompanion(name)) {
-                            addFormat(sql, "Companion/" + name);
-                        }
-                    }
-                    return null;
+        final List<String> formatNames = new ArrayList<String>();
+        for (final IFormatReader formatReader : new ImageReader().getReaders()) {
+            String name = formatReader.getClass().getSimpleName();
+            if (name.endsWith("Reader")) {
+                name = name.substring(0, name.length() - 6);
+                if ("Fake".equals(name)) {
+                    continue;
                 }
-
-            });
-        } catch (Exception e) {
-            final String msg = "Error synchronizing enumerations";
-            log.error(msg, e); // slf4j migration: fatal() to error()
-            InternalException ie = new InternalException(msg);
-            throw ie;
-        }
-    }
-
-    /**
-     * Adds an ome.model.enums.Format object if 1) the format value is not
-     * omitted, 2) it doesn't already exist.
-     * 
-     * @param jdbc
-     * @param name
-     * @return true if the format was added.
-     */
-    private boolean addFormat(SqlAction sql, String name) {
-
-        if (shouldBeOmitted(name)) {
-            log.debug("Omitting: " + name);
-            return false;
-        }
-
-        long count = sql.countFormat(name);
-
-        if (count > 0) {
-            log.debug("Found reader: " + name);
-            return false;
-        }
-
-        int inserts = sql.insertFormat(name);
-        if (inserts != 1) {
-            throw new InternalException("Expected 1 insert. Found " + inserts
-                    + " while adding: " + name);
+                formatNames.add(name);
+                if (formatReader.hasCompanionFiles()) {
+                    formatNames.add("Companion/" + name);
+                }
+            }
         }
-
-        log.info("Added format: " + name);
-        return true;
-
+        ensureEnum.ensure(Format.class, formatNames);
     }
 
     @Override