Re: [OBO-Edit Working Group] Controlling the amount of memory to command-line utilities

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Hi John - the command-line version doesn't seem to be working:

taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$ ./obo2obo 
-J-Xm1024M -fixdbxrefs gene_ontology_edit.obo -o 
gene_ontology_edit_fixed.obo
READPATHS = [-J-Xm1024M, gene_ontology_edit.obo]
exception java.io.FileNotFoundException: /Users/jane/Jane's 
applications/OBO-Edit1_1beta7/-J-Xm1024M (No such file or directory)
org.geneontology.dataadapter.DataAdapterException: Load error
        at 
org.geneontology.oboedit.dataadapter.OBOFileAdapter.doOperation(Unknown 
Source)
        at 
org.geneontology.oboedit.launcher.OBO2OBO.convertFiles(Unknown Source)
        at org.geneontology.oboedit.launcher.OBO2OBO.main(Unknown Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)
Caused by: java.io.FileNotFoundException: /Users/jane/Jane's 
applications/OBO-Edit1_1beta7/-J-Xm1024M (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:106)
        at java.io.FileInputStream.<init>(FileInputStream.java:66)
        at 
sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)
        at 
sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)
        at 
org.geneontology.io.ProgressableURLInputStream.<init>(ProgressableURLInputStream.java:10)
        at org.geneontology.io.IOUtil.getProgressableStream(IOUtil.java:130)
        at 
org.geneontology.oboedit.dataadapter.OBOParseEngine.detectXML(Unknown 
Source)
        at 
org.geneontology.oboedit.dataadapter.OBOParseEngine.doParse(Unknown Source)
        at 
org.geneontology.oboedit.dataadapter.OBOParseEngine.parse(Unknown Source)
        ... 9 more
taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$

I also tried creating the obo2obo.vmoptions file:

taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$ ls
ARTISTIC_LICENSE                extensions                      
obo2obo.command                 oboedit.vmoptions
LICENSE                         gene_ontology_edit.obo          
obo2obo.vmoptions               obomerge
OBO-Edit Uninstaller.app        obo2flat                        
obodiff                         obomerge.command
README                          obo2flat.command                
obodiff.command                 runtime
docs                            obo2obo                         oboedit.app
taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$

with -xm1024M. But that still gives me an out of memory error (although 
a slightly different one now):

taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$ ./obo2obo 
-fixdbxrefs gene_ontology_edit.obo -o gene_ontology_edit_fixed.obo
READPATHS = [gene_ontology_edit.obo]
exception java.lang.OutOfMemoryError: Java heap space
org.geneontology.dataadapter.DataAdapterException: Load error
        at 
org.geneontology.oboedit.dataadapter.OBOFileAdapter.doOperation(Unknown 
Source)
        at 
org.geneontology.oboedit.launcher.OBO2OBO.convertFiles(Unknown Source)
        at org.geneontology.oboedit.launcher.OBO2OBO.main(Unknown Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
taughannock:~/Jane's applications/OBO-Edit1_1beta7 jane$

cheers,

Jane

John Day-Richter wrote:
> A correction to my last email!
>
> To increase memory using "Installer version (option 1)", the
> command-line flag should be:
>
> -J-Xm<megs>M
>
> Where <megs> is the number of megabytes of memory.
>
>     -John
>
> John Day-Richter wrote:
>   
>> The command-line utilities don't use the OBO-Edit memory settings.
>> Here's how to increase the memory:
>>
>> * Installer version (option 1):
>>
>> add the command-line flag
>>
>>     -Jxm<megs>M
>>
>> where <megs> is the number of megabytes of memory to use. So
>>
>> obo2obo -Jxm1024M <other args>
>>
>> would run obo2obo with 1024 megabytes of memory.
>>
>> * Installer version (option 2):
>>
>> Create a text file called <utilityname>.vmoptions in the same directory
>> as the utility (so for obo2obo, create a file called
>> "obo2obo.vmoptions"). Edit the file so that the contents are:
>>
>> -xm<megs>M
>>
>> Where megs is the number of megabytes of memory to use.
>>
>> * Platform-independent version:
>>
>> Edit the launcher script for the command-line utility using a text
>> editor. The last line of the file will look like this:
>>
>> $JAVAPATH -mx$MEMSETTING -classpath $GO_CLASSPATH
>>
>> immediately BEFORE that line, add the line
>>
>> MEMSETTING=<megs>M
>>
>> Where <megs> is the number of megabytes of memory to use.
>>
>> (Note that the platform-independent version will no-longer support this
>> method after the next release of OBO-Edit. As of 1.100-beta8, the
>> platform independent version will work like the installer version).
>>
>>     -John
>>
>> Jane Lomax wrote:
>>   
>>     
>>> And the same problem with the paresecomments flag - doesn't seem to be
>>> loading the file properly:
>>>
>>> [osx:~/OBO-Edit1_1beta7] jlomax% ./obo2obo -parsecomments
>>> gene_ontology_edit.obo -o gene_ontology_fixed.obo
>>> READPATHS = [gene_ontology_edit.obo]
>>> exception java.lang.OutOfMemoryError
>>> org.geneontology.dataadapter.DataAdapterException: Load error
>>>         at
>>> org.geneontology.oboedit.dataadapter.OBOFileAdapter.doOperation(Unknown
>>> Source)
>>>         at
>>> org.geneontology.oboedit.launcher.OBO2OBO.convertFiles(Unknown Source)
>>>         at org.geneontology.oboedit.launcher.OBO2OBO.main(Unknown Source)
>>>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>         at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>>         at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>>         at java.lang.reflect.Method.invoke(Method.java:324)
>>>         at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
>>>         at com.install4j.runtime.Launcher.main(Unknown Source)
>>> Caused by: java.lang.OutOfMemoryError
>>> [osx:~/OBO-Edit1_1beta7] jlomax%
>>>
>>>
>>> cheers,
>>>
>>> Jane
>>>
>>>
>>> On 19 Oct 2006, at 17:22, John Day-Richter wrote:
>>>
>>>     
>>>       
>>>> Try the -parsecomments and -writecomments options in obo2obo. These
>>>> don't seem to be documented in the user's guide, but you can see an
>>>> explanation of their usage when you run obo2obo with no arguments.
>>>>
>>>> I'll add these to the User's Guide this afternoon.
>>>>
>>>>     -John
>>>>
>>>> ja...@eb... wrote:
>>>>
>>>>       
>>>>         
>>>>> Cheers for that John - we'll get the file fixed up.
>>>>>
>>>>> About the gene_ontology_edit.obo 1.2 file...the obsolete
>>>>> replacements are
>>>>> still in the comments, not tags. Did we intend obo2obo to do this
>>>>> inital
>>>>> conversion of comments to tags? And if not, is there an easy way to
>>>>> make
>>>>> obo2obo do it? Will save Amelia writing another script ;)
>>>>>
>>>>> ta,
>>>>>
>>>>> jane
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>         
>>>>>           
>>>>>> I sent this message earlier today with a large attachment. It looks
>>>>>> like
>>>>>> the original got bounced by our servers, so I'm resending:
>>>>>>
>>>>>>     *    *    *    *
>>>>>>
>>>>>> I actually think OBO-Edit works correctly now. These problems must
>>>>>> have
>>>>>> been introduced by an old version of OBO-Edit, and have been hanging
>>>>>> around the file for a while. When the file is formatted correctly,
>>>>>> OBO-Edit reads and writes it just fine. So it's just a matter of
>>>>>> fixing
>>>>>> the file.
>>>>>>
>>>>>> I've adapted obo2obo with an undocumented feature that can fix most of
>>>>>> these automatically (I'm releasing this update tonight). See below for
>>>>>> tips on how to diagnose the problem and fix the file.
>>>>>>
>>>>>>     -John
>>>>>>
>>>>>> * Finding the problem : Broken dbxrefs can be found with the search:
>>>>>>
>>>>>> [Self] [Dbxref] [matches wildcard] [:*]
>>>>>>
>>>>>> * Fixing the problem: Run obo2obo with the undocumented switch
>>>>>> "-fixdbxrefs", like so:
>>>>>>
>>>>>> obo2obo -fixdbxrefs gene_ontology.obo -o gene_ontology_fixed.obo
>>>>>>
>>>>>> You'll see a lot of output lines like this:
>>>>>>
>>>>>>     * Repairing broken dbxref at GO:0018901, merging dbxrefs
>>>>>> UM-BBD_pathwayID:2 and :4d
>>>>>>     * Repairing broken dbxref at GO:0047512, merging dbxrefs
>>>>>> MetaCyc:(S
>>>>>> and
>>>>>>         :S)-BUTANEDIOL-DEHYDROGENASE-RXN
>>>>>>
>>>>>> You may want to scan through these to make sure that the merge is
>>>>>> correct. Sometimes, there is a broken dbxref that obo2obo can't repair
>>>>>> automatically. Then you'll see a line like this:
>>>>>>
>>>>>>     *!! Possible broken ref at GO:0018980 could not be automatically
>>>>>> repaired.
>>>>>>
>>>>>> Usually this message means that a dbxref got broken into several
>>>>>> pieces,
>>>>>> and obo2obo doesn't want to try to guess at putting it back together.
>>>>>> You'll need to edit the ontology to repair this dbxref.  You should do
>>>>>> this fix in OBO-Edit, NOT by hand. If you do decide to fix the file by
>>>>>> hand, heed the following:
>>>>>>
>>>>>> * WARNING ABOUT FIXING THE FILE BY HAND! Note that if the file is
>>>>>> fixed
>>>>>> by hand, you can't just stick the two pieces of the dbxref together
>>>>>> and
>>>>>> add a comma. You need to add a BACKSLASH-COMMA "\,". Otherwise the
>>>>>> problem will appear again immediately, because OBO-Edit will think
>>>>>> that
>>>>>> the unescaped comma means the end of a dbxref has been reached.
>>>>>> That was
>>>>>> the whole source of the problem in the first place.
>>>>>>
>>>>>>     -John
>>>>>>
>>>>>> Amelia Ireland wrote:
>>>>>>
>>>>>>
>>>>>>           
>>>>>>             
>>>>>>> Back in Gotham City at 10:53 on 17 Oct 2006, ja...@eb... wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>             
>>>>>>>               
>>>>>>>> John, Mike - any idea what's going on here? Is this an obo2obo
>>>>>>>> problem?
>>>>>>>>
>>>>>>>>
>>>>>>>>               
>>>>>>>>                 
>>>>>>> No, it's OBO-Edit - it messes up dbxrefs with commas in them. Those
>>>>>>> dbxrefs are identical in the _edit file. I fixed all those the other
>>>>>>> day... grrrrr!
>>>>>>>
>>>>>>> John, could we get this bug fixed in the next OBO-Edit release,
>>>>>>> please?
>>>>>>>
>>>>>>> Cheers,
>>>>>>> A.
>>>>>>>
>>>>>>> -- 
>>>>>>> Amelia Ireland
>>>>>>> GO Editorial Office,
>>>>>>> European Bioinformatics Institute, UK.
>>>>>>> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>             
>>>>>>>               
>>>>>>           
>>>>>>             
>>>>>         
>>>>>           
>>>     
>>>       
>> -------------------------------------------------------------------------
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>>
>>   
>>     

Re: [OBO-Edit Working Group] Controlling the amount of memory to command-line utilities

The DEPRECATED legacy location of the GO, see http://geneontology.org

Re: [OBO-Edit Working Group] Controlling the amount of memory to command-line utilities