(1) Search of assay contant data (2) Hierarchy concept mbrusnia  2015-07-22 16:35
Status: Closed
 
(1) Search is not working for me.
 
https://www.labkey.org/wiki/home/Documentation/page.view?name=luceneSearch
I used the above document to search to take out all assay runs and batches that contains a string “OTD*”.
I checked all categories and scopes to make sure it will return the information but it wasn’t.
Could you tell me why my search is not returning obvious data?

(2) Hierarchy concept
In our view, Batch can have multi runs.
However, after select a batch in view batches, it shows the run file. When I use “Import Data” under “view runs”,
It still creates a new batch and put the new imported file as one run associated with a new batch.
I can’t find a document how to tide multi runs to a given batch.
I also have used select batch -> import data -> "save and import another run"
The file has a new entry and the file name is also not overlap with any other run I have already uploaded.
However, I got the following error that was not making sense for me
500: Unexpected server error
The same file was uploaded twice - all files must be unique
rg.labkey.api.exp.ExperimentException: The same file was uploaded twice - all files must be unique
       at org.labkey.api.study.assay.AssayFileWriter.savePostedFiles(AssayFileWriter.java:192)
       at org.labkey.api.study.actions.AssayRunUploadForm.getAdditionalPostedFiles(AssayRunUploadForm.java:253)
       at org.labkey.api.study.actions.AssayRunUploadForm.getPropertyMapFromRequest(AssayRunUploadForm.java:130)
       at org.labkey.api.study.actions.AssayRunUploadForm.getRunProperties(AssayRunUploadForm.java:111)
       at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.validatePost(UploadWizardAction.java:682)
       at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.handleStep(UploadWizardAction.java:628)
       at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:169)
       at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:95)
       at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:80)
       at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:179)
       at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414)
       at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1032)
       at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1085)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:182)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
       at java.lang.Thread.run(Thread.java:745)

request attributes
LABKEY.OriginalURL = http://optides.fhcrc.org:8080/labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH
LABKEY.StartTime = 1437607929205
LABKEY.action = uploadWizard
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.labkey.api.module.SpringModule$1@5975c4f: display name [Study WebApplicationContext]; startup date [Mon May 04 04:53:43 PDT 2015]; parent: org.springframework.web.context.support.XmlWebApplicationContext@5762e5ed
LABKEY.controller = assay
LABKEY.Counter = 0
X-LABKEY-CSRF = 3fea1251744a79902feea5443850b61b
LABKEY.container = /Optides
LABKEY.RequestURL = /labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH
LABKEY.OriginalURLHelper = /labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH

I would appreciate if you can help me how I can associate multi run to one batch file.
 
 
Jon (LabKey DevOps) responded:  2015-07-23 15:54
Hello,

I'd like to get some clarification on your question regarding search.

Is your crawler running under the Full Text Search page? You can access this under Admin > Site > Admin Console and then click on "Full-Text Search" You will see whether it's running or not there. Also, at the bottom of the same page, you'll see the index statistics. Is there anything listed there? Can you provide us with a screenshot?

Information on the index page is here: https://www.labkey.org/wiki/home/Documentation/page.view?name=searchAdmin

Also, when you say, you're search is to "take out all assay runs and batches", do you mean that when you search for the word OTD*, you're expecting to see everything related to your assays that start with OTD? Or are you saying you want to omit those in your search?

Regarding the second question, only one file to an assay via the import. But you can re-import the file though as long as it has a different file name. Please visit https://www.labkey.org/wiki/home/Documentation/page.view?name=generalAssays and review the last section regarding re-importing a file.

Regards,

Jon
 
mbrusnia responded:  2015-07-24 15:42
Dear Jon,

1. Full-Text Search
Based on your feedback, it looks like it searched but did not find. (see attached fig 1 and fig 2)
I should use "pulled out" from Assay tables and its rows containing the "OTD*" (not "take out")
So I am still puzzling why the search result did not yield anything.

2. Regarding the import
Now I am thinking that we have some configuration issues rather than user misunderstanding.
I would appreciate if you can verify.
I have removed all the files that were updated with a given assay (see attached fig3) and you can see empty run views (fig4).
Now, any files when I tried to import using "import data" function.
I get the error message that I get yesterday (fig 5).

I had created a new project and defined the same assay design. Then when I try to load the first run with any file I uploaded to the other project (please notice that I already deleted all the files associated with the previous project), I still get the same error message (fig5).

The behavior and error message doesn't make sense to me. I wonder whether there is any configuration issues.
 
Jon (LabKey DevOps) responded:  2015-07-27 10:38
Hello,

So if you go to the upper-right box and type in OTD*, you get no results at all? So you get a search screen with no results rather than something that looks like my screenshot? (See attached)

Also, can you provide me with a copy of your assay? I'd like to see if I can reproduce the problem on my end locally.

Regards,

Jon
 
kevink responded:  2015-07-27 11:02
Hi Mi-Youn,

I've created an issue for the assay serach issue here:

https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=23870

I'll contact you off the forum to discuss the assay runs and batchs issue.

Thanks,
Kevin