I'm trying to import some flow data from FCS Express and so far no success. How do I find the Protocol ID? The Denovo software documentation says "The Protocol ID is an integer generated automatically by LabKey Server and can be found by following the directions in the FCS Express Set Up: Prepare the FCS Express Report section of the accompanying LabKey tutorial.". But, I can't find anything about this in the LabKey tutorial. The LabKey tutorial says to enter the number "16". I need to know how to get this number. I'm guessing that my import is not successful because I'm not entering the correct protocol ID.

(I think I just sent an empty message arggg)
I am having problems generating graphs from a page that starts like this

Flow Experiment Runs > 96 WellBatch0 - PanSurf1-4 >
FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'

Run Name:    96 WellBatch0 - PanSurf1-4
Analysis Folder:    Flow Experiment Runs
Well Name:    Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs

and ends like this.
FCS Files derived from this file and associated FCS Analyses:
Name     Run Name     Analysis Folder
FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'     Panel L1.wsp     Flow Experiment Runs
FCSAnalysis 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'     Panel L1.wsp     Flow Experiment Runs

More Graphs
Keywords from the FCS file
Download FCS file
Experiment Run Graph Details

the complete error message is shown below.
but the jar is indeed there
root@labkey:/usr/local/labkey/labkeywebapp/WEB-INF/lib# ls jfree* jcom*
jcommon-1.0.17.jar jfreechart-1.0.14.jar

any help would be appreciated.

 ERROR WellController 2014-05-12 10:32:51,576 http-8080-6 : Error generating graph
java.lang.NoClassDefFoundError: Could not initialize class org.jfree.chart.JFreeChart
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:138)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:166)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:177)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraphs(FCSAnalyzer.java:199)
    at org.labkey.flow.script.FlowAnalyzer.generateGraph(FlowAnalyzer.java:80)
    at org.labkey.flow.controllers.well.WellController$GenerateGraphAction.getView(WellController.java:358)
    at org.labkey.flow.controllers.well.WellController$GenerateGraphAction.getView(WellController.java:349)
    at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:58)
    at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:177)
    at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
    at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:354)
    at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:989)
    at org.labkey.api.view.ViewServlet.service(ViewServlet.java:165)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:800)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:171)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:861)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:606)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:724)

We use an FCS file keyword to hold the specimen id, and use a study specimen repo. When I import FCS files into a flow folder, I can then Customize View of FCSFiles table to show info about the Specimen (like ParticipantId, SequenceNum, DrawTimestamp, etc.) because I set the SpecimenId Column setting in the ICS Meta Data screen to by the appropriate keyword, and chose the appropriate target study during import. In Customize View, there is a SpecimenId property which has a Specimen property which has ParticipantId, SequenceNum properties, etc. Nice.

Now I import a FlowJo workspace, and have it resolve to existing FCS files - the ones I imported above. That works fine. When I customize view of the resulting FCSAnalyses, there is an "FCSFile" property which itself has an "Original FCSFile" property. As I understand it, the "FCSFile" property refers to the info about the file found in the FlowJo workspace, while the "Original FCSFile" property refers to the originally imported FCS file. The latter is the same as what shows up in the FCSFiles table (same wellId in the URL).

However, when I customize view of FCSAnalyses, and try to use FCSFile.OriginalFCSFile.SpecimenId.Specimen.*, those all show up blank - even though they are properly resolved when I use SpecimenId.Specimen.* in the FCSFiles table. If I instead use FCSFile.SpecimenId.Specimen.*, the data show up. The problem with this is the following:

Sometimes the operator entered the wrong value as the keyword value for specimenId. To fix this, we modify the keyword value in the FCSFile, and (re)import the FCSFile run. However, the FCSFile used in the FlowJo workspace might be the version with the wrong specimenId. This is why we prefer to use FCSFile.OriginalFCSFile.SpecimenId.Specimen.* rather than FCSFile.SpecimenId.Specimen.* - the former has been corrected, while the latter might not have been.

Note that when I customize view of FCSAnalyses to show FCSFile.OriginalFCSFile.Keyword.*, those show up fine, and have the values from the "corrected" file. It just seems to be the SpecimenId that does not show up.

This also affects Copy to Study: When I try to copy-to-study the analysis results, it uses the "bad" specimenIds found in the FlowJo workspace, not the corrected ones found in the FCSFiles table.

Do I understand things correctly regarding how this should work? Why are the FCSFile.OriginalFCSFile.SpecimenId.Specimen.* values showing up blank when I customize view of FCSAnalyses, but showing up fine when I customize view of FCSFiles? Is there any way to use the proper specimenId values during copy to study?

Thanks.

Andy Straw
University of Rochester

Just imported a FlowJo workspace for one of our users. The workspace has well over 50 gates, which results in well over 100 stat columns in the FCSAnalyses table (for each gate, there's a Count, a %Parent, and for some, a Geometric Mean stat). This makes using "Customize View" on the FCSAnalyses table very tedious. For example, if all you care about are the Count stats, you have to check every other (or every third) sub-field under the Statistic field, and check over 50 check boxes. Usually, we want fewer columns, so we don't have to check so many, but finding the stats we want, especially when they have long, hierarchical gate names, is still very tedious.

Is there an easy way to get a list of all the Statistic columns in a given FCSAnalyses table?

Is there an easy way to define a view programmatically, rather than using the the "Customize View" GUI?

I can imagine solving my problem by automating some or all of these steps: 1.) getting a list of all the stats, 2.) filtering that list down to the ones users want to see, 3.) defining a view using that filtered list of columns.

How do others deal with this?

Thanks for any related info or suggestions.

Andy Straw
University of Rochester

After importing a run of FCS files, we noticed that the keyword we use to hold the specimen id was wrong in one of the files. I deleted the run (essentially, did an "un-import"), updated the file to have the correct value for that keyword, then re-imported the run/folder. After the re-import, the keyword value for that file was still the old value, as shown in the FCSFiles view, and as shown in the details view of the specific FCSFile record. I downloaded the file via the "Files" web part, and checked the value of the keyword in the file: the value was the new value. Saw this on two different files in two different runs. I tried this several times, and saw the same behavior every time for these two files/runs. I had to manually edit the keyword value on the FCSFile details page to correct them.

I have done similar corrections in the past (delete run, change keyword values, re-import run), and never saw this behavior.

Why would the import not pick up the changed keyword value?

Andy

When using the "analysis import" feature of the Flow module, if we choose the option to match the analysis with existing FCS files, we get a page in the import wizard where all the files found in the analysis are displayed, one per row in a table, with one column being a drop-down list, and the selected item in the list is the proposed matching FCS file. (The idea being that if the automated matching algorithm guessed wrong, the user could manually correct the choice.) If the number of files in the analysis is large, and/or the number of existing FCS files is large, Firefox has a tough time displaying the page. In fact, when trying recently to import an analysis that covered 684 FCS files, Firefox crashed for us. (Fortunately, we were able to get Chrome to work. The other alternative was for us to break our analysis archive into smaller pieces, and import each piece separately, but that is not a desirable work-around.)

I'm guessing the fact that we had many rows (684), and each row had a drop-down with at least 684 items in it, somehow caused problems for the browser. I've seen problems with smaller analyses (~150 FCS files) - in these cases, it just takes a LONG time for the browser to display the page.

I'm not sure what the solution is to this issue. However, we have found that we never manually correct the choice made by the automated algorithm, so perhaps the drop-down is not needed (or could be optional somehow)?

Suggestions welcome.

Andy Straw
University of Rochester Medical Center

We have some queries that broke when we upgraded to either 12.2 or 12.3. The queries were user-defined queries in the assay schema that were trying to join some data from general purpose assays with data from the FCSFiles table of the flow schema. The error we got when trying to save or execute the queries was that there was no flow.FCSFiles table. I notice that there is now a sub-schema under assay called Flow. I'm guessing that the query parser is treating our reference to flow.FCSFiles as a reference to the flow sub-schema of assay (which does not have an FCSFiles table), rather than the top-level flow schema (which does have an FCSFiles table). I was able to fix the broken query by doing either of the following:

1. Moved the query from the assay schema to the flow schema, and then prepended "assay." to the names of the general purpose assays referenced in the query. (This was not a preferred approach for us.)

2. Left the query in the assay schema, but prepended the container name to the reference to "flow.FCSFiles", something like "/MyProject/MyFolder/MySubfolder".flow.FCSFiles.

We don't like #2 either, since moving the query or changing the folder structure breaks it. Is there a way to namespace the reference to the flow.FCSFiles table to force it to be the "top-level" flow schema, rather than the sub-schema of the current (assay) schema?

Thanks.

Andy Straw
University of Rochester

https://www.labkey.org/wiki/home/Documentation/page.view?name=addSampleDescriptions

Today I took the ‘Import a Flow Workspace Tutorial’, and then looked at the ‘Add Sample Descriptions’ page.

1. On the ‘Add Sample Descriptions’ page, I was unable to locate the Excel file in the “Workspaces” folder of the demo data (labkey-flow-demo). The “Workspaces” folder only contains 3 files: an XML file, a JO file, and a JOT file. How can I locate the Excel file?
 
2. My understanding is that adding sample information and other metadata to a Flow Cytometry project is only optional; it is done by selecting ‘Upload Sample Descriptions’ and/or ‘Other settings’ on the Flow Dashboard. Am I correct?

I'm creating queries against the FCSFiles table. The queries work as expected, but in the table of FCSFiles that are displayed as the result of the queries, the value in the "Name" column (which displays the name of the FCS file) is not a link to the FCSFile details, as it is in the built-in FCSFiles table.

How do I remedy this? I looked at FCSFiles schema in the schema browser, but couldn't find anything special in the schema or meta data.

Note that the "Run" column in my query results _IS_ a link to the run details.

A simple query like the following shows what I mean (Run column are links; Name column are NOT links):

select FCSFiles.Run, FCSFiles.Name from FCSFiles

Please help. Thanks.

Andy Straw
Univ. of Rochester

I just set up my MacBook with LabKey 12.2. When I try to import a run/folder of FCS files, I get an error. These are the same FCS files I have imported successfully on my Windows 7 dev box, and our RedHat Linux servers. Log of the import job is attached.

What might I be doing wrong, or how might I have things configured wrong on my MacBook?

Thanks.

Andy Straw
University of Rochester

Hello,

I installed the Labkey server for my Windows 7 machine and the installation was successful. I tried the flow analysis demo and it seemed working fine. However, there is no the link of [show graphs] and I could not get the graphs like in the following documentation page.

https://www.labkey.org/wiki/home/Documentation/page.view?name=examineGraphs

Is there any settings I need to change or any changes to the flow analysis module? Two snapshots of the page I got are attached.

Thanks,
Yongguo

we are now assessing using the labkey platform to manage our database.

After importing a FlowJo workspace file into the database, we proceed to 'Associate FCS Files'. I tried many times but could not link the FlowJo workspace with the fcs files. The error message was 'None of the samples used by the workspace were found in the selected directory 'null'.'

Anyone has the same experience or knows how to solve the problem?

Hello,

Is there a good sql script to be able to subtract a particular row from a series of other rows? I would like to subtract a mock/background row from several other test rows based upon participantId, visitid or date, cohort etc.

any recommedations.

crashed during analysis, log file attached

I was going back through old CPAS runs and changing compensation gates
when I got this error message after selecting show compensation, move
or define gates, and then selecting the run I wanted: "The page at
http://wilsonlab.gs.washington.edu says: The call failed on the
server; see server log for details" Do you know what this might mean
or how to fix it?

Thank you!

I wrote a simple commandline tool to dump the keywords from a set of FCS files. Used together with findstr or grep this can be used to search a directory of fcs files.

For more information, see FCS keyword utility in our documentation.

This is a feature on my wishlist. There are four different staining panels and each requires its own compensation matrix. I would like to be able to analyze this. There are keywords that identify which FCS files are for each staining panel. I hope this feature may be able to be added.
Thanks,
Steve

Could you help me understand a little bit more about how compensation is done in CPAS? Is the formula pretty much the same as what Flow Jo uses for compensation? I assume so, because compensation in CPAS looks basically identical to compensation in Flow Jo, but I was just wondering how that is calculated. Along these lines, when we edit our compensation matrix and set the positive and negative peaks based on single color controls, one must assign a value for the positive gate and another line for the negative gate. Does CPAS look at the positive line and consider everything to the right of it positive and then look at the negative line and consider everything to the left of it negative? I guess I was just wondering why those peaks have to be set twice, given that you could just cut the histogram in half (like in Flow Jo) and it will know that cells on the left are negative and cells on the right are positive. If we should be setting two separate peaks for positive and negative populations, then what happens to the cells that fall in the middle - are they just excluded? Thanks for your help!

How to upload flow experiments into CPAS?

Thanks

A "Flow" web part is added to a project. When "Build Query" button is clicked, the system returns "404: Page Not Found". (e.g. link /cpas/Flow/test11-contact/showQueryBuilder.view?)

Is feature available in v1.1?

Chee-Hong, BII, SG