Apparently it is not possible to attach two files having the same name.
So here is the mascot log

Hi Rune,
What version of Mascot do you have? I think it might not be finding the expected finish line in the Mascot results.

            // handle response.
            // check for "Finished uploading search details..."
            //for Mascot version earlier than 2.2.03
            //final String endOfUploadMarker = "Finished uploading search details...";
            //for Mascot version 2.2.03
            //final String endOfUploadMarker = "Finished uploading search details and file...";
            final String endOfUploadMarker = "Finished uploading search details";

It prints "Finished uploading search details and file..."
So where do I check whether this is what my labkey installation expects?

They all expect that so the version is not the problem. But, the results that it is retreiving do appear to be missing that line. If you post the mascot.xml and the organism name I will try it here.

Note that this was changed to fix this exact problem in CPAS v8.1. If you are not running CPAS v8.1, you should consider upgrading to get the fix for this version of Mascot.

--Brendan

I am using a local mascot server http://mascot4.bmb.sdu.dk/mascot
It has the attached database installed
I haven't chosen any organism (because the database is very small), but the sample only contain ALBU_BOVIN.

It could also be the return below causing that error.
        // Check that we didn't run out of retries.
        if (statusCode == -1) {
            post.releaseConnection();
            return false;
        }

Hi Rune,
I was looking at the 8.1 code, and did't realize that there had been recent changes to the Mascot implementation, so Brendan is correct (unless of course you are already using 8.1).
Bill

I am using 8.1.
I am trying out some debugging. I have tried inserting some debugging messages in MascotSearchTask and MascotClientImpl (the versions from trunk).
Then I updated the ms2.jar file in LabKey Server\modules\moduleLibDir\ms2 so that it contained my new .class files.
I of course restarted the tomcat server, but somehow it seems the server isn't using my new files....

I'm not sure why the mod is not loading but I'm sure that when Seattle wakes up they will have some ideas. I did run your file, but against Sprot. It did retrieve the .dat file but it didn't make it past Protein Prophet. Your mzXML (211 scans) and database(22 sequences) are pretty small to work well with the Prophets.

Can you try your search with a known sample first? This would eliminate a lot of variables. Since you have the code checked out look in the C:\CPAS\sampledata\xarfiles\ms2pipe\bov_sample and C:\CPAS\sampledata\xarfiles\ms2pipe\databases directories for the Bovine_mini.fasta and CAexample_mini.mzXML.

add <note label="pipeline prophet, min probability" type="input">0</note> to your input XML and everthing else can be default.
Thanks,
Bill

Hi Rune,

Sorry to hear about the troubles you have. We are running Mascot 2.2.03 locally.

Please provide your labkey error log. This log could provide clues on whether the failure is at the query submission or at the stage of checking that Mascot has started its search.

If you have access to your Mascot server search log, you could check if the request has been acted upon. If so, it means the failure is at the state after the statusCode check you mentioned. Otherwise, you need to access the error log on Mascot server for clue.

If you are familiar with HTTP and HTML, you can use WireShark to monitor the network traffics between LabKey server and Mascot Server and determine the point of failure.

If you prefer to work with the Java code, uncomment the line "//getLogger().info("Mascot Server: "+str);" in the while loop ...
            while ((str = in.readLine()) != null)
            {
                //getLogger().info("Mascot Server: "+str);
                if (str.contains(endOfUploadMarker))
                {
                    uploadFinished = true;
                    getLogger().info("Mascot search task status: query upload completed");
                    //WCH: we cannot break for Mascot on Windows platform
                    //break;
                }
            }

This dump each line of what Mascot Server responds after the search has been submitted in the search log. You can then easily determine if the marker has been found.

*Chee-Hong.

I just discovered why I couldn't test my modified files by replacing the jar file.
The .jar files used in the labkey installation is restored silently by Windows File Protection (WFP).
So I have just now begun to hate WFP.. It could at least pop up and tell me when I try to replace the protected file, so that I don't use so much time trying to figure out what is going on.

Oh well, I checked the mascot search log, and the file didn't go through.
No additional info in the labkey logs.

Copying JAR files directly into the moduleLibDir is not a supported deployment scenario. When our webapp starts up as part of Tomcat initialization, it will overwrite files in the moduleLibDir subdirectories that don't match the files included in the .module files. .module files are also ZIP files, and contain the build JARs with the module classes, third party JARs, static webapp files like .gif and .png, and so forth.

If you'd like to try running against modified code, try copying the ms2.module file into the modules directory. I'd strongly recommend that you sync to the 8.1 branch (https://hedgehog.fhcrc.org/tor/stedi/branches/release8.1) if you're deploying to an 8.1 server - you will likely run into numerous version conflicts mixing 8.1 code and the trunk code.

Thanks,
Josh

Ahh, thank you Josh.
So it wasn't WFP teasing me after all.
Thanks for the link to the 8.1 branch, I don't have enough access righs to view the branches folder, so I could not discover the branch name myself.
Maybe I should contact someone about rights for the branches...

When you write: "try copying the ms2.module file into the modules directory.", do you mean copy my modified ms2.jar file into the ms2.modules file?

I got wireshark up and running and found the problem.
The interface should really display these errors in the log files.
And I have attached a patch that will show more verbose information when encountering errors.

The problem was that I had typed invalid parameters in the default parameter file.

Btw. that part of LabKey really needs another interface.
A better editor for parameter files.

It sounds like you're past this point now, but yes, you want a ms2.module file that contains your updated ms2.jar file. Assuming that you're doing a standard Ant build using the build.xml in <LABKEY_ROOT>/server, it will create an updated ms2.module for you in <LABKEY_ROOT>/build/labkeyWebapp/modules. You'd then copy that ms2.module into your deployment's module directory if you're not running a development build.

Version 8.2 will include the first phase of an improved interface for defining search protocols with a GUI to set the various options. We're working on getting rid of editing the XML text area at all, as well as giving better feedback on unrecognized or incorrectly formatting parameters.

Thanks for your patch - I'll get it checked into the trunk for 8.2.

Thanks,
Josh