Talk:Promethease

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Promethease is a wiki expert system. New bug reports are welcome below, closed bugs are in the page history.

Contents

[edit] My Report won't open

I have a report of over 10MB which won't open. When I first open the report, only a ‘black’ Active X alert if present (CPU running 100%), then the report screen is presented with the Active X alert ‘white’, I click the alert bar and click Yes to the question about running Active X, get a continuous hour glass with 100% CPU operation.

Plain old IE should have no problem with it. But perhaps you've got layers of antivirus (and or viruses) battling it out. Please try the same file in another browser. I'd suggest chrome or firefox



[edit] Recognized file formats:

Promethease knows how to read these specific specific file formats:

If you cooked up your own file you may end up with a warning about it being unrecognized. Since all of the formats from the various companies are just tab or csv delimited, promethease relies on these headers to know which format to expect. Please make your file look like one of these including the header.

[edit] Extra process

It seems like running promethease causes another process to start running called nsB50A.tmp (or any other 4 hex digits after the ns). This is typical of various rootkit/worm/trojans. Any idea?


No virus, just part of the mechanism for making the application simple. It needs many DLLs and support files, but I don't want people to have to deal with an installer, especially for these earliest versions. I like single file .exe apps such as putty. The single file .exe is actually a NSIS installer. When you run the app, that unzips the necessary support files into a temp directory and launches the UI. When you click the 'begin analysis' button a second thread begins. This second process does the very long running communication with the SNPedia.com server (which will often block due to network speed/unreliability) to run without interrupting the UI thread which needs to remain responsive. I've seen cases where killing the UI doesn't immediately propagate to the SNPedia thread, but in general killing the UI should kill both threads quickly. I'd encourage you to run a packet sniffer to observe the traffic and watch how truely boring it is.

[edit] Firewall issue

One user has experienced the message 

WARNING: No messages found in Special:Allmessages. Maybe the server is down. Retrying in 1 minutes...

which was isolated as specific to a single machine, possibly firewall related. If you experience similar please leave a note.

  • I also received the same message on 3 separate occasions (12/11, 12/12). I successfully ran promethease on this computer about a week ago. All firewall settings are disabled.

I had some problems running Promethease with a firewall on (on Windows XP). Only the first report section (Interesting SNPs) would be generated and the program would hang indefinitely after the message "Reading SNPedia genoset overiew" and "Getting Category:Is a medicine..".

My working temporary solution was to drop the firewall for a few seconds after the message "WARNING: No messages found in Special:Allmessages. Maybe the server is down. Retrying in 1 minutes..".

I think there may be something different about the first outbound trip to snpedia when the category phase begins.

Program will not analyze files in the root directory, stating they cannot be found.




[edit] Strange log entries

There is one bit of the log output that I do not understand. Stepstone 22:44, 24 January 2010 (UTC) 

caching allsnpediasnpset
reading 23andMe genotypes
filtering down to the 10150 snpedia snps
retrieve [[Rs3094315]] from SNPedia
Reading Genotypes snps overiew
  File "threading.pyo", line 497, in __bootstrap
  File "threading.pyo", line 525, in __bootstrap_inner
  File "prometheaseui.pyo", line 96, in run
  File "SNPediaWalker.pyo", line 2260, in multiReport
  File "SNPediaWalker.pyo", line 2129, in pooledSection
  File "SNPediaWalker.pyo", line 1454, in pgeSortedGenos
  File "genoparser.pyo", line 45, in parseold
  File "newgenotype.pyo", line 220, in setFromSNPedia
  File "newgenotype.pyo", line 370, in orientto
  File "newgenotype.pyo", line 556, in flip
  File "SNPediaWalker.pyo", line 4206, in allsnpediagenos
  File "SNPediaWalker.pyo", line 4124, in allsnpediagenos_nc
cache miss for Genotype
Getting [[Category:Genotype]]...
caching allsnpediagenos


The message above does not indicate a problem. It is an accurate debugging message and does belong in the log with the current release. Cariaso 12:19, 25 January 2010 (UTC)

[edit] Unicode

Thanks for the clarification. It ran well (and gave me a lot of interesting information about issues that are of utmost importance for me!) and gave me a readable report, but of course it just had to do the Unicode thing one last time (perhaps because I have an "ä" in my Windows username?). Stepstone 22:02, 25 January 2010 (UTC)

Indeed, Unicode has been the theme of the last few fixes. At present it seems to work well for all known cases, I won't be surprised if a few unicode bugs are still hiding. Cariaso 21:46, 27 January 2010 (UTC)

[edit] Fails and then requires payment again?

Promethease (on Vista) failed after creating most of a report. When trying to run again in the hopes it worked this time, it then asked me again to pay again to speed it up and get the features I used.

I tried to continue again without paying again, but it didn't give me the same inheritance option for my spouse I used the first time when I paid.

The promethease.log was overwritten on re-startup so I don't have useful info for you, but it did get pretty far. The callstack it showed mentioned interaction with my 23andme primary ZIP file, a mention of file detection, and finally the StopIteration exception.

I'm happy to pay another time if needed, but if it fails again I'd be really depressed.

  • Any way to get it to work with the advanced spouse option?
  • Any way to avoid having to pay again? (Amazon transaction ID: 14QI8O88K743ET1DJGSMZPP9LP98FQMN5PL)
  • Any info I can provide to help you further?


This is now refunded. When reporting a bug it is helpful to know

  1. Amazon transaction ID - Only if you paid
  2. The name Amazon.com knows you by - Only if you paid. (Easier for me to see than the transaction ID)
  3. Information from promethease.log (future versions will make this easier to find)
  4. Your Promethease version number (it should look like '0.1.76' or similar)

Running again is unlikely to make it work. Instead email bugs@promethease.com and perhaps the next version will be able to fix the issue affecting you (and probably many other people). Cariaso 22:10, 6 February 2010 (UTC)

[edit] 

 retrieve Promethease/config/F1Box from SNPedia
 pulling allsnpediasnpset from cache
 open #######Removed##########
 23andMe formatted file
 reading 23andMe genotypes
 23andMe formatted file
 reading 23andMe genotypes
 pulling allsnpediasnpset from cache
 23andMe formatted file
 reading 23andMe genotypes
 23andMe formatted file
 reading 23andMe genotypes
 Exception in thread Thread-6:
 Traceback (most recent call last):
 File "threading.pyo", line 525, in __bootstrap_inner
 File "prometheaseui.pyo", line 97, in run
 File "SNPediaWalker.pyo", line 2294, in multiReport
 File "SNPediaWalker.pyo", line 1742, in pairBreedBox
 File "SNPediaWalker.pyo", line 1908, in pairBreedGroups
 IndexError: list index out of range
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