1 package org.vamsas.test.simpleclient;
3 import java.io.InputStream;
4 import java.io.PrintStream;
5 import java.io.PrintWriter;
7 import org.vamsas.client.ClientDocument;
8 import org.vamsas.client.Vobject;
9 import org.vamsas.client.simpleclient.VamsasArchiveReader;
10 import org.vamsas.objects.core.Alignment;
11 import org.vamsas.objects.core.AppData;
12 import org.vamsas.objects.core.ApplicationData;
13 import org.vamsas.objects.core.DataSet;
14 import org.vamsas.objects.core.Entry;
15 import org.vamsas.objects.core.Instance;
16 import org.vamsas.objects.core.Provenance;
17 import org.vamsas.objects.core.Tree;
18 import org.vamsas.objects.core.User;
19 import org.vamsas.objects.core.VAMSAS;
20 import org.vamsas.objects.core.VamsasDocument;
22 * this class contains static methods for writing info to stdout about a vamsas document
23 * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
24 * Methods return true or false - indicating if the Vobject was valid or not
25 * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document
29 public class ArchiveReports {
31 * print an informative summary on a VamsasDocument
33 * @param document - the document itself
34 * @param archive - document source archive for resolving any appData refs
37 public static boolean reportProvenance(Provenance p, PrintStream outstr) {
39 outstr.println("No Provenance");
42 Entry[] pe = p.getEntry();
43 for (int i=0; i<pe.length; i++)
44 outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
47 public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
49 boolean nulldata=false;
50 if (appD.getDataReference()!=null) {
51 String appData=appD.getDataReference();
52 if (appData==null) { outstr.println("Empty DataReference - not valid ?"); }
54 if (appData.length()>1) {
55 outstr.print("a reference ("+appData+")");
57 if ((jstrm=archive.getAppdataStream(appData))!=null)
58 outstr.println(" which resolves to a JarEntry.");
60 outstr.println(" which does not resolve to a JarEntry.");
61 outstr.println("Unresolved appdata reference '"+appData+"'");
67 if (appD.getData()==null)
70 outstr.println("an embedded chunk of "+appD.getData().length+" bytes.");
73 outstr.println("Null AppData reference/data chunk.");
78 public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
80 // Report on root appData
81 appDataEntryReport(appD, archive, cascade, outstr);
82 if (appD.getInstanceCount()>0) {
83 Instance inst[] = appD.getInstance();
84 for (int i=0,j=inst.hashCode(); i<j; i++) {
85 outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
86 appDataEntryReport(inst[i],archive,cascade,outstr);
89 if (appD.getUserCount()>0) {
90 User users[] = appD.getUser();
91 for (int i=0,j=users.length; i<j; i++) {
92 outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
93 appDataEntryReport(users[i], archive, cascade, outstr);
100 public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
101 if (document!=null) {
102 outstr.println("Vamsas Document version '"+document.getVersion()+"'");
103 reportProvenance(document.getProvenance(), outstr);
104 outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
105 if (document.getVAMSASCount()>0 && cascade)
106 rootReport(document.getVAMSAS(), true, outstr);
107 if (document.getApplicationDataCount()>0) {
108 outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n");
109 ApplicationData appd[] = document.getApplicationData();
110 for (int i=0,j=appd.length; i<j; i++) {
111 outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
112 outstr.print("AppData is :");
113 appDataReport(appd[i], archive, cascade, outstr);
119 outstr.println("Document Object is null");
125 * summarises all the datasets in a vamsas document.
127 * @param cascade TODO
131 public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
133 for (int i=0; i<roots.length; i++) {
136 outstr.print("Vamsas Root "+i+" (id="
137 +((r.getId()!=null) ? r.getId():"<none>")
138 +") contains "+(ds=r.getDataSetCount())+" DataSets, "
139 + (tr=r.getTreeCount())+" Global trees\n");
141 for (int j=0; j<ds; j++) {
142 outstr.println("Dataset "+j);
143 cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
145 for (int j=0; j<tr; j++) {
146 outstr.println("Global tree "+j);
147 cascade = treeReport(r.getTree(j), true, outstr) && cascade;
155 public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
157 reportProvenance(ds.getProvenance(), outstr);
158 outstr.println("Dataset contains : "+ds.getSequenceCount()
159 +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
161 alignmentReport(ds.getAlignment(), true, outstr);
164 public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
166 if (al!=null && al.length>0) {
167 for (int i=0; i<al.length; i++) {
168 outstr.println("Alignment "+i);
170 reportProvenance(al[i].getProvenance(), outstr);
171 outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
172 +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
174 for (int t=0; t<al[i].getTreeCount(); t++)
175 treeReport(al[i].getTree(t), true, outstr);
181 public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
182 outstr.println("Tree: '"+t.getTitle()+"'");
183 return !cascade || reportProvenance(t.getProvenance(), outstr);