private void deleteBlock(CachedUrl cu) throws IOException {
   log.info("deleting " + cu.getUrl());
   CachedUrlSetSpec cuss = new SingleNodeCachedUrlSetSpec(cu.getUrl());
   ArchivalUnit au = cu.getArchivalUnit();
   CachedUrlSet cus = au.makeCachedUrlSet(cuss);
   NodeManager nm = au.getPlugin().getDaemon().getNodeManager(au);
   nm.deleteNode(cus);
 }
  public void testFunctionalFromTarHierarchy() throws Exception {
    log.debug3("in testFromTarHierarchy");
    // load the tarballs
    InputStream file_input = null;
    try {
      file_input = getResourceAsStream(realTARFile_A);
      // UrlCacher uc = au.makeUrlCacher(TAR_A_BASE);
      // uc.storeContent(file_input, tarHeader);
      UrlCacher uc = tarAu.makeUrlCacher(new UrlData(file_input, tarHeader, TAR_A_BASE));
      uc.storeContent();
      IOUtil.safeClose(file_input);

      file_input = getResourceAsStream(realTARFile_B);
      // uc = au.makeUrlCacher(TAR_B_BASE);
      // uc.storeContent(file_input, tarHeader);
      uc = tarAu.makeUrlCacher(new UrlData(file_input, tarHeader, TAR_B_BASE));
      uc.storeContent();
      IOUtil.safeClose(file_input);

    } catch (IOException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } finally {
      IOUtil.safeClose(file_input);
    }

    CachedUrlSet cus = tarAu.getAuCachedUrlSet();
    for (CachedUrl cu : cus.getCuIterable()) {
      log.debug3("AU - cu is: " + cu.getUrl());
      cu.release();
    }

    // We need to start from the level of the ArticleMetadataExtractor
    MyListEmitter emitter = new MyListEmitter();
    ArticleMetadataExtractor amEx =
        new ElsevierDeferredArticleMetadataExtractor(ArticleFiles.ROLE_ARTICLE_METADATA);

    Iterator<ArticleFiles> it = tarAu.getArticleIterator(MetadataTarget.Any());
    while (it.hasNext()) {
      ArticleFiles af = it.next();
      log.debug3("Metadata test - articlefiles " + af.toString());
      // CachedUrl cu = af.getFullTextCu();
      CachedUrl cu = af.getRoleCu(ArticleFiles.ROLE_ARTICLE_METADATA);
      log.debug3("metadata cu is " + cu.getUrl());
      // List<ArticleMetadata> mdlist = mle.extract(MetadataTarget.Any(), cu);
      amEx.extract(MetadataTarget.Any(), af, emitter);
      List<ArticleMetadata> returnList = emitter.getAmList();

      assertNotNull(returnList);
      log.debug3("size of returnList is " + returnList.size());
      Iterator<ArticleMetadata> mdIt = returnList.iterator();
      ArticleMetadata mdRecord = null;
      while (mdIt.hasNext()) {
        mdRecord = (ArticleMetadata) mdIt.next();
        validateCompleteMetadataRecord(mdRecord);
      }
    }
  }
  public void testArticleCountAndType() throws Exception {
    int expCount = 28;
    PluginTestUtil.crawlSimAu(sau);
    String pat1 = "branch(\\d+)/(\\d+file\\.html)";
    String rep1 = "aps/journal/v123/n$1/full/$2";
    PluginTestUtil.copyAu(sau, nau, ".*[^.][^p][^d][^f]$", pat1, rep1);
    String pat2 = "branch(\\d+)/(\\d+file\\.pdf)";
    String rep2 = "aps/journal/v123/n$1/pdf/$2";
    PluginTestUtil.copyAu(sau, nau, ".*\\.pdf$", pat2, rep2);

    // Remove some URLs
    int deleted = 0;
    for (Iterator it = nau.getAuCachedUrlSet().contentHashIterator(); it.hasNext(); ) {
      CachedUrlSetNode cusn = (CachedUrlSetNode) it.next();
      if (cusn instanceof CachedUrl) {
        CachedUrl cu = (CachedUrl) cusn;
        String url = cu.getUrl();
        if (url.contains("/journal/")
            && (url.endsWith("1file.html") || url.endsWith("2file.pdf"))) {
          deleteBlock(cu);
          ++deleted;
        }
      }
    }
    assertEquals(8, deleted);

    Iterator<ArticleFiles> it = nau.getArticleIterator();
    int count = 0;
    int countHtmlOnly = 0;
    int countPdfOnly = 0;
    while (it.hasNext()) {
      ArticleFiles af = it.next();
      log.info(af.toString());
      CachedUrl cu = af.getFullTextCu();
      String url = cu.getUrl();
      assertNotNull(cu);
      String contentType = cu.getContentType();
      log.debug("count " + count + " url " + url + " " + contentType);
      count++;
      if (af.getRoleUrl(ArticleFiles.ROLE_FULL_TEXT_PDF) == null) {
        ++countHtmlOnly;
      }
      if (af.getRoleUrl(ArticleFiles.ROLE_FULL_TEXT_PDF) == url) {
        ++countPdfOnly;
      }
    }
    log.debug("Article count is " + count);
    assertEquals(expCount, count);
    assertEquals(4, countHtmlOnly);
    assertEquals(4, countPdfOnly);
  }
 private String getUrlContent(CachedUrl url) throws IOException {
   InputStream content = url.getUnfilteredInputStream();
   ByteArrayOutputStream baos = new ByteArrayOutputStream();
   StreamUtil.copy(content, baos);
   content.close();
   String contentStr = new String(baos.toByteArray());
   baos.close();
   return contentStr;
 }
  protected void checkFilter(SimulatedArchivalUnit sau) throws Exception {
    log.debug("checkFilter()");
    CachedUrl cu = sau.makeCachedUrl(sau.getUrlRoot() + "/001file.html");

    enableFilter(sau, true);
    InputStream is = cu.openForHashing();
    String expected = "001file.html This is file 1, depth 0, branch 0. foobar ";
    assertEquals(expected, StringUtil.fromInputStream(is));
    is.close();
    enableFilter(sau, false);
    cu = sau.makeCachedUrl(sau.getUrlRoot() + "/001file.html");
    is = cu.openForHashing();
    expected =
        "<HTML><HEAD><TITLE>001file.html</TITLE></HEAD><BODY>\n"
            + "This is file 1, depth 0, branch 0.<br><!-- comment -->    "
            + "Citation String   foobar<br><script>"
            + "(defun fact (n) (cond ((= n 0) 1) (t (fact (sub1 n)))))</script>\n"
            + "</BODY></HTML>";
    assertEquals(expected, StringUtil.fromInputStream(is));
    is.close();
  }