[kepler-dev] Fwd: [kepler-code] r20864 - in trunk/modules: provenance/src/org/kepler/provenance/sql provenance/src/org/kepler/util workflow-run-manager/src/org/kepler/workflowrunmanager
Derik Barseghian
barseghian at nceas.ucsb.edu
Fri Oct 2 18:57:18 PDT 2009
Hi devs,
I don't think anyone besides me is using them, but if you've created
run-archives with the workflow-run-manager module, you'll now get
errors trying to open them.
I recommend deleting them and making new ones. If you really want to
keep using an old one, let me know, you just have to add the hostId
entry in the WorkflowRun file.
Derik
Begin forwarded message:
> From: barseghian at ecoinformatics.org
> Date: October 2, 2009 6:50:28 PM PDT
> To: kepler-cvs at kepler-project.org
> Subject: [kepler-code] r20864 - in trunk/modules: provenance/src/org/
> kepler/provenance/sql provenance/src/org/kepler/util workflow-run-
> manager/src/org/kepler/workflowrunmanager
>
> Author: barseghian
> Date: 2009-10-02 18:50:27 -0700 (Fri, 02 Oct 2009)
> New Revision: 20864
>
> Modified:
> trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLQueryV8.java
> trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLRecordingV8.java
> trunk/modules/provenance/src/org/kepler/util/WorkflowRun.java
> trunk/modules/workflow-run-manager/src/org/kepler/
> workflowrunmanager/WorkflowRunManager.java
> Log:
> now recording host_id in WorkflowRun. You'll want to delete any
> existing run-archives to avoid errors.
>
> Modified: trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLQueryV8.java
> ===================================================================
> --- trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLQueryV8.java 2009-10-02 23:41:25 UTC (rev 20863)
> +++ trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLQueryV8.java 2009-10-03 01:50:27 UTC (rev 20864)
> @@ -323,7 +323,7 @@
> String queryStr =
> "SELECT wf.name wf_name, wf.lsid wf_lsid,
> wfexec.user, " +
> "wfexec.id wfexec_id, wfexec.start_time, " +
> - "wfexec.end_time, wfexec.lsid run_lsid, " +
> + "wfexec.end_time, wfexec.lsid run_lsid,
> wfexec.host_id host_id, " +
> "err.id error_id, err.message error_message " +
> "FROM " + workflowStr + " wf, " + wfExecStr + "
> wfexec " +
> "LEFT JOIN " + errorStr + " err ON
> wfexec.id=err.exec_id " +
> @@ -388,7 +388,7 @@
> WorkflowRun run = null;
> try
> {
> - run = new WorkflowRun(runLSID,
> result.getString("user"), result.getString("wf_name"),
> result.getString("wf_lsid"), startTime, duration, execId, errorMsgs);
> + run = new WorkflowRun(runLSID,
> result.getString("user"), result.getString("wf_name"),
> result.getString("wf_lsid"), startTime, duration, execId, errorMsgs,
> result.getString("host_id"));
> }
> catch(Exception e)
> {
>
> Modified: trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLRecordingV8.java
> ===================================================================
> --- trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLRecordingV8.java 2009-10-02 23:41:25 UTC (rev 20863)
> +++ trunk/modules/provenance/src/org/kepler/provenance/sql/
> SQLRecordingV8.java 2009-10-03 01:50:27 UTC (rev 20864)
> @@ -721,15 +721,19 @@
> {
>
> Queryable q = null;
> - try {
> + try
> + {
> q = getQueryable(); //this will make sure we're connect to db
> - } catch (QueryException e1) {
> + }
> + catch (QueryException e1)
> + {
> // TODO Auto-generated catch block
> e1.printStackTrace();
> }
>
> ObjectManager om = ObjectManager.getInstance();
> - try {
> + try
> + {
>
> //TODO should annotationStr be available in workflowRun?
> String annotationStr = "";
> @@ -761,7 +765,7 @@
> _psWorkflowExecStart.setString(2, run.getUser());
> _psWorkflowExecStart.setTimestamp(3, run.getStartTime());
> _psWorkflowExecStart.setString(4, wfMD5Str);
> - _psWorkflowExecStart.setString(5,
> "FIXMEHardCodeMachineName"); //TODO run.getMachineName);
> + _psWorkflowExecStart.setString(5, run.getHostId());
> _psWorkflowExecStart.setString(6, annotationStr);
> _psWorkflowExecStart.setString(7,
> run.getRunLSID().toString());
> workflowExecId = _dbType.insert(_psWorkflowExecStart,
> @@ -855,7 +859,8 @@
> //NamedObj reportLayout =
> ObjectManager
> .getInstance().getHighestObjectRevision(reportLayoutLSID);
>
> String expression = attribute.getExpression();
> - if (expression == null){ //hopefully won't happen
> + if (expression == null) //hopefully won't happen
> + {
> return;
> }
>
>
> Modified: trunk/modules/provenance/src/org/kepler/util/
> WorkflowRun.java
> ===================================================================
> --- trunk/modules/provenance/src/org/kepler/util/WorkflowRun.java
> 2009-10-02 23:41:25 UTC (rev 20863)
> +++ trunk/modules/provenance/src/org/kepler/util/WorkflowRun.java
> 2009-10-03 01:50:27 UTC (rev 20864)
> @@ -50,7 +50,7 @@
> private KeplerLSID runLSID = null; //this is the value of entityId
> in the xml serialization
> private KeplerLSID wfLSID = null;
> private Integer execId = null;
> - //private url provenanceStore = null;
> + private String hostId = null;
> //private String tags = null;
> //private RIO[] RIOs = null; //Report Instance Objects associated
> w/ this run.
> private String workflowName = null;
> @@ -66,6 +66,7 @@
> private StringAttribute execIdAttribute = null;
> private StringAttribute karLSIDAttribute = null;
> private StringAttribute errorMessageAttribute = null;
> + private StringAttribute hostIdAttribute = null;
> public static final String DURATION_ATTRIBUTE_NAME = "duration";
> public static final String STARTTIME_ATTRIBUTE_NAME = "startTime";
> public static final String USER_ATTRIBUTE_NAME = "user";
> @@ -73,6 +74,7 @@
> public static final String WORKFLOWNAME_ATTRIBUTE_NAME =
> "workflowName";
> public static final String EXECID_ATTRIBUTE_NAME = "execId";
> public static final String ERRORMESSAGES_ATTRIBUTE_NAME =
> "errorMessages";
> + public static final String HOSTID_ATTRIBUTE_NAME = "hostId";
>
>
> //override NamedObj default _elementName of entity, so that we can
> read the moml back in
> @@ -104,6 +106,7 @@
> execId = new Integer(-111);
> karLSID = null;
> errorMessages = new LinkedHashMap<Integer, String>();
> + hostId = "";
>
> _setAttributes();
> }
> @@ -124,6 +127,7 @@
> execId = new Integer(-111);
> karLSID = null;
> errorMessages = new LinkedHashMap<Integer, String>();
> + hostId = "";
>
> _setAttributes();
> }
> @@ -131,9 +135,9 @@
> /*
> * Constructor that also takes and sets kar lsid (lsid of kar it's
> contained by)
> */
> - public WorkflowRun(KeplerLSID runlsid, String theUser, String
> workflow, String wflsid, Timestamp start, Long dur, Integer execid,
> Map errorMsgs, KeplerLSID karlsid) throws Exception
> + public WorkflowRun(KeplerLSID runlsid, String theUser, String
> workflow, String wflsid, Timestamp start, Long dur, Integer execid,
> Map errorMsgs, String host_id, KeplerLSID karlsid) throws Exception
> {
> - this(runlsid, theUser, workflow, wflsid, start, dur, execid,
> errorMsgs);
> + this(runlsid, theUser, workflow, wflsid, start, dur, execid,
> errorMsgs, host_id);
>
> karLSID = karlsid;
>
> @@ -154,7 +158,7 @@
> }
>
>
> - public WorkflowRun(KeplerLSID runlsid, String theUser, String
> workflow, String wflsid, Timestamp start, Long dur, Integer execid,
> Map errorMsgs) throws Exception
> + public WorkflowRun(KeplerLSID runlsid, String theUser, String
> workflow, String wflsid, Timestamp start, Long dur, Integer execid,
> Map errorMsgs, String host_id) throws Exception
> {
> super("WorkflowRun");
>
> @@ -182,6 +186,7 @@
> execId = execid;
> errorMessages = errorMsgs;
> karLSID = null;
> + hostId = host_id;
>
> _setAttributes();
>
> @@ -284,6 +289,11 @@
> return errorMessages;
> }
>
> + public String getHostId()
> + {
> + return hostId;
> + }
> +
> public String toString()
> {
> return this.exportMoML();
> @@ -391,6 +401,7 @@
> String workflowLSIDStr =
> ((StringAttribute
> )no.getAttribute(WORKFLOWLSID_ATTRIBUTE_NAME)).getExpression();
> String workflowNameStr =
> ((StringAttribute
> )no.getAttribute(WORKFLOWNAME_ATTRIBUTE_NAME)).getExpression();
> String errorMessagesStr =
> ((StringAttribute
> )no.getAttribute(ERRORMESSAGES_ATTRIBUTE_NAME)).getExpression();
> + String hostIdStr =
> ((StringAttribute
> )no.getAttribute(HOSTID_ATTRIBUTE_NAME)).getExpression();
>
> //TODO cleanup error messages formatting:
> Map errorMsgs = new LinkedHashMap<Integer, String>();
> @@ -449,7 +460,7 @@
> //System.out.println("WorkflowRun("+runLSIDStr+","+userStr
> +","+workflowNameStr+","+workflowLSIDStr+","+startTimeStr
> +","+durationStr+","+execIdStr+","+karLsid+")");
>
> //workflowRun = new WorkflowRun(runLSID, userStr,
> workflowNameStr, workflowLSIDStr, startTime, duration, execId);
> - workflowRun = new WorkflowRun(runLSID, userStr,
> workflowNameStr, workflowLSIDStr, startTime, duration, execId,
> errorMsgs, karLsid);
> + workflowRun = new WorkflowRun(runLSID, userStr,
> workflowNameStr, workflowLSIDStr, startTime, duration, execId,
> errorMsgs, hostIdStr, karLsid);
>
> //must now inherit from the NamedObj any non-standard
> WorkflowRun attributes that were found in the workflowrun-string
> (e.g. those added by reporting)
> // we currently just catch and ignore exceptions from non
> StringAttributes, like _parser. //TODO see if we want such attribs
> @@ -552,7 +563,9 @@
> workflowNameAttribute = new StringAttribute(this,
> WORKFLOWNAME_ATTRIBUTE_NAME);
> execIdAttribute = new StringAttribute(this,
> EXECID_ATTRIBUTE_NAME);
> errorMessageAttribute = new StringAttribute(this,
> ERRORMESSAGES_ATTRIBUTE_NAME);
> + hostIdAttribute = new StringAttribute(this,
> HOSTID_ATTRIBUTE_NAME);
>
> +
>
> durationAttribute.setContainer(this);
> durationAttribute.setExpression(duration.toString());
> @@ -583,6 +596,8 @@
> {
>
> errorMessageAttribute.setExpression(errorMessages.toString());
> }
> + hostIdAttribute.setContainer(this);
> + hostIdAttribute.setExpression(hostId);
>
> }
> catch (IllegalActionException e)
>
> Modified: trunk/modules/workflow-run-manager/src/org/kepler/
> workflowrunmanager/WorkflowRunManager.java
> ===================================================================
> --- trunk/modules/workflow-run-manager/src/org/kepler/
> workflowrunmanager/WorkflowRunManager.java 2009-10-02 23:41:25 UTC
> (rev 20863)
> +++ trunk/modules/workflow-run-manager/src/org/kepler/
> workflowrunmanager/WorkflowRunManager.java 2009-10-03 01:50:27 UTC
> (rev 20864)
> @@ -220,8 +220,6 @@
> }
>
>
> -
> - //TODO expand this to take all args:
> public ArrayList<WorkflowRun> WRMQuery(String workflowName, String
> userName, String startTimeSearchString, String durationSearchString,
> String execIdSearchString){
>
> ArrayList<WorkflowRun> results = new ArrayList<WorkflowRun>();
>
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