X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Ftest%2Fsimpleclient%2FArchiveReports.java;h=83989afe42c78b329c7979f8bae0025de0944237;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=94d06bfd5277d5602a7b91daf3258f10afe7898e;hpb=3b92275c26c14a678519f1d7d2ffaa477eb76cdb;p=vamsas.git

diff --git a/src/uk/ac/vamsas/test/simpleclient/ArchiveReports.java b/src/uk/ac/vamsas/test/simpleclient/ArchiveReports.java
index 94d06bf..83989af 100644
--- a/src/uk/ac/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/uk/ac/vamsas/test/simpleclient/ArchiveReports.java
@@ -1,187 +1,268 @@
-package uk.ac.vamsas.test.simpleclient;
-
-import java.io.InputStream;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-
-
-import uk.ac.vamsas.client.ClientDocument;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.Alignment;
-import uk.ac.vamsas.objects.core.AppData;
-import uk.ac.vamsas.objects.core.ApplicationData;
-import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Instance;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.Tree;
-import uk.ac.vamsas.objects.core.User;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-/**
- * this class contains static methods for writing info to stdout about a vamsas document
- * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
- * Methods return true or false - indicating if the Vobject was valid or not
- * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
- * @author jimp
- *
- */
-public class ArchiveReports {
-    /**
-     * print an informative summary on a VamsasDocument
-     * @param outstr TODO
-     * @param document - the document itself
-     * @param archive - document source archive for resolving any appData refs
-     * @return
-     */
-  public static boolean reportProvenance(Provenance p, PrintStream outstr) {
-    if (p==null) {
-      outstr.println("No Provenance");
-      return false;
-    }
-    Entry[] pe = p.getEntry();
-    for (int i=0; i<pe.length; i++)
-      outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
-    return true;
-  }
-  public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (appD!=null) {
-      boolean nulldata=false;
-      if (appD.getDataReference()!=null) {
-        String appData=appD.getDataReference();
-        if (appData==null) { outstr.println("Empty DataReference - not valid ?"); } 
-        else 
-          if (appData.length()>1) {
-          outstr.print("a reference ("+appData+")");
-          InputStream jstrm;
-          if ((jstrm=archive.getAppdataStream(appData))!=null)
-            outstr.println(" which resolves to a JarEntry.");
-          else {
-            outstr.println(" which does not resolve to a JarEntry.");
-            outstr.println("Unresolved appdata reference '"+appData+"'");
-          }
-        } else {
-          nulldata=true;
-        }
-      } else {
-        if (appD.getData()==null)
-          nulldata &= true;
-          else
-          outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
-      }
-      if (nulldata)
-        outstr.println("Null AppData reference/data chunk.");
-    }
-    return true;
-  }
-  
-  public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (appD!=null) {
-      // Report on root appData
-      appDataEntryReport(appD, archive, cascade, outstr);
-      if (appD.getInstanceCount()>0) {
-        Instance inst[] = appD.getInstance();
-        for (int i=0,j=inst.hashCode(); i<j; i++) {
-          outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
-          appDataEntryReport(inst[i],archive,cascade,outstr);
-        }
-      }
-      if (appD.getUserCount()>0) {
-        User users[] = appD.getUser();
-        for (int i=0,j=users.length; i<j; i++) {
-          outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
-          appDataEntryReport(users[i], archive, cascade, outstr);
-        }
-      }
-    }
-
-    return true;
-  }
-  public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
-    if (document!=null) {
-      outstr.println("Vamsas Document version '"+document.getVersion()+"'");
-      reportProvenance(document.getProvenance(), outstr);
-      outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
-      if (document.getVAMSASCount()>0 && cascade)
-        rootReport(document.getVAMSAS(), true, outstr);
-      if (document.getApplicationDataCount()>0) {
-        outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
-        ApplicationData appd[] = document.getApplicationData();
-        for (int i=0,j=appd.length; i<j; i++) {
-          outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
-          outstr.print("AppData is :");
-          appDataReport(appd[i], archive, cascade, outstr);
-        }
-          
-      }
-      return true;
-    } else {
-      outstr.println("Document Object is null");
-    }
-    return false;
-  }
-
-  /**
-   * summarises all the datasets in a vamsas document.
-   * @param roots
-   * @param cascade TODO
-   * @param outstr TODO
-   * @return
-   */
-  public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
-    if (roots!=null) {
-      for (int i=0; i<roots.length; i++) {
-        VAMSAS r = roots[i];
-        int ds, tr;
-        outstr.print("Vamsas Root "+i+" (id="
-            +((r.getId()!=null) ? r.getId():"<none>")
-            +") contains "+(ds=r.getDataSetCount())+" DataSets, "
-            + (tr=r.getTreeCount())+" Global trees\n");
-        if (cascade) {
-          for (int j=0; j<ds; j++) {
-            outstr.println("Dataset "+j);
-            cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
-          }
-          for (int j=0; j<tr; j++) {
-            outstr.println("Global tree "+j);
-            cascade = treeReport(r.getTree(j), true, outstr) && cascade;
-          }
-        }
-      }
-      return true;
-    }
-    return false;
-  }
-  public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
-    if (cascade)
-      reportProvenance(ds.getProvenance(), outstr);
-    outstr.println("Dataset contains : "+ds.getSequenceCount()
-        +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
-    if (cascade)
-      alignmentReport(ds.getAlignment(), true, outstr);
-    return true;
-  }
-  public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
-    boolean val=true;
-    if (al!=null && al.length>0) {
-      for (int i=0; i<al.length; i++) {
-        outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
-        if (cascade)
-          reportProvenance(al[i].getProvenance(), outstr);
-        outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
-            +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
-        if (cascade) {
-          for (int t=0; t<al[i].getTreeCount(); t++)
-            treeReport(al[i].getTree(t), true, outstr);
-        }
-      }
-    }
-    return val;
-  }
-  public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
-    outstr.println("Tree: '"+t.getTitle()+"'");
-    return !cascade || reportProvenance(t.getProvenance(), outstr);
-  }
-
-}
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package uk.ac.vamsas.test.simpleclient;
+
+import java.io.InputStream;
+import java.io.PrintStream;
+import java.io.PrintWriter;
+
+import uk.ac.vamsas.client.ClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AppData;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Instance;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.Tree;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+
+/**
+ * this class contains static methods for writing info to stdout about a vamsas
+ * document Methods have a 'cascade' switch to indicate if sub-objects should
+ * have info printed on them. Methods return true or false - indicating if the
+ * Vobject was valid or not TODO: LATER: propagate true/false return so that an
+ * invalid vamsas Vobject invalidates the whole document
+ * 
+ * @author jimp
+ * 
+ */
+public class ArchiveReports {
+  /**
+   * print an informative summary on a VamsasDocument
+   * 
+   * @param outstr
+   *          TODO
+   * @param document
+   *          - the document itself
+   * @param archive
+   *          - document source archive for resolving any appData refs
+   * @return
+   */
+  public static boolean reportProvenance(Provenance p, PrintStream outstr) {
+    if (p == null) {
+      outstr.println("No Provenance");
+      return false;
+    }
+    Entry[] pe = p.getEntry();
+    for (int i = 0; i < pe.length; i++) {
+      outstr.print(pe[i].getDate() + "\t'" + pe[i].getUser() + "'\t"
+          + pe[i].getApp() + "\t'" + pe[i].getAction() + "' ");
+      outputVobjectState(pe[i], outstr);
+    }
+    return true;
+  }
+
+  public static boolean appDataEntryReport(AppData appD,
+      VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
+    if (appD != null) {
+      boolean nulldata = false;
+      if (appD.getDataReference() != null) {
+        String appData = appD.getDataReference();
+        if (appData == null) {
+          outstr.println("Empty DataReference - not valid ?");
+        } else if (appData.length() > 1) {
+          outstr.print("a reference (" + appData + ")");
+          InputStream jstrm;
+          if ((jstrm = archive.getAppdataStream(appData)) != null)
+            outstr.println(" which resolves to a JarEntry.");
+          else {
+            outstr.println(" which does not resolve to a JarEntry.");
+            outstr.println("Unresolved appdata reference '" + appData + "'");
+          }
+        } else {
+          nulldata = true;
+        }
+      } else {
+        if (appD.getData() == null)
+          nulldata &= true;
+        else
+          outstr.println("an embedded chunk of " + appD.getData().length
+              + " bytes.");
+      }
+      if (nulldata)
+        outstr.println("Null AppData reference/data chunk.");
+    }
+    return true;
+  }
+
+  public static boolean appDataReport(ApplicationData appD,
+      VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
+    if (appD != null) {
+      // Report on root appData
+      appDataEntryReport(appD, archive, cascade, outstr);
+      if (appD.getInstanceCount() > 0) {
+        Instance inst[] = appD.getInstance();
+        for (int i = 0, j = inst.hashCode(); i < j; i++) {
+          outstr.println("Data for App Instance URN: '" + inst[i].getUrn());
+          appDataEntryReport(inst[i], archive, cascade, outstr);
+        }
+      }
+      if (appD.getUserCount() > 0) {
+        User users[] = appD.getUser();
+        for (int i = 0, j = users.length; i < j; i++) {
+          outstr.println("Data for User '" + users[i].getFullname() + "' of '"
+              + users[i].getOrganization() + "'");
+          appDataEntryReport(users[i], archive, cascade, outstr);
+        }
+      }
+    }
+
+    return true;
+  }
+
+  public static boolean reportDocument(VamsasDocument document,
+      VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
+    if (document != null) {
+      outstr.println("Vamsas Document version '" + document.getVersion() + "'");
+      reportProvenance(document.getProvenance(), outstr);
+      outstr.print("Document contains " + document.getVAMSASCount()
+          + " VAMSAS Elements and " + document.getApplicationDataCount()
+          + " Application data elements.\n");
+      if (document.getVAMSASCount() > 0 && cascade)
+        rootReport(document.getVAMSAS(), true, outstr);
+      if (document.getApplicationDataCount() > 0) {
+        outstr.print("There are " + document.getApplicationDataCount()
+            + " ApplicationData references.\n");
+        ApplicationData appd[] = document.getApplicationData();
+        for (int i = 0, j = appd.length; i < j; i++) {
+          outstr.print("Application " + i + ": '" + appd[i].getName()
+              + "'\nVersion '" + appd[i].getVersion() + "'\n");
+          outstr.print("AppData is :");
+          appDataReport(appd[i], archive, cascade, outstr);
+        }
+
+      }
+      return true;
+    } else {
+      outstr.println("Document Object is null");
+    }
+    return false;
+  }
+
+  /**
+   * summarises all the datasets in a vamsas document.
+   * 
+   * @param roots
+   * @param cascade
+   *          TODO
+   * @param outstr
+   *          TODO
+   * @return
+   */
+  public static boolean rootReport(VAMSAS[] roots, boolean cascade,
+      PrintStream outstr) {
+    if (roots != null) {
+      for (int i = 0; i < roots.length; i++) {
+        VAMSAS r = roots[i];
+        int ds, tr;
+        outstr.print("Vamsas Root " + i + " (id="
+            + ((r.getId() != null) ? r.getId() : "<none>") + ") contains "
+            + (ds = r.getDataSetCount()) + " DataSets, "
+            + (tr = r.getTreeCount()) + " Global trees\n");
+        outputVobjectState(r, outstr);
+        if (cascade) {
+          for (int j = 0; j < ds; j++) {
+            outstr.println("Dataset " + j);
+            cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade;
+          }
+          for (int j = 0; j < tr; j++) {
+            outstr.println("Global tree " + j);
+            cascade = treeReport(r.getTree(j), true, outstr) && cascade;
+          }
+        }
+      }
+      return true;
+    }
+    return false;
+  }
+
+  public static void outputVobjectState(Vobject v, PrintStream outstr) {
+    outstr.print(" (Object is: ");
+    boolean comma = false;
+    if (v.is__stored_in_document()) {
+      outstr.print(" stored");
+      comma = true;
+    }
+    if (v.isNewInDocument()) {
+      if (comma)
+        outstr.print(",");
+      comma = true;
+      outstr.print(" new in document");
+    }
+    if (v.isUpdated()) {
+      if (comma)
+        outstr.print(",");
+      comma = true;
+      outstr.print(" updated since last read");
+    }
+    outstr.println(")");
+  }
+
+  public static boolean datasetReport(DataSet ds, boolean cascade,
+      PrintStream outstr) {
+    if (cascade)
+      reportProvenance(ds.getProvenance(), outstr);
+    outputVobjectState(ds, outstr);
+    outstr.println("Dataset contains : " + ds.getSequenceCount()
+        + " sequences, " + ds.getAlignmentCount() + " alignments and "
+        + ds.getTreeCount() + " trees.");
+    if (cascade)
+      alignmentReport(ds.getAlignment(), true, outstr);
+    return true;
+  }
+
+  public static boolean alignmentReport(Alignment[] al, boolean cascade,
+      PrintStream outstr) {
+    boolean val = true;
+    if (al != null && al.length > 0) {
+      for (int i = 0; i < al.length; i++) {
+        outstr.println("Alignment "
+            + i
+            + (al[i].isRegistered() ? " (" + al[i].getVorbaId() + ")"
+                : " (unregistered)"));
+        outputVobjectState(al[i], outstr);
+        if (cascade)
+          reportProvenance(al[i].getProvenance(), outstr);
+        outstr.println("Involves " + al[i].getAlignmentSequenceCount()
+            + " sequences, has " + al[i].getAlignmentAnnotationCount()
+            + " annotations and " + al[i].getTreeCount() + " trees.");
+        if (cascade) {
+          for (int t = 0; t < al[i].getTreeCount(); t++)
+            treeReport(al[i].getTree(t), true, outstr);
+        }
+      }
+    }
+    return val;
+  }
+
+  public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
+    outstr.print("Tree: '" + t.getTitle() + "' ");
+    outputVobjectState(t, outstr);
+    return !cascade || reportProvenance(t.getProvenance(), outstr);
+  }
+
+}