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Messages - drinehart

1
XCMS / Re: MRM data?
Please try xcmsonline-mrm.scripps.edu.  Your XCMS Online account should provide access.

Duane Rinehart
TSRI
2
XCMS Online / Re: Invalid checksum
We have been updating XCMS Online recently, specifically the data pre-processing modules to use sha1 instead of md5 checksums on certain files.  Unfortunately there was a bug in the way it was implemented that forced the system to check your files (stored MD5 checksum in database) with the locally-calculated sha1 checksum.  Since these values did not match, the system errored out the job.

I made a correction to the aforementioned check and reran the job 1002782 (with error) but now there is another problem - I only see 35 files in the source dataset #47917.  You would need to reupload the missing files or delete them from the dataset as they are not on disk.  On a bright note, I added an additional check to the stored datasets page to display a file as inactive if it is not physically on disk.  You can then re-upload the missing/corrupted files.

Duane
3
XCMS Online / Re: Storage Quota problem?
The error message you receive is generic until we can provide more specific feedback about job submission errors.  That said, you are correct in that exceeding your storage quota will prevent a job from submitting.  Currently there are "soft quotas" you can exceed during an upload (assuming you were below quota prior to starting the upload) but there is another quota check prior to job submission.  That is where your job certainly failed.  You will need more storage space in order to proceed.

To remedy the situation you can delete datasets (make sure you have the original) and/or job results (you can download the zip file with all results, including images AND export the result table if you added annotations to features) and then submit the job.  If this scenario is still not workable because of the aggregate size of the samples you would need to do one of the following:

-process on-site with XCMS (distributed through http://www.bioconductor.org/)
-request more space for your account (see contact form on XCMS Online)
-purchase XCMS Server (send e-mail to xcmsserver@gmail.com for more information)

Duane
4
XCMS Online / Re: Problem uploading files
The uploader is a Java applet and as such relies on the Java runtime environment (JRE) being installed on the end-user computer.  We have had some issues with the Java version transition from 1.6 (Sun) to 1.7 (Oracle), which were supposed to fix security vulnerabilities.  Browsers such as Firefox also have plugins that call the JRE but they too were updated and broke the system.

I added some JRE version checking to help users ensure they have the latest JRE version (along with links to download).  We are also in the process of creating a testing page that will provide visual feedback (green/red checkboxes) to clearly and quickly identify potential problems.  Once completed, we will post a link on the front splash page and in the FAQ.

As of 11-JAN-2013 we are having the least number of reported problems from users with Firefox, IE9 and Chrome.

Duane
6
XCMS Online / Re: Problem uploading files
Currently we are experiencing sporadic problems related to the uploader window not closing.  This results in the dataset status never changing to "UPLOAD_COMPLETE".  As such jobs never submit; they stay in queued status as the system is waiting for all datasets to complete uploading.  This is part of a pre-submit feature however it recently became unstable.  We are currently working on debugging this module and hope to have a resolution soon.

Have you tried uploading the missing files outside of the job submit workflow (i.e., in the stored datasets area)?

Duane Rinehart
7
XCMS Online / Re: Stored Datasets Error
You are correct in that this was a bug (which was fixed recently).  I was working on the individual file display for datasets (part of same class).  I just ported changes to production server.

Thank you for using XCMS Online!

Duane
8
XCMS Online / Re: save methods XCMS online
After you have created a parameter set the new parameter set will appear in available parameters when you create new jobs.  These parameters may be edited by clicking the "View/Edit" button (when creating a new job) and will have the "Save Current" button at the bottom so you can modify the parameter set prior to running the job.  There is one situation where the parameter set will be set to "read only" (and you therefore will not be able to modify it - which is why the "Save Current" button has been removed) and that is when the specific parameter set has been used to run an active job.  This is part of the design because many users wish to consult the parameter set that was used for a particular job after the job has been run.  (i.e., a user is wondering why certain features do not appear in the result set and checks the see what ppm or retention time settings were used to explain the difference between the expected result and the actual result.)

Saving a new parameter set with the same name will not overwrite the original as the index (number to the left of the parameter set name in the dropdown list) must be unique in the database.  Again this is by design.

If you delete the jobs that "rely" on a specific parameter set you wish to change, the parameter should then switch to "read-write" mode, enabling you to edit or delete it (which is the second part of your question).  Parameter sets do not automatically delete when the job that used said parameter set is deleted, allowing a user to reuse them.  The delete button only shows up when the "read-write" mode is enabled (similar to the ability to edit).

Many other users have found appending "a", "b" or a number to the end of a parameter set name to be sufficient when they want to create variations on a base parameter set.

Duane
10
XCMS Online / Re: Data Upload
I recently added the ability to upload a single file to an existing dataset.  For corrupt files, please delete the bad file(s) and use the "Add Files" button on the View/Edit Dataset page.

Duane
11
XCMS Online / Re: File Count and Storage Space Count Errors
I was able to reproduce and isolate the problem related to file counts - it appears to be related to resuming uploads (ability to return to page and resume partially-completed upload).  I temporarily disabled this functionality until I can test further.

I recently enabled the ability to add individual files to a dataset.  If a single file is corrupt, you can delete this file and upload again to the same dataset.  There is a button on the "Stored Datasets" page to accomplish this.  You will need to select a dataset to see the "Add Files" button at the bottom of the page.  Alternatively you can edit an individual dataset by clicking the link on the "View Results" page.

Note: This code has been internally tested but not externally tested yet.  In addition, the user manual does not document this feature yet.

Duane
12
XCMS Online / Re: File Count and Storage Space Count Errors
With respect to the file count on dataset uploads, I started testing to reproduce (and fix) this error.  Currently we are working on the upload module, adding some enhanced functionality so it is possible this issue has already been resolved.  I will post an update after testing is completed.  No additional information is need on your part as I have located your account and datasets.

For the available storage capacity, I was able to make programming modifications to correctly calculate available space.

In response to your question about the difference between "File read: OK." and "VALID MD5", when files are uploaded a checksum is calculated prior to upload on your computer.  This code is transferred to the server and stored in our database.  After all segments of the upload are transferred and the file is reconstructed on the server, the complete file is used to calculate an MD5 checksum.  This code is compared with the one previously calculated on the client prior to upload.  If the codes are identical, the files are also identical, implicating a successful transfer of the complete file without corruption.  (This means the file you transferred was received on the server but it does not say anything about the file itself.)  This is where files can become "corrupted".

XCMS Online currently supports certain file formats (e.g. mzXML, CDF, .d, etc. - see website for complete list).  If other formats are uploaded (e.g. RAW, .D, WIFF, etc.), we may receive them (valid MD5) but the system can not read/process them.  After a job is started, the files must be "read" into memory.  This stage results in the status message "File read: OK", if the file was in a format the XCMS Online system can interpret.  This is where files could be considered "useless", at least until we implement a converter for the file type in question.

The Chaos MD5 program is only capable of calculating an MD5 checksum for a single file.  The MD5 checksum we calculate is based on a single file as well: the zipped version of the .d directory.  For mzXML or CDF files, we zip those as well prior to calculating the MD5.  It is possible to calculate the MD5 on the non-zipped version prior to zipping but we have found this to be overkill at present (because most errors we have seen do not relate to zipping/unzipping).  The MD5 codes should match what was uploaded (assuming they are the same).  One of the features our development team is implementing is the ability to upload a single file to be included in a dataset.  This will likely help where a large dataset has a single problematic file (because the user will not have to upload all the dataset files again).

Thank you for using the system and for your patience as well refine the system, which is still in beta version.

Duane
13
XCMS Online / Re: Total Ion Chromatograms
For #2, the issue should be fixed however the previous code could still be in the browser's cache.  You may wish to refresh the page (F5 key) while on the "Create Job" page.

Duane