Examples of MisoPerlDaemonInterrogationMechanism

uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism
A concrete interrogation mechanism that interrogates a queryable SequencerReference with a MisoPerlDaemonQuery that produces a MisoPerlDaemonResult @author Rob Davey @date 07-Oct-2010 @since 0.0.2

Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

  }


  @Override
  public List<Status> listAllStatus(SequencerReference sr) throws InterrogationException {
    List<Status> s = new ArrayList<Status>();
    JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), statusQuery).parseResult());
    if (response != null && response.has("response")) {
      JSONArray a = response.getJSONArray("response");
      for (JSONObject j : (Iterable<JSONObject>) a) {
        if (j.has("file") && j.has("xml")) {
          try {

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    return sts;
  }


  @Override
  public List<String> listRunsByHealthType(SequencerReference sr, HealthType healthType) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), new MisoPerlDaemonQuery("Illumina", healthType.getKey().toLowerCase())).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*/([\\d]+_[A-z0-9]+_[\\d]+_[A-z0-9_]*)/.*";

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    return s;
  }


  @Override
  public List<String> listAllCompleteRuns(SequencerReference sr) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), completeRunsQuery).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*/([\\d]+_[A-z0-9]+_[\\d]+_[A-z0-9_]*)/.*";

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    return s;
  }


  @Override
  public List<String> listAllIncompleteRuns(SequencerReference sr) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), incompleteRunsQuery).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*/([\\d]+_[A-z0-9]+_[\\d]+_[A-z0-9_]*)/.*";

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

  @Override
  public Status getRunStatus(SequencerReference sr, String runName) throws InterrogationException {
    MisoPerlDaemonQuery runStatusQuery = new MisoPerlDaemonQuery("Illumina", runName, "status");


    try {
      JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), runStatusQuery).parseResult());
      if (response != null && response.has("response")) {
        JSONArray a = response.getJSONArray("response");
        if (a.iterator().hasNext()) {
          JSONObject j = (JSONObject) a.iterator().next();
          if (j.has("file") && j.has("xml")) {

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

  public JSONObject getRunInformation(SequencerReference sr, String runName) throws InterrogationException {
    MisoPerlDaemonQuery runInfoQuery = new MisoPerlDaemonQuery("Illumina", runName, "status");


    JSONObject json = new JSONObject();
    try {
      JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), runInfoQuery).parseResult());
      if (response != null && response.has("response")) {
        JSONArray a = response.getJSONArray("response");
        if (a.iterator().hasNext()) {
          JSONObject j = (JSONObject) a.iterator().next();
          if (j.has("file") && j.has("xml")) {

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    return (sr.getPlatform().getPlatformType().equals(PlatformType.LS454));
  }


  public List<Status> listAllStatus(SequencerReference sr) throws InterrogationException {
    List<Status> s = new ArrayList<Status>();
    JSONObject response = JSONObject.fromObject(doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), statusQuery).parseResult());
    if (response != null && response.has("response")) {
      JSONArray a = response.getJSONArray("response");
      for (JSONObject j : (Iterable<JSONObject>) a) {
        if (j.has("file") && j.has("xml")) {
          try {

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    return null;
  }


  @Override
  public List<String> listRunsByHealthType(SequencerReference sr, HealthType healthType) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), new MisoPerlDaemonQuery("454", healthType.getKey().toLowerCase())).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*/([\\d]+_[A-z0-9]+_[\\d]+_[A-z0-9_]*)/.*";

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    Collections.sort(s);
    return s;
  }


  public List<String> listAllCompleteRuns(SequencerReference sr) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), completeRunsQuery).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*\\/(R_\\d{4}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_[A-z0-9]+_[A-z0-9]+_[A-z0-9_\\-]+)\\/.*";

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.mechanism.interrogator.MisoPerlDaemonInterrogationMechanism

    Collections.sort(s);
    return s;
  }


  public List<String> listAllIncompleteRuns(SequencerReference sr) throws InterrogationException {
    String response = doQuery(sr, new MisoPerlDaemonInterrogationMechanism(), incompleteRunsQuery).parseResult();
    List<String> s = new ArrayList<String>();
    if (response != null) {
      String[] ss = response.split(",");
      for (String sss : ss) {
        String regex = ".*\\/(R_\\d{4}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_\\d{2}_[A-z0-9]+_[A-z0-9]+_[A-z0-9_\\-]+)\\/.*";

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