1 package org.vamsas.test.simpleclient;
3 import java.io.InputStream;
4 import java.io.PrintStream;
5 import java.io.PrintWriter;
8 import uk.ac.vamsas.client.ClientDocument;
9 import uk.ac.vamsas.client.Vobject;
10 import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
11 import uk.ac.vamsas.objects.core.Alignment;
12 import uk.ac.vamsas.objects.core.AppData;
13 import uk.ac.vamsas.objects.core.ApplicationData;
14 import uk.ac.vamsas.objects.core.DataSet;
15 import uk.ac.vamsas.objects.core.Entry;
16 import uk.ac.vamsas.objects.core.Instance;
17 import uk.ac.vamsas.objects.core.Provenance;
18 import uk.ac.vamsas.objects.core.Tree;
19 import uk.ac.vamsas.objects.core.User;
20 import uk.ac.vamsas.objects.core.VAMSAS;
21 import uk.ac.vamsas.objects.core.VamsasDocument;
23 * this class contains static methods for writing info to stdout about a vamsas document
24 * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
25 * Methods return true or false - indicating if the Vobject was valid or not
26 * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
30 public class ArchiveReports {
32 * print an informative summary on a VamsasDocument
34 * @param document - the document itself
35 * @param archive - document source archive for resolving any appData refs
38 public static boolean reportProvenance(Provenance p, PrintStream outstr) {
40 outstr.println("No Provenance");
43 Entry[] pe = p.getEntry();
44 for (int i=0; i<pe.length; i++)
45 outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
48 public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
50 boolean nulldata=false;
51 if (appD.getDataReference()!=null) {
52 String appData=appD.getDataReference();
53 if (appData==null) { outstr.println("Empty DataReference - not valid ?"); }
55 if (appData.length()>1) {
56 outstr.print("a reference ("+appData+")");
58 if ((jstrm=archive.getAppdataStream(appData))!=null)
59 outstr.println(" which resolves to a JarEntry.");
61 outstr.println(" which does not resolve to a JarEntry.");
62 outstr.println("Unresolved appdata reference '"+appData+"'");
68 if (appD.getData()==null)
71 outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
74 outstr.println("Null AppData reference/data chunk.");
79 public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
81 // Report on root appData
82 appDataEntryReport(appD, archive, cascade, outstr);
83 if (appD.getInstanceCount()>0) {
84 Instance inst[] = appD.getInstance();
85 for (int i=0,j=inst.hashCode(); i<j; i++) {
86 outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
87 appDataEntryReport(inst[i],archive,cascade,outstr);
90 if (appD.getUserCount()>0) {
91 User users[] = appD.getUser();
92 for (int i=0,j=users.length; i<j; i++) {
93 outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
94 appDataEntryReport(users[i], archive, cascade, outstr);
101 public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
102 if (document!=null) {
103 outstr.println("Vamsas Document version '"+document.getVersion()+"'");
104 reportProvenance(document.getProvenance(), outstr);
105 outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
106 if (document.getVAMSASCount()>0 && cascade)
107 rootReport(document.getVAMSAS(), true, outstr);
108 if (document.getApplicationDataCount()>0) {
109 outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
110 ApplicationData appd[] = document.getApplicationData();
111 for (int i=0,j=appd.length; i<j; i++) {
112 outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
113 outstr.print("AppData is :");
114 appDataReport(appd[i], archive, cascade, outstr);
120 outstr.println("Document Object is null");
126 * summarises all the datasets in a vamsas document.
128 * @param cascade TODO
132 public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
134 for (int i=0; i<roots.length; i++) {
137 outstr.print("Vamsas Root "+i+" (id="
138 +((r.getId()!=null) ? r.getId():"<none>")
139 +") contains "+(ds=r.getDataSetCount())+" DataSets, "
140 + (tr=r.getTreeCount())+" Global trees\n");
142 for (int j=0; j<ds; j++) {
143 outstr.println("Dataset "+j);
144 cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
146 for (int j=0; j<tr; j++) {
147 outstr.println("Global tree "+j);
148 cascade = treeReport(r.getTree(j), true, outstr) && cascade;
156 public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
158 reportProvenance(ds.getProvenance(), outstr);
159 outstr.println("Dataset contains : "+ds.getSequenceCount()
160 +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
162 alignmentReport(ds.getAlignment(), true, outstr);
165 public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
167 if (al!=null && al.length>0) {
168 for (int i=0; i<al.length; i++) {
169 outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
171 reportProvenance(al[i].getProvenance(), outstr);
172 outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
173 +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
175 for (int t=0; t<al[i].getTreeCount(); t++)
176 treeReport(al[i].getTree(t), true, outstr);
182 public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
183 outstr.println("Tree: '"+t.getTitle()+"'");
184 return !cascade || reportProvenance(t.getProvenance(), outstr);