[BioMart Users] test scripts for biomart 0.8

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[BioMart Users] test scripts for biomart 0.8

Jorge Zamora Berna
Hi,

are the any scripts to test marts built with 0.8? I mean scripts that automatically query the mart and report the queries that failed.

Thanks,
Jorge


     
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Re: [BioMart Users] test scripts for biomart 0.8

Syed Haider
Hi Jorge,

With rc4, unfortunately there are'nt any yet. With rc6, we should be add
these scripts

Best,
Syed

On 21/02/2011 19:10, Jorge Zamora Berna wrote:

> Hi,
>
> are the any scripts to test marts built with 0.8? I mean scripts that automatically query the mart and report the queries that failed.
>
> Thanks,
> Jorge
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora Berna
Hi Syed,

will wait for it!

Thanks,
Jorge


--- El lun, 21/2/11, Syed Haider <[hidden email]> escribió:

> De: Syed Haider <[hidden email]>
> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
> Para: "Jorge Zamora Berna" <[hidden email]>
> CC: "[hidden email]" <[hidden email]>
> Fecha: lunes, 21 de febrero, 2011 21:36
> Hi Jorge,
>
> With rc4, unfortunately there are'nt any yet. With rc6, we
> should be add
> these scripts
>
> Best,
> Syed
>
> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
> > Hi,
> >
> > are the any scripts to test marts built with 0.8? I
> mean scripts that automatically query the mart and report
> the queries that failed.
> >
> > Thanks,
> > Jorge
> >
> >
> >
> > _______________________________________________
> > Users mailing list
> > [hidden email]
> > https://lists.biomart.org/mailman/listinfo/users
>


     
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Re: [BioMart Users] test scripts for biomart 0.8

Arek Kasprzyk-2
In reply to this post by Syed Haider
I believe that there is a soak script that the guys here use routinely  
to check for working filters and atts. Is that what you are after?

a

On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]> wrote:

> Hi Jorge,
>
> With rc4, unfortunately there are'nt any yet. With rc6, we should be  
> add
> these scripts
>
> Best,
> Syed
>
> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>> Hi,
>>
>> are the any scripts to test marts built with 0.8? I mean scripts  
>> that automatically query the mart and report the queries that failed.
>>
>> Thanks,
>> Jorge
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora Berna
Hi Arek,

Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?

Thanks a lot,
Jorge

/release-0_8-candidate_4/test/org/biomart/soak$ ls
SoakTest.java
/release-0_8-candidate_4/test/org/biomart/diff$ ls
Diff.java





--- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:

> De: Arek Kasprzyk <[hidden email]>
> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
> Para: "Syed Haider" <[hidden email]>
> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
> Fecha: martes, 22 de febrero, 2011 07:18
> I believe that there is a soak script
> that the guys here use routinely 
> to check for working filters and atts. Is that what you are
> after?
>
> a
>
> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
> wrote:
>
> > Hi Jorge,
> >
> > With rc4, unfortunately there are'nt any yet. With
> rc6, we should be 
> > add
> > these scripts
> >
> > Best,
> > Syed
> >
> > On 21/02/2011 19:10, Jorge Zamora Berna wrote:
> >> Hi,
> >>
> >> are the any scripts to test marts built with 0.8?
> I mean scripts 
> >> that automatically query the mart and report the
> queries that failed.
> >>
> >> Thanks,
> >> Jorge
> >>
> >>
> >>
> >> _______________________________________________
> >> Users mailing list
> >> [hidden email]
> >> https://lists.biomart.org/mailman/listinfo/users
> > _______________________________________________
> > Users mailing list
> > [hidden email]
> > https://lists.biomart.org/mailman/listinfo/users
>


     
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Re: [BioMart Users] test scripts for biomart 0.8

Arek Kasprzyk-2

Jonathan is your man :)

a


On 2011-02-22, at 17:14, "Jorge Zamora Berna" <[hidden email]> wrote:

> Hi Arek,
>
> Yes, actually I found the folders where I believe the scripts are  
> located (SoakTest.java, Diff.java). Could you please give us some  
> help on how to use them?
>
> Thanks a lot,
> Jorge
>
> /release-0_8-candidate_4/test/org/biomart/soak$ ls
> SoakTest.java
> /release-0_8-candidate_4/test/org/biomart/diff$ ls
> Diff.java
>
>
>
>
>
> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escrib
> ió:
>
>> De: Arek Kasprzyk <[hidden email]>
>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>> Para: "Syed Haider" <[hidden email]>
>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]
>> >
>> Fecha: martes, 22 de febrero, 2011 07:18
>> I believe that there is a soak script
>> that the guys here use routinely
>> to check for working filters and atts. Is that what you are
>> after?
>>
>> a
>>
>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>> wrote:
>>
>>> Hi Jorge,
>>>
>>> With rc4, unfortunately there are'nt any yet. With
>> rc6, we should be
>>> add
>>> these scripts
>>>
>>> Best,
>>> Syed
>>>
>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>> Hi,
>>>>
>>>> are the any scripts to test marts built with 0.8?
>> I mean scripts
>>>> that automatically query the mart and report the
>> queries that failed.
>>>>
>>>> Thanks,
>>>> Jorge
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
>
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[hidden email]
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Re: [BioMart Users] test scripts for biomart 0.8

Jonathan Guberman
In reply to this post by Jorge Zamora Berna
Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.

To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").

To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).

To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.

Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.

There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.

I hope that helps!

Jonathan

On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:

> Hi Arek,
>
> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>
> Thanks a lot,
> Jorge
>
> /release-0_8-candidate_4/test/org/biomart/soak$ ls
> SoakTest.java
> /release-0_8-candidate_4/test/org/biomart/diff$ ls
> Diff.java
>
>
>
>
>
> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>
>> De: Arek Kasprzyk <[hidden email]>
>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>> Para: "Syed Haider" <[hidden email]>
>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>> Fecha: martes, 22 de febrero, 2011 07:18
>> I believe that there is a soak script
>> that the guys here use routinely  
>> to check for working filters and atts. Is that what you are
>> after?
>>
>> a
>>
>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>> wrote:
>>
>>> Hi Jorge,
>>>
>>> With rc4, unfortunately there are'nt any yet. With
>> rc6, we should be  
>>> add
>>> these scripts
>>>
>>> Best,
>>> Syed
>>>
>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>> Hi,
>>>>
>>>> are the any scripts to test marts built with 0.8?
>> I mean scripts  
>>>> that automatically query the mart and report the
>> queries that failed.
>>>>
>>>> Thanks,
>>>> Jorge
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora-2

Hi Jonathan,

I'm trying the soak test but it fails when I try to compile  (javac -g
SoakTest.java) I get the following errors. any idea why it fails?

Thanks,
Jorge

SoakTest.java:13: error: The import org.apache cannot be resolved
    import org.apache.commons.codec.EncoderException;
           ^^^^^^^^^^
SoakTest.java:14: error: The import org.apache cannot be resolved
    import org.apache.commons.codec.net.URLCodec;
           ^^^^^^^^^^
SoakTest.java:15: error: The import org.jdom cannot be resolved
    import org.jdom.Document;
           ^^^^^^^^
SoakTest.java:16: error: The import org.jdom cannot be resolved
    import org.jdom.Element;
           ^^^^^^^^
SoakTest.java:17: error: The import org.jdom cannot be resolved
    import org.jdom.JDOMException;
           ^^^^^^^^
SoakTest.java:18: error: The import org.jdom cannot be resolved
    import org.jdom.input.SAXBuilder;
           ^^^^^^^^
SoakTest.java:27: error: URLCodec cannot be resolved to a type
    URLCodec safeURL = new URLCodec();
    ^^^^^^^^
SoakTest.java:27: error: URLCodec cannot be resolved to a type
    URLCodec safeURL = new URLCodec();
                           ^^^^^^^^
SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
    SAXBuilder builder = new SAXBuilder();
    ^^^^^^^^^^
SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
    SAXBuilder builder = new SAXBuilder();
                             ^^^^^^^^^^
SoakTest.java:35: error: Document cannot be resolved to a type
    Document martDoc = builder.build(martsURL);
    ^^^^^^^^
SoakTest.java:37: error: Element cannot be resolved to a type
    Element martRoot = martDoc.getRootElement();
    ^^^^^^^
SoakTest.java:39: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List martPointers = martRoot.getChildren("mart");
    ^^^^
SoakTest.java:40: warning: Iterator is a raw type. References to generic
type Iterator<E> should be parameterized
    Iterator mpIterator = martPointers.iterator();
    ^^^^^^^^
SoakTest.java:47: error: Element cannot be resolved to a type
    Element martPointer = (Element) mpIterator.next();
    ^^^^^^^
SoakTest.java:47: error: Element cannot be resolved to a type
    Element martPointer = (Element) mpIterator.next();
                           ^^^^^^^
SoakTest.java:63: error: Document cannot be resolved to a type
    Document datasetsDoc = builder.build(datasetsURL);
    ^^^^^^^^
SoakTest.java:65: error: Element cannot be resolved to a type
    Element datasetsRoot = datasetsDoc.getRootElement();
    ^^^^^^^
SoakTest.java:67: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List datasets = datasetsRoot.getChildren("dataset");
    ^^^^
SoakTest.java:68: warning: Iterator is a raw type. References to generic
type Iterator<E> should be parameterized
    Iterator datasetsIterator = datasets.iterator();
    ^^^^^^^^
SoakTest.java:70: error: Element cannot be resolved to a type
    Element dataset = (Element) datasetsIterator.next();
    ^^^^^^^
SoakTest.java:70: error: Element cannot be resolved to a type
    Element dataset = (Element) datasetsIterator.next();
                       ^^^^^^^
SoakTest.java:78: error: Document cannot be resolved to a type
    Document attributeDoc = builder.build(attributeURL);
    ^^^^^^^^
SoakTest.java:80: error: Element cannot be resolved to a type
    Element attributeRoot = attributeDoc.getRootElement();
    ^^^^^^^
SoakTest.java:82: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List attributes = attributeRoot.getChildren("attribute");
    ^^^^
SoakTest.java:83: warning: Iterator is a raw type. References to generic
type Iterator<E> should be parameterized
    Iterator attributeIterator = attributes.iterator();
    ^^^^^^^^
SoakTest.java:86: error: Element cannot be resolved to a type
    Element attribute = (Element) attributeIterator.next();
    ^^^^^^^
SoakTest.java:86: error: Element cannot be resolved to a type
    Element attribute = (Element) attributeIterator.next();
                         ^^^^^^^
SoakTest.java:94: error: Document cannot be resolved to a type
    Document filterDoc = builder.build(filterURL);
    ^^^^^^^^
SoakTest.java:96: error: Element cannot be resolved to a type
    Element filterRoot = filterDoc.getRootElement();
    ^^^^^^^
SoakTest.java:98: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List filters = filterRoot.getChildren("filter");
    ^^^^
SoakTest.java:99: warning: Iterator is a raw type. References to generic
type Iterator<E> should be parameterized
    Iterator filterIterator = filters.iterator();
    ^^^^^^^^
SoakTest.java:101: error: Element cannot be resolved to a type
    Element filter = (Element) filterIterator.next();
    ^^^^^^^
SoakTest.java:101: error: Element cannot be resolved to a type
    Element filter = (Element) filterIterator.next();
                      ^^^^^^^
SoakTest.java:113: error: JDOMException cannot be resolved to a type
    } catch (JDOMException e) {
             ^^^^^^^^^^^^^
SoakTest.java:116: error: EncoderException cannot be resolved to a type
    } catch (EncoderException e) {
             ^^^^^^^^^^^^^^^^
SoakTest.java:132: error: URLCodec cannot be resolved to a type
    HashSet<String> failInfo, URLCodec safeURL, String martName,
                              ^^^^^^^^
SoakTest.java:134: error: Element cannot be resolved to a type
    Element filter) throws MalformedURLException, EncoderException {
    ^^^^^^^
SoakTest.java:134: error: EncoderException cannot be resolved to a type
    Element filter) throws MalformedURLException, EncoderException {
                                                  ^^^^^^^^^^^^^^^^
SoakTest.java:141: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List subFilters = filter.getChildren("filter");
    ^^^^
SoakTest.java:142: warning: Iterator is a raw type. References to
generic type Iterator<E> should be parameterized
    Iterator subFiltersIterator = subFilters.iterator();
    ^^^^^^^^
SoakTest.java:144: error: Element cannot be resolved to a type
    Element subFilter = (Element) subFiltersIterator.next();
    ^^^^^^^
SoakTest.java:144: error: Element cannot be resolved to a type
    Element subFilter = (Element) subFiltersIterator.next();
                         ^^^^^^^
SoakTest.java:193: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List values = filter.getChildren("value");
    ^^^^
SoakTest.java:194: warning: Iterator is a raw type. References to
generic type Iterator<E> should be parameterized
    Iterator valueIterator = values.iterator();
    ^^^^^^^^
SoakTest.java:196: error: Element cannot be resolved to a type
    Element value = (Element) valueIterator.next();
    ^^^^^^^
SoakTest.java:196: error: Element cannot be resolved to a type
    Element value = (Element) valueIterator.next();
                     ^^^^^^^
SoakTest.java:244: error: URLCodec cannot be resolved to a type
    HashSet<String> failInfo, URLCodec safeURL, String martName,
                              ^^^^^^^^
SoakTest.java:246: error: Element cannot be resolved to a type
    Element attribute) throws MalformedURLException, EncoderException {
    ^^^^^^^
SoakTest.java:246: error: EncoderException cannot be resolved to a type
    Element attribute) throws MalformedURLException, EncoderException {
                                                     ^^^^^^^^^^^^^^^^
SoakTest.java:247: warning: List is a raw type. References to generic
type List<E> should be parameterized
    List subAttributes = attribute.getChildren("attribute");
    ^^^^
SoakTest.java:293: warning: Iterator is a raw type. References to
generic type Iterator<E> should be parameterized
    Iterator subAttributesIterator = subAttributes.iterator();
    ^^^^^^^^
SoakTest.java:295: error: Element cannot be resolved to a type
    Element subAttribute = (Element) subAttributesIterator.next();
    ^^^^^^^
SoakTest.java:295: error: Element cannot be resolved to a type
    Element subAttribute = (Element) subAttributesIterator.next();
                            ^^^^^^^
54 problems (40 errors, 14 warnings)






















Jonathan Guberman wrote:

> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>
> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>
> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>
> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>
> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>
> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>
> I hope that helps!
>
> Jonathan
>
> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>
>  
>> Hi Arek,
>>
>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>
>> Thanks a lot,
>> Jorge
>>
>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>> SoakTest.java
>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>> Diff.java
>>
>>
>>
>>
>>
>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>
>>    
>>> De: Arek Kasprzyk <[hidden email]>
>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>> Para: "Syed Haider" <[hidden email]>
>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>> Fecha: martes, 22 de febrero, 2011 07:18
>>> I believe that there is a soak script
>>> that the guys here use routinely  
>>> to check for working filters and atts. Is that what you are
>>> after?
>>>
>>> a
>>>
>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>> wrote:
>>>
>>>      
>>>> Hi Jorge,
>>>>
>>>> With rc4, unfortunately there are'nt any yet. With
>>>>        
>>> rc6, we should be  
>>>      
>>>> add
>>>> these scripts
>>>>
>>>> Best,
>>>> Syed
>>>>
>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>        
>>>>> Hi,
>>>>>
>>>>> are the any scripts to test marts built with 0.8?
>>>>>          
>>> I mean scripts  
>>>      
>>>>> that automatically query the mart and report the
>>>>>          
>>> queries that failed.
>>>      
>>>>> Thanks,
>>>>> Jorge
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [hidden email]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>          
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>        
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>    
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>  


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Re: [BioMart Users] test scripts for biomart 0.8

Jonathan Guberman
Jorge,

You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar

Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest

On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:

>
> Hi Jonathan,
>
> I'm trying the soak test but it fails when I try to compile  (javac -g
> SoakTest.java) I get the following errors. any idea why it fails?
>
> Thanks,
> Jorge
>
> SoakTest.java:13: error: The import org.apache cannot be resolved
>    import org.apache.commons.codec.EncoderException;
>           ^^^^^^^^^^
> SoakTest.java:14: error: The import org.apache cannot be resolved
>    import org.apache.commons.codec.net.URLCodec;
>           ^^^^^^^^^^
> SoakTest.java:15: error: The import org.jdom cannot be resolved
>    import org.jdom.Document;
>           ^^^^^^^^
> SoakTest.java:16: error: The import org.jdom cannot be resolved
>    import org.jdom.Element;
>           ^^^^^^^^
> SoakTest.java:17: error: The import org.jdom cannot be resolved
>    import org.jdom.JDOMException;
>           ^^^^^^^^
> SoakTest.java:18: error: The import org.jdom cannot be resolved
>    import org.jdom.input.SAXBuilder;
>           ^^^^^^^^
> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>    URLCodec safeURL = new URLCodec();
>    ^^^^^^^^
> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>    URLCodec safeURL = new URLCodec();
>                           ^^^^^^^^
> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>    SAXBuilder builder = new SAXBuilder();
>    ^^^^^^^^^^
> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>    SAXBuilder builder = new SAXBuilder();
>                             ^^^^^^^^^^
> SoakTest.java:35: error: Document cannot be resolved to a type
>    Document martDoc = builder.build(martsURL);
>    ^^^^^^^^
> SoakTest.java:37: error: Element cannot be resolved to a type
>    Element martRoot = martDoc.getRootElement();
>    ^^^^^^^
> SoakTest.java:39: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List martPointers = martRoot.getChildren("mart");
>    ^^^^
> SoakTest.java:40: warning: Iterator is a raw type. References to generic
> type Iterator<E> should be parameterized
>    Iterator mpIterator = martPointers.iterator();
>    ^^^^^^^^
> SoakTest.java:47: error: Element cannot be resolved to a type
>    Element martPointer = (Element) mpIterator.next();
>    ^^^^^^^
> SoakTest.java:47: error: Element cannot be resolved to a type
>    Element martPointer = (Element) mpIterator.next();
>                           ^^^^^^^
> SoakTest.java:63: error: Document cannot be resolved to a type
>    Document datasetsDoc = builder.build(datasetsURL);
>    ^^^^^^^^
> SoakTest.java:65: error: Element cannot be resolved to a type
>    Element datasetsRoot = datasetsDoc.getRootElement();
>    ^^^^^^^
> SoakTest.java:67: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List datasets = datasetsRoot.getChildren("dataset");
>    ^^^^
> SoakTest.java:68: warning: Iterator is a raw type. References to generic
> type Iterator<E> should be parameterized
>    Iterator datasetsIterator = datasets.iterator();
>    ^^^^^^^^
> SoakTest.java:70: error: Element cannot be resolved to a type
>    Element dataset = (Element) datasetsIterator.next();
>    ^^^^^^^
> SoakTest.java:70: error: Element cannot be resolved to a type
>    Element dataset = (Element) datasetsIterator.next();
>                       ^^^^^^^
> SoakTest.java:78: error: Document cannot be resolved to a type
>    Document attributeDoc = builder.build(attributeURL);
>    ^^^^^^^^
> SoakTest.java:80: error: Element cannot be resolved to a type
>    Element attributeRoot = attributeDoc.getRootElement();
>    ^^^^^^^
> SoakTest.java:82: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List attributes = attributeRoot.getChildren("attribute");
>    ^^^^
> SoakTest.java:83: warning: Iterator is a raw type. References to generic
> type Iterator<E> should be parameterized
>    Iterator attributeIterator = attributes.iterator();
>    ^^^^^^^^
> SoakTest.java:86: error: Element cannot be resolved to a type
>    Element attribute = (Element) attributeIterator.next();
>    ^^^^^^^
> SoakTest.java:86: error: Element cannot be resolved to a type
>    Element attribute = (Element) attributeIterator.next();
>                         ^^^^^^^
> SoakTest.java:94: error: Document cannot be resolved to a type
>    Document filterDoc = builder.build(filterURL);
>    ^^^^^^^^
> SoakTest.java:96: error: Element cannot be resolved to a type
>    Element filterRoot = filterDoc.getRootElement();
>    ^^^^^^^
> SoakTest.java:98: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List filters = filterRoot.getChildren("filter");
>    ^^^^
> SoakTest.java:99: warning: Iterator is a raw type. References to generic
> type Iterator<E> should be parameterized
>    Iterator filterIterator = filters.iterator();
>    ^^^^^^^^
> SoakTest.java:101: error: Element cannot be resolved to a type
>    Element filter = (Element) filterIterator.next();
>    ^^^^^^^
> SoakTest.java:101: error: Element cannot be resolved to a type
>    Element filter = (Element) filterIterator.next();
>                      ^^^^^^^
> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>    } catch (JDOMException e) {
>             ^^^^^^^^^^^^^
> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>    } catch (EncoderException e) {
>             ^^^^^^^^^^^^^^^^
> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>    HashSet<String> failInfo, URLCodec safeURL, String martName,
>                              ^^^^^^^^
> SoakTest.java:134: error: Element cannot be resolved to a type
>    Element filter) throws MalformedURLException, EncoderException {
>    ^^^^^^^
> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>    Element filter) throws MalformedURLException, EncoderException {
>                                                  ^^^^^^^^^^^^^^^^
> SoakTest.java:141: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List subFilters = filter.getChildren("filter");
>    ^^^^
> SoakTest.java:142: warning: Iterator is a raw type. References to
> generic type Iterator<E> should be parameterized
>    Iterator subFiltersIterator = subFilters.iterator();
>    ^^^^^^^^
> SoakTest.java:144: error: Element cannot be resolved to a type
>    Element subFilter = (Element) subFiltersIterator.next();
>    ^^^^^^^
> SoakTest.java:144: error: Element cannot be resolved to a type
>    Element subFilter = (Element) subFiltersIterator.next();
>                         ^^^^^^^
> SoakTest.java:193: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List values = filter.getChildren("value");
>    ^^^^
> SoakTest.java:194: warning: Iterator is a raw type. References to
> generic type Iterator<E> should be parameterized
>    Iterator valueIterator = values.iterator();
>    ^^^^^^^^
> SoakTest.java:196: error: Element cannot be resolved to a type
>    Element value = (Element) valueIterator.next();
>    ^^^^^^^
> SoakTest.java:196: error: Element cannot be resolved to a type
>    Element value = (Element) valueIterator.next();
>                     ^^^^^^^
> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>    HashSet<String> failInfo, URLCodec safeURL, String martName,
>                              ^^^^^^^^
> SoakTest.java:246: error: Element cannot be resolved to a type
>    Element attribute) throws MalformedURLException, EncoderException {
>    ^^^^^^^
> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>    Element attribute) throws MalformedURLException, EncoderException {
>                                                     ^^^^^^^^^^^^^^^^
> SoakTest.java:247: warning: List is a raw type. References to generic
> type List<E> should be parameterized
>    List subAttributes = attribute.getChildren("attribute");
>    ^^^^
> SoakTest.java:293: warning: Iterator is a raw type. References to
> generic type Iterator<E> should be parameterized
>    Iterator subAttributesIterator = subAttributes.iterator();
>    ^^^^^^^^
> SoakTest.java:295: error: Element cannot be resolved to a type
>    Element subAttribute = (Element) subAttributesIterator.next();
>    ^^^^^^^
> SoakTest.java:295: error: Element cannot be resolved to a type
>    Element subAttribute = (Element) subAttributesIterator.next();
>                            ^^^^^^^
> 54 problems (40 errors, 14 warnings)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Jonathan Guberman wrote:
>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>
>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>
>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>
>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>
>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>
>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>
>> I hope that helps!
>>
>> Jonathan
>>
>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>
>>
>>> Hi Arek,
>>>
>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>
>>> Thanks a lot,
>>> Jorge
>>>
>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>> SoakTest.java
>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>> Diff.java
>>>
>>>
>>>
>>>
>>>
>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>
>>>
>>>> De: Arek Kasprzyk <[hidden email]>
>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>> Para: "Syed Haider" <[hidden email]>
>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>> I believe that there is a soak script
>>>> that the guys here use routinely
>>>> to check for working filters and atts. Is that what you are
>>>> after?
>>>>
>>>> a
>>>>
>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>> wrote:
>>>>
>>>>
>>>>> Hi Jorge,
>>>>>
>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>
>>>> rc6, we should be
>>>>
>>>>> add
>>>>> these scripts
>>>>>
>>>>> Best,
>>>>> Syed
>>>>>
>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>
>>>> I mean scripts
>>>>
>>>>>> that automatically query the mart and report the
>>>>>>
>>>> queries that failed.
>>>>
>>>>>> Thanks,
>>>>>> Jorge
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Users mailing list
>>>>>> [hidden email]
>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [hidden email]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>
>>>
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora-2
Hi Jonathan,

Thanks for the clarification.

Now I set my mart url, set the testCounter to 1 and the testValues to
'true', then compiled, executed and this I what I got :

Success! 1

doest it means that all filters and attributes in the marts available
from my url are OK?

Thanks a lot,

Jorge




To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.

Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.

There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.





Jonathan Guberman wrote:

> Jorge,
>
> You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
> javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar
>
> Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
> java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest
>
> On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:
>
>  
>> Hi Jonathan,
>>
>> I'm trying the soak test but it fails when I try to compile  (javac -g
>> SoakTest.java) I get the following errors. any idea why it fails?
>>
>> Thanks,
>> Jorge
>>
>> SoakTest.java:13: error: The import org.apache cannot be resolved
>>    import org.apache.commons.codec.EncoderException;
>>           ^^^^^^^^^^
>> SoakTest.java:14: error: The import org.apache cannot be resolved
>>    import org.apache.commons.codec.net.URLCodec;
>>           ^^^^^^^^^^
>> SoakTest.java:15: error: The import org.jdom cannot be resolved
>>    import org.jdom.Document;
>>           ^^^^^^^^
>> SoakTest.java:16: error: The import org.jdom cannot be resolved
>>    import org.jdom.Element;
>>           ^^^^^^^^
>> SoakTest.java:17: error: The import org.jdom cannot be resolved
>>    import org.jdom.JDOMException;
>>           ^^^^^^^^
>> SoakTest.java:18: error: The import org.jdom cannot be resolved
>>    import org.jdom.input.SAXBuilder;
>>           ^^^^^^^^
>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>    URLCodec safeURL = new URLCodec();
>>    ^^^^^^^^
>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>    URLCodec safeURL = new URLCodec();
>>                           ^^^^^^^^
>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>    SAXBuilder builder = new SAXBuilder();
>>    ^^^^^^^^^^
>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>    SAXBuilder builder = new SAXBuilder();
>>                             ^^^^^^^^^^
>> SoakTest.java:35: error: Document cannot be resolved to a type
>>    Document martDoc = builder.build(martsURL);
>>    ^^^^^^^^
>> SoakTest.java:37: error: Element cannot be resolved to a type
>>    Element martRoot = martDoc.getRootElement();
>>    ^^^^^^^
>> SoakTest.java:39: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List martPointers = martRoot.getChildren("mart");
>>    ^^^^
>> SoakTest.java:40: warning: Iterator is a raw type. References to generic
>> type Iterator<E> should be parameterized
>>    Iterator mpIterator = martPointers.iterator();
>>    ^^^^^^^^
>> SoakTest.java:47: error: Element cannot be resolved to a type
>>    Element martPointer = (Element) mpIterator.next();
>>    ^^^^^^^
>> SoakTest.java:47: error: Element cannot be resolved to a type
>>    Element martPointer = (Element) mpIterator.next();
>>                           ^^^^^^^
>> SoakTest.java:63: error: Document cannot be resolved to a type
>>    Document datasetsDoc = builder.build(datasetsURL);
>>    ^^^^^^^^
>> SoakTest.java:65: error: Element cannot be resolved to a type
>>    Element datasetsRoot = datasetsDoc.getRootElement();
>>    ^^^^^^^
>> SoakTest.java:67: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List datasets = datasetsRoot.getChildren("dataset");
>>    ^^^^
>> SoakTest.java:68: warning: Iterator is a raw type. References to generic
>> type Iterator<E> should be parameterized
>>    Iterator datasetsIterator = datasets.iterator();
>>    ^^^^^^^^
>> SoakTest.java:70: error: Element cannot be resolved to a type
>>    Element dataset = (Element) datasetsIterator.next();
>>    ^^^^^^^
>> SoakTest.java:70: error: Element cannot be resolved to a type
>>    Element dataset = (Element) datasetsIterator.next();
>>                       ^^^^^^^
>> SoakTest.java:78: error: Document cannot be resolved to a type
>>    Document attributeDoc = builder.build(attributeURL);
>>    ^^^^^^^^
>> SoakTest.java:80: error: Element cannot be resolved to a type
>>    Element attributeRoot = attributeDoc.getRootElement();
>>    ^^^^^^^
>> SoakTest.java:82: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List attributes = attributeRoot.getChildren("attribute");
>>    ^^^^
>> SoakTest.java:83: warning: Iterator is a raw type. References to generic
>> type Iterator<E> should be parameterized
>>    Iterator attributeIterator = attributes.iterator();
>>    ^^^^^^^^
>> SoakTest.java:86: error: Element cannot be resolved to a type
>>    Element attribute = (Element) attributeIterator.next();
>>    ^^^^^^^
>> SoakTest.java:86: error: Element cannot be resolved to a type
>>    Element attribute = (Element) attributeIterator.next();
>>                         ^^^^^^^
>> SoakTest.java:94: error: Document cannot be resolved to a type
>>    Document filterDoc = builder.build(filterURL);
>>    ^^^^^^^^
>> SoakTest.java:96: error: Element cannot be resolved to a type
>>    Element filterRoot = filterDoc.getRootElement();
>>    ^^^^^^^
>> SoakTest.java:98: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List filters = filterRoot.getChildren("filter");
>>    ^^^^
>> SoakTest.java:99: warning: Iterator is a raw type. References to generic
>> type Iterator<E> should be parameterized
>>    Iterator filterIterator = filters.iterator();
>>    ^^^^^^^^
>> SoakTest.java:101: error: Element cannot be resolved to a type
>>    Element filter = (Element) filterIterator.next();
>>    ^^^^^^^
>> SoakTest.java:101: error: Element cannot be resolved to a type
>>    Element filter = (Element) filterIterator.next();
>>                      ^^^^^^^
>> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>>    } catch (JDOMException e) {
>>             ^^^^^^^^^^^^^
>> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>>    } catch (EncoderException e) {
>>             ^^^^^^^^^^^^^^^^
>> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>>    HashSet<String> failInfo, URLCodec safeURL, String martName,
>>                              ^^^^^^^^
>> SoakTest.java:134: error: Element cannot be resolved to a type
>>    Element filter) throws MalformedURLException, EncoderException {
>>    ^^^^^^^
>> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>>    Element filter) throws MalformedURLException, EncoderException {
>>                                                  ^^^^^^^^^^^^^^^^
>> SoakTest.java:141: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List subFilters = filter.getChildren("filter");
>>    ^^^^
>> SoakTest.java:142: warning: Iterator is a raw type. References to
>> generic type Iterator<E> should be parameterized
>>    Iterator subFiltersIterator = subFilters.iterator();
>>    ^^^^^^^^
>> SoakTest.java:144: error: Element cannot be resolved to a type
>>    Element subFilter = (Element) subFiltersIterator.next();
>>    ^^^^^^^
>> SoakTest.java:144: error: Element cannot be resolved to a type
>>    Element subFilter = (Element) subFiltersIterator.next();
>>                         ^^^^^^^
>> SoakTest.java:193: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List values = filter.getChildren("value");
>>    ^^^^
>> SoakTest.java:194: warning: Iterator is a raw type. References to
>> generic type Iterator<E> should be parameterized
>>    Iterator valueIterator = values.iterator();
>>    ^^^^^^^^
>> SoakTest.java:196: error: Element cannot be resolved to a type
>>    Element value = (Element) valueIterator.next();
>>    ^^^^^^^
>> SoakTest.java:196: error: Element cannot be resolved to a type
>>    Element value = (Element) valueIterator.next();
>>                     ^^^^^^^
>> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>>    HashSet<String> failInfo, URLCodec safeURL, String martName,
>>                              ^^^^^^^^
>> SoakTest.java:246: error: Element cannot be resolved to a type
>>    Element attribute) throws MalformedURLException, EncoderException {
>>    ^^^^^^^
>> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>>    Element attribute) throws MalformedURLException, EncoderException {
>>                                                     ^^^^^^^^^^^^^^^^
>> SoakTest.java:247: warning: List is a raw type. References to generic
>> type List<E> should be parameterized
>>    List subAttributes = attribute.getChildren("attribute");
>>    ^^^^
>> SoakTest.java:293: warning: Iterator is a raw type. References to
>> generic type Iterator<E> should be parameterized
>>    Iterator subAttributesIterator = subAttributes.iterator();
>>    ^^^^^^^^
>> SoakTest.java:295: error: Element cannot be resolved to a type
>>    Element subAttribute = (Element) subAttributesIterator.next();
>>    ^^^^^^^
>> SoakTest.java:295: error: Element cannot be resolved to a type
>>    Element subAttribute = (Element) subAttributesIterator.next();
>>                            ^^^^^^^
>> 54 problems (40 errors, 14 warnings)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Jonathan Guberman wrote:
>>    
>>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>>
>>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>>
>>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>>
>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>
>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>
>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>
>>> I hope that helps!
>>>
>>> Jonathan
>>>
>>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>>
>>>
>>>      
>>>> Hi Arek,
>>>>
>>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>>
>>>> Thanks a lot,
>>>> Jorge
>>>>
>>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>>> SoakTest.java
>>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>>> Diff.java
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>>
>>>>
>>>>        
>>>>> De: Arek Kasprzyk <[hidden email]>
>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>> Para: "Syed Haider" <[hidden email]>
>>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>>> I believe that there is a soak script
>>>>> that the guys here use routinely
>>>>> to check for working filters and atts. Is that what you are
>>>>> after?
>>>>>
>>>>> a
>>>>>
>>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>>> wrote:
>>>>>
>>>>>
>>>>>          
>>>>>> Hi Jorge,
>>>>>>
>>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>>
>>>>>>            
>>>>> rc6, we should be
>>>>>
>>>>>          
>>>>>> add
>>>>>> these scripts
>>>>>>
>>>>>> Best,
>>>>>> Syed
>>>>>>
>>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>>
>>>>>>            
>>>>>>> Hi,
>>>>>>>
>>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>>
>>>>>>>              
>>>>> I mean scripts
>>>>>
>>>>>          
>>>>>>> that automatically query the mart and report the
>>>>>>>
>>>>>>>              
>>>>> queries that failed.
>>>>>
>>>>>          
>>>>>>> Thanks,
>>>>>>> Jorge
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Users mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>
>>>>>>>              
>>>>>> _______________________________________________
>>>>>> Users mailing list
>>>>>> [hidden email]
>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>
>>>>>>            
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>
>>>>        
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>>      
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>
>>    
>
>  


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Re: [BioMart Users] test scripts for biomart 0.8

Jonathan Guberman
It appears that you've only tested one Mart, not all of them. To test all of them, testCounter must be set to -1 (minus 1), not 1.

On 2011-02-22, at 12:02 PM, Jorge Zamora wrote:

> Hi Jonathan,
>
> Thanks for the clarification.
>
> Now I set my mart url, set the testCounter to 1 and the testValues to
> 'true', then compiled, executed and this I what I got :
>
> Success! 1
>
> doest it means that all filters and attributes in the marts available
> from my url are OK?
>
> Thanks a lot,
>
> Jorge
>
>
>
>
> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>
> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>
> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>
>
>
>
>
> Jonathan Guberman wrote:
>> Jorge,
>>
>> You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
>> javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar
>>
>> Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
>> java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest
>>
>> On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:
>>
>>
>>> Hi Jonathan,
>>>
>>> I'm trying the soak test but it fails when I try to compile  (javac -g
>>> SoakTest.java) I get the following errors. any idea why it fails?
>>>
>>> Thanks,
>>> Jorge
>>>
>>> SoakTest.java:13: error: The import org.apache cannot be resolved
>>>   import org.apache.commons.codec.EncoderException;
>>>          ^^^^^^^^^^
>>> SoakTest.java:14: error: The import org.apache cannot be resolved
>>>   import org.apache.commons.codec.net.URLCodec;
>>>          ^^^^^^^^^^
>>> SoakTest.java:15: error: The import org.jdom cannot be resolved
>>>   import org.jdom.Document;
>>>          ^^^^^^^^
>>> SoakTest.java:16: error: The import org.jdom cannot be resolved
>>>   import org.jdom.Element;
>>>          ^^^^^^^^
>>> SoakTest.java:17: error: The import org.jdom cannot be resolved
>>>   import org.jdom.JDOMException;
>>>          ^^^^^^^^
>>> SoakTest.java:18: error: The import org.jdom cannot be resolved
>>>   import org.jdom.input.SAXBuilder;
>>>          ^^^^^^^^
>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>   URLCodec safeURL = new URLCodec();
>>>   ^^^^^^^^
>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>   URLCodec safeURL = new URLCodec();
>>>                          ^^^^^^^^
>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>   SAXBuilder builder = new SAXBuilder();
>>>   ^^^^^^^^^^
>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>   SAXBuilder builder = new SAXBuilder();
>>>                            ^^^^^^^^^^
>>> SoakTest.java:35: error: Document cannot be resolved to a type
>>>   Document martDoc = builder.build(martsURL);
>>>   ^^^^^^^^
>>> SoakTest.java:37: error: Element cannot be resolved to a type
>>>   Element martRoot = martDoc.getRootElement();
>>>   ^^^^^^^
>>> SoakTest.java:39: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List martPointers = martRoot.getChildren("mart");
>>>   ^^^^
>>> SoakTest.java:40: warning: Iterator is a raw type. References to generic
>>> type Iterator<E> should be parameterized
>>>   Iterator mpIterator = martPointers.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>   Element martPointer = (Element) mpIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>   Element martPointer = (Element) mpIterator.next();
>>>                          ^^^^^^^
>>> SoakTest.java:63: error: Document cannot be resolved to a type
>>>   Document datasetsDoc = builder.build(datasetsURL);
>>>   ^^^^^^^^
>>> SoakTest.java:65: error: Element cannot be resolved to a type
>>>   Element datasetsRoot = datasetsDoc.getRootElement();
>>>   ^^^^^^^
>>> SoakTest.java:67: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List datasets = datasetsRoot.getChildren("dataset");
>>>   ^^^^
>>> SoakTest.java:68: warning: Iterator is a raw type. References to generic
>>> type Iterator<E> should be parameterized
>>>   Iterator datasetsIterator = datasets.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>   Element dataset = (Element) datasetsIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>   Element dataset = (Element) datasetsIterator.next();
>>>                      ^^^^^^^
>>> SoakTest.java:78: error: Document cannot be resolved to a type
>>>   Document attributeDoc = builder.build(attributeURL);
>>>   ^^^^^^^^
>>> SoakTest.java:80: error: Element cannot be resolved to a type
>>>   Element attributeRoot = attributeDoc.getRootElement();
>>>   ^^^^^^^
>>> SoakTest.java:82: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List attributes = attributeRoot.getChildren("attribute");
>>>   ^^^^
>>> SoakTest.java:83: warning: Iterator is a raw type. References to generic
>>> type Iterator<E> should be parameterized
>>>   Iterator attributeIterator = attributes.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>   Element attribute = (Element) attributeIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>   Element attribute = (Element) attributeIterator.next();
>>>                        ^^^^^^^
>>> SoakTest.java:94: error: Document cannot be resolved to a type
>>>   Document filterDoc = builder.build(filterURL);
>>>   ^^^^^^^^
>>> SoakTest.java:96: error: Element cannot be resolved to a type
>>>   Element filterRoot = filterDoc.getRootElement();
>>>   ^^^^^^^
>>> SoakTest.java:98: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List filters = filterRoot.getChildren("filter");
>>>   ^^^^
>>> SoakTest.java:99: warning: Iterator is a raw type. References to generic
>>> type Iterator<E> should be parameterized
>>>   Iterator filterIterator = filters.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>   Element filter = (Element) filterIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>   Element filter = (Element) filterIterator.next();
>>>                     ^^^^^^^
>>> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>>>   } catch (JDOMException e) {
>>>            ^^^^^^^^^^^^^
>>> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>>>   } catch (EncoderException e) {
>>>            ^^^^^^^^^^^^^^^^
>>> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>>>   HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>                             ^^^^^^^^
>>> SoakTest.java:134: error: Element cannot be resolved to a type
>>>   Element filter) throws MalformedURLException, EncoderException {
>>>   ^^^^^^^
>>> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>>>   Element filter) throws MalformedURLException, EncoderException {
>>>                                                 ^^^^^^^^^^^^^^^^
>>> SoakTest.java:141: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List subFilters = filter.getChildren("filter");
>>>   ^^^^
>>> SoakTest.java:142: warning: Iterator is a raw type. References to
>>> generic type Iterator<E> should be parameterized
>>>   Iterator subFiltersIterator = subFilters.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>   Element subFilter = (Element) subFiltersIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>   Element subFilter = (Element) subFiltersIterator.next();
>>>                        ^^^^^^^
>>> SoakTest.java:193: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List values = filter.getChildren("value");
>>>   ^^^^
>>> SoakTest.java:194: warning: Iterator is a raw type. References to
>>> generic type Iterator<E> should be parameterized
>>>   Iterator valueIterator = values.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>   Element value = (Element) valueIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>   Element value = (Element) valueIterator.next();
>>>                    ^^^^^^^
>>> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>>>   HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>                             ^^^^^^^^
>>> SoakTest.java:246: error: Element cannot be resolved to a type
>>>   Element attribute) throws MalformedURLException, EncoderException {
>>>   ^^^^^^^
>>> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>>>   Element attribute) throws MalformedURLException, EncoderException {
>>>                                                    ^^^^^^^^^^^^^^^^
>>> SoakTest.java:247: warning: List is a raw type. References to generic
>>> type List<E> should be parameterized
>>>   List subAttributes = attribute.getChildren("attribute");
>>>   ^^^^
>>> SoakTest.java:293: warning: Iterator is a raw type. References to
>>> generic type Iterator<E> should be parameterized
>>>   Iterator subAttributesIterator = subAttributes.iterator();
>>>   ^^^^^^^^
>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>   Element subAttribute = (Element) subAttributesIterator.next();
>>>   ^^^^^^^
>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>   Element subAttribute = (Element) subAttributesIterator.next();
>>>                           ^^^^^^^
>>> 54 problems (40 errors, 14 warnings)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Jonathan Guberman wrote:
>>>
>>>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>>>
>>>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>>>
>>>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>>>
>>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>>
>>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>>
>>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>>
>>>> I hope that helps!
>>>>
>>>> Jonathan
>>>>
>>>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>>>
>>>>
>>>>
>>>>> Hi Arek,
>>>>>
>>>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>>>
>>>>> Thanks a lot,
>>>>> Jorge
>>>>>
>>>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>>>> SoakTest.java
>>>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>>>> Diff.java
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>>>
>>>>>
>>>>>
>>>>>> De: Arek Kasprzyk <[hidden email]>
>>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>>> Para: "Syed Haider" <[hidden email]>
>>>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>>>> I believe that there is a soak script
>>>>>> that the guys here use routinely
>>>>>> to check for working filters and atts. Is that what you are
>>>>>> after?
>>>>>>
>>>>>> a
>>>>>>
>>>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Jorge,
>>>>>>>
>>>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>>>
>>>>>>>
>>>>>> rc6, we should be
>>>>>>
>>>>>>
>>>>>>> add
>>>>>>> these scripts
>>>>>>>
>>>>>>> Best,
>>>>>>> Syed
>>>>>>>
>>>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>>>
>>>>>>>>
>>>>>> I mean scripts
>>>>>>
>>>>>>
>>>>>>>> that automatically query the mart and report the
>>>>>>>>
>>>>>>>>
>>>>>> queries that failed.
>>>>>>
>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Jorge
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Users mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Users mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>
>>>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [hidden email]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>
>>>>
>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>>
>>>
>>
>>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>

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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora-2
Hi Jonathan,

Yes, I meant -1. Actually what I'm testing in our ICGC mart, that is one
mart. However is it possible to have more comprehensive log? I just say
this since our mart is using open ID and wouldn't expect the test script
access the mart from the url without authentication.

Thanks,
Jorge




Jonathan Guberman wrote:

> It appears that you've only tested one Mart, not all of them. To test all of them, testCounter must be set to -1 (minus 1), not 1.
>
> On 2011-02-22, at 12:02 PM, Jorge Zamora wrote:
>
>  
>> Hi Jonathan,
>>
>> Thanks for the clarification.
>>
>> Now I set my mart url, set the testCounter to 1 and the testValues to
>> 'true', then compiled, executed and this I what I got :
>>
>> Success! 1
>>
>> doest it means that all filters and attributes in the marts available
>> from my url are OK?
>>
>> Thanks a lot,
>>
>> Jorge
>>
>>
>>
>>
>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>
>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>
>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>
>>
>>
>>
>>
>> Jonathan Guberman wrote:
>>    
>>> Jorge,
>>>
>>> You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
>>> javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar
>>>
>>> Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
>>> java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest
>>>
>>> On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:
>>>
>>>
>>>      
>>>> Hi Jonathan,
>>>>
>>>> I'm trying the soak test but it fails when I try to compile  (javac -g
>>>> SoakTest.java) I get the following errors. any idea why it fails?
>>>>
>>>> Thanks,
>>>> Jorge
>>>>
>>>> SoakTest.java:13: error: The import org.apache cannot be resolved
>>>>   import org.apache.commons.codec.EncoderException;
>>>>          ^^^^^^^^^^
>>>> SoakTest.java:14: error: The import org.apache cannot be resolved
>>>>   import org.apache.commons.codec.net.URLCodec;
>>>>          ^^^^^^^^^^
>>>> SoakTest.java:15: error: The import org.jdom cannot be resolved
>>>>   import org.jdom.Document;
>>>>          ^^^^^^^^
>>>> SoakTest.java:16: error: The import org.jdom cannot be resolved
>>>>   import org.jdom.Element;
>>>>          ^^^^^^^^
>>>> SoakTest.java:17: error: The import org.jdom cannot be resolved
>>>>   import org.jdom.JDOMException;
>>>>          ^^^^^^^^
>>>> SoakTest.java:18: error: The import org.jdom cannot be resolved
>>>>   import org.jdom.input.SAXBuilder;
>>>>          ^^^^^^^^
>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>   URLCodec safeURL = new URLCodec();
>>>>   ^^^^^^^^
>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>   URLCodec safeURL = new URLCodec();
>>>>                          ^^^^^^^^
>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>   SAXBuilder builder = new SAXBuilder();
>>>>   ^^^^^^^^^^
>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>   SAXBuilder builder = new SAXBuilder();
>>>>                            ^^^^^^^^^^
>>>> SoakTest.java:35: error: Document cannot be resolved to a type
>>>>   Document martDoc = builder.build(martsURL);
>>>>   ^^^^^^^^
>>>> SoakTest.java:37: error: Element cannot be resolved to a type
>>>>   Element martRoot = martDoc.getRootElement();
>>>>   ^^^^^^^
>>>> SoakTest.java:39: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List martPointers = martRoot.getChildren("mart");
>>>>   ^^^^
>>>> SoakTest.java:40: warning: Iterator is a raw type. References to generic
>>>> type Iterator<E> should be parameterized
>>>>   Iterator mpIterator = martPointers.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>   Element martPointer = (Element) mpIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>   Element martPointer = (Element) mpIterator.next();
>>>>                          ^^^^^^^
>>>> SoakTest.java:63: error: Document cannot be resolved to a type
>>>>   Document datasetsDoc = builder.build(datasetsURL);
>>>>   ^^^^^^^^
>>>> SoakTest.java:65: error: Element cannot be resolved to a type
>>>>   Element datasetsRoot = datasetsDoc.getRootElement();
>>>>   ^^^^^^^
>>>> SoakTest.java:67: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List datasets = datasetsRoot.getChildren("dataset");
>>>>   ^^^^
>>>> SoakTest.java:68: warning: Iterator is a raw type. References to generic
>>>> type Iterator<E> should be parameterized
>>>>   Iterator datasetsIterator = datasets.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>   Element dataset = (Element) datasetsIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>   Element dataset = (Element) datasetsIterator.next();
>>>>                      ^^^^^^^
>>>> SoakTest.java:78: error: Document cannot be resolved to a type
>>>>   Document attributeDoc = builder.build(attributeURL);
>>>>   ^^^^^^^^
>>>> SoakTest.java:80: error: Element cannot be resolved to a type
>>>>   Element attributeRoot = attributeDoc.getRootElement();
>>>>   ^^^^^^^
>>>> SoakTest.java:82: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List attributes = attributeRoot.getChildren("attribute");
>>>>   ^^^^
>>>> SoakTest.java:83: warning: Iterator is a raw type. References to generic
>>>> type Iterator<E> should be parameterized
>>>>   Iterator attributeIterator = attributes.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>   Element attribute = (Element) attributeIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>   Element attribute = (Element) attributeIterator.next();
>>>>                        ^^^^^^^
>>>> SoakTest.java:94: error: Document cannot be resolved to a type
>>>>   Document filterDoc = builder.build(filterURL);
>>>>   ^^^^^^^^
>>>> SoakTest.java:96: error: Element cannot be resolved to a type
>>>>   Element filterRoot = filterDoc.getRootElement();
>>>>   ^^^^^^^
>>>> SoakTest.java:98: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List filters = filterRoot.getChildren("filter");
>>>>   ^^^^
>>>> SoakTest.java:99: warning: Iterator is a raw type. References to generic
>>>> type Iterator<E> should be parameterized
>>>>   Iterator filterIterator = filters.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>   Element filter = (Element) filterIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>   Element filter = (Element) filterIterator.next();
>>>>                     ^^^^^^^
>>>> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>>>>   } catch (JDOMException e) {
>>>>            ^^^^^^^^^^^^^
>>>> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>>>>   } catch (EncoderException e) {
>>>>            ^^^^^^^^^^^^^^^^
>>>> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>>>>   HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>                             ^^^^^^^^
>>>> SoakTest.java:134: error: Element cannot be resolved to a type
>>>>   Element filter) throws MalformedURLException, EncoderException {
>>>>   ^^^^^^^
>>>> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>>>>   Element filter) throws MalformedURLException, EncoderException {
>>>>                                                 ^^^^^^^^^^^^^^^^
>>>> SoakTest.java:141: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List subFilters = filter.getChildren("filter");
>>>>   ^^^^
>>>> SoakTest.java:142: warning: Iterator is a raw type. References to
>>>> generic type Iterator<E> should be parameterized
>>>>   Iterator subFiltersIterator = subFilters.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>   Element subFilter = (Element) subFiltersIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>   Element subFilter = (Element) subFiltersIterator.next();
>>>>                        ^^^^^^^
>>>> SoakTest.java:193: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List values = filter.getChildren("value");
>>>>   ^^^^
>>>> SoakTest.java:194: warning: Iterator is a raw type. References to
>>>> generic type Iterator<E> should be parameterized
>>>>   Iterator valueIterator = values.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>   Element value = (Element) valueIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>   Element value = (Element) valueIterator.next();
>>>>                    ^^^^^^^
>>>> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>>>>   HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>                             ^^^^^^^^
>>>> SoakTest.java:246: error: Element cannot be resolved to a type
>>>>   Element attribute) throws MalformedURLException, EncoderException {
>>>>   ^^^^^^^
>>>> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>>>>   Element attribute) throws MalformedURLException, EncoderException {
>>>>                                                    ^^^^^^^^^^^^^^^^
>>>> SoakTest.java:247: warning: List is a raw type. References to generic
>>>> type List<E> should be parameterized
>>>>   List subAttributes = attribute.getChildren("attribute");
>>>>   ^^^^
>>>> SoakTest.java:293: warning: Iterator is a raw type. References to
>>>> generic type Iterator<E> should be parameterized
>>>>   Iterator subAttributesIterator = subAttributes.iterator();
>>>>   ^^^^^^^^
>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>   Element subAttribute = (Element) subAttributesIterator.next();
>>>>   ^^^^^^^
>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>   Element subAttribute = (Element) subAttributesIterator.next();
>>>>                           ^^^^^^^
>>>> 54 problems (40 errors, 14 warnings)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Jonathan Guberman wrote:
>>>>
>>>>        
>>>>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>>>>
>>>>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>>>>
>>>>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>>>>
>>>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>>>
>>>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>>>
>>>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>>>
>>>>> I hope that helps!
>>>>>
>>>>> Jonathan
>>>>>
>>>>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>> Hi Arek,
>>>>>>
>>>>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>>>>
>>>>>> Thanks a lot,
>>>>>> Jorge
>>>>>>
>>>>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>>>>> SoakTest.java
>>>>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>>>>> Diff.java
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>> De: Arek Kasprzyk <[hidden email]>
>>>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>>>> Para: "Syed Haider" <[hidden email]>
>>>>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>>>>> I believe that there is a soak script
>>>>>>> that the guys here use routinely
>>>>>>> to check for working filters and atts. Is that what you are
>>>>>>> after?
>>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>> Hi Jorge,
>>>>>>>>
>>>>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>> rc6, we should be
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>> add
>>>>>>>> these scripts
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Syed
>>>>>>>>
>>>>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>> I mean scripts
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>>> that automatically query the mart and report the
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>> queries that failed.
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>>> Thanks,
>>>>>>>>> Jorge
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Users mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>> _______________________________________________
>>>>>>>> Users mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>> _______________________________________________
>>>>>> Users mailing list
>>>>>> [hidden email]
>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>
>>>>>>
>>>>>>            
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [hidden email]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>
>>>>>
>>>>>          
>>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
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>>>>
>>>>
>>>>        
>>>      
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>
>>    
>
>  


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Re: [BioMart Users] test scripts for biomart 0.8

Jonathan Guberman
There is more comprehensive logging: it should be outputting the status for each filter and attribute to STDERR as it goes. The two possibilities are the your STDERR isn't displaying for some reason, or that, because of the openID authentication, it can't see any filters and attributes and therefore can't test it (and therefore passes by default, because nothing goes wrong).

The simplest way to check if that is the case is to manually look at the martService URLs to see if they return results.

On 2011-02-22, at 12:15 PM, Jorge Zamora wrote:

> Hi Jonathan,
>
> Yes, I meant -1. Actually what I'm testing in our ICGC mart, that is one
> mart. However is it possible to have more comprehensive log? I just say
> this since our mart is using open ID and wouldn't expect the test script
> access the mart from the url without authentication.
>
> Thanks,
> Jorge
>
>
>
>
> Jonathan Guberman wrote:
>> It appears that you've only tested one Mart, not all of them. To test all of them, testCounter must be set to -1 (minus 1), not 1.
>>
>> On 2011-02-22, at 12:02 PM, Jorge Zamora wrote:
>>
>>
>>> Hi Jonathan,
>>>
>>> Thanks for the clarification.
>>>
>>> Now I set my mart url, set the testCounter to 1 and the testValues to
>>> 'true', then compiled, executed and this I what I got :
>>>
>>> Success! 1
>>>
>>> doest it means that all filters and attributes in the marts available
>>> from my url are OK?
>>>
>>> Thanks a lot,
>>>
>>> Jorge
>>>
>>>
>>>
>>>
>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>
>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>
>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>
>>>
>>>
>>>
>>>
>>> Jonathan Guberman wrote:
>>>
>>>> Jorge,
>>>>
>>>> You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
>>>> javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar
>>>>
>>>> Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
>>>> java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest
>>>>
>>>> On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:
>>>>
>>>>
>>>>
>>>>> Hi Jonathan,
>>>>>
>>>>> I'm trying the soak test but it fails when I try to compile  (javac -g
>>>>> SoakTest.java) I get the following errors. any idea why it fails?
>>>>>
>>>>> Thanks,
>>>>> Jorge
>>>>>
>>>>> SoakTest.java:13: error: The import org.apache cannot be resolved
>>>>>  import org.apache.commons.codec.EncoderException;
>>>>>         ^^^^^^^^^^
>>>>> SoakTest.java:14: error: The import org.apache cannot be resolved
>>>>>  import org.apache.commons.codec.net.URLCodec;
>>>>>         ^^^^^^^^^^
>>>>> SoakTest.java:15: error: The import org.jdom cannot be resolved
>>>>>  import org.jdom.Document;
>>>>>         ^^^^^^^^
>>>>> SoakTest.java:16: error: The import org.jdom cannot be resolved
>>>>>  import org.jdom.Element;
>>>>>         ^^^^^^^^
>>>>> SoakTest.java:17: error: The import org.jdom cannot be resolved
>>>>>  import org.jdom.JDOMException;
>>>>>         ^^^^^^^^
>>>>> SoakTest.java:18: error: The import org.jdom cannot be resolved
>>>>>  import org.jdom.input.SAXBuilder;
>>>>>         ^^^^^^^^
>>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>>  URLCodec safeURL = new URLCodec();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>>  URLCodec safeURL = new URLCodec();
>>>>>                         ^^^^^^^^
>>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>>  SAXBuilder builder = new SAXBuilder();
>>>>>  ^^^^^^^^^^
>>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>>  SAXBuilder builder = new SAXBuilder();
>>>>>                           ^^^^^^^^^^
>>>>> SoakTest.java:35: error: Document cannot be resolved to a type
>>>>>  Document martDoc = builder.build(martsURL);
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:37: error: Element cannot be resolved to a type
>>>>>  Element martRoot = martDoc.getRootElement();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:39: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List martPointers = martRoot.getChildren("mart");
>>>>>  ^^^^
>>>>> SoakTest.java:40: warning: Iterator is a raw type. References to generic
>>>>> type Iterator<E> should be parameterized
>>>>>  Iterator mpIterator = martPointers.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>>  Element martPointer = (Element) mpIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>>  Element martPointer = (Element) mpIterator.next();
>>>>>                         ^^^^^^^
>>>>> SoakTest.java:63: error: Document cannot be resolved to a type
>>>>>  Document datasetsDoc = builder.build(datasetsURL);
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:65: error: Element cannot be resolved to a type
>>>>>  Element datasetsRoot = datasetsDoc.getRootElement();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:67: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List datasets = datasetsRoot.getChildren("dataset");
>>>>>  ^^^^
>>>>> SoakTest.java:68: warning: Iterator is a raw type. References to generic
>>>>> type Iterator<E> should be parameterized
>>>>>  Iterator datasetsIterator = datasets.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>>  Element dataset = (Element) datasetsIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>>  Element dataset = (Element) datasetsIterator.next();
>>>>>                     ^^^^^^^
>>>>> SoakTest.java:78: error: Document cannot be resolved to a type
>>>>>  Document attributeDoc = builder.build(attributeURL);
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:80: error: Element cannot be resolved to a type
>>>>>  Element attributeRoot = attributeDoc.getRootElement();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:82: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List attributes = attributeRoot.getChildren("attribute");
>>>>>  ^^^^
>>>>> SoakTest.java:83: warning: Iterator is a raw type. References to generic
>>>>> type Iterator<E> should be parameterized
>>>>>  Iterator attributeIterator = attributes.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>>  Element attribute = (Element) attributeIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>>  Element attribute = (Element) attributeIterator.next();
>>>>>                       ^^^^^^^
>>>>> SoakTest.java:94: error: Document cannot be resolved to a type
>>>>>  Document filterDoc = builder.build(filterURL);
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:96: error: Element cannot be resolved to a type
>>>>>  Element filterRoot = filterDoc.getRootElement();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:98: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List filters = filterRoot.getChildren("filter");
>>>>>  ^^^^
>>>>> SoakTest.java:99: warning: Iterator is a raw type. References to generic
>>>>> type Iterator<E> should be parameterized
>>>>>  Iterator filterIterator = filters.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>>  Element filter = (Element) filterIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>>  Element filter = (Element) filterIterator.next();
>>>>>                    ^^^^^^^
>>>>> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>>>>>  } catch (JDOMException e) {
>>>>>           ^^^^^^^^^^^^^
>>>>> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>>>>>  } catch (EncoderException e) {
>>>>>           ^^^^^^^^^^^^^^^^
>>>>> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>>>>>  HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>>                            ^^^^^^^^
>>>>> SoakTest.java:134: error: Element cannot be resolved to a type
>>>>>  Element filter) throws MalformedURLException, EncoderException {
>>>>>  ^^^^^^^
>>>>> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>>>>>  Element filter) throws MalformedURLException, EncoderException {
>>>>>                                                ^^^^^^^^^^^^^^^^
>>>>> SoakTest.java:141: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List subFilters = filter.getChildren("filter");
>>>>>  ^^^^
>>>>> SoakTest.java:142: warning: Iterator is a raw type. References to
>>>>> generic type Iterator<E> should be parameterized
>>>>>  Iterator subFiltersIterator = subFilters.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>>  Element subFilter = (Element) subFiltersIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>>  Element subFilter = (Element) subFiltersIterator.next();
>>>>>                       ^^^^^^^
>>>>> SoakTest.java:193: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List values = filter.getChildren("value");
>>>>>  ^^^^
>>>>> SoakTest.java:194: warning: Iterator is a raw type. References to
>>>>> generic type Iterator<E> should be parameterized
>>>>>  Iterator valueIterator = values.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>>  Element value = (Element) valueIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>>  Element value = (Element) valueIterator.next();
>>>>>                   ^^^^^^^
>>>>> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>>>>>  HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>>                            ^^^^^^^^
>>>>> SoakTest.java:246: error: Element cannot be resolved to a type
>>>>>  Element attribute) throws MalformedURLException, EncoderException {
>>>>>  ^^^^^^^
>>>>> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>>>>>  Element attribute) throws MalformedURLException, EncoderException {
>>>>>                                                   ^^^^^^^^^^^^^^^^
>>>>> SoakTest.java:247: warning: List is a raw type. References to generic
>>>>> type List<E> should be parameterized
>>>>>  List subAttributes = attribute.getChildren("attribute");
>>>>>  ^^^^
>>>>> SoakTest.java:293: warning: Iterator is a raw type. References to
>>>>> generic type Iterator<E> should be parameterized
>>>>>  Iterator subAttributesIterator = subAttributes.iterator();
>>>>>  ^^^^^^^^
>>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>>  Element subAttribute = (Element) subAttributesIterator.next();
>>>>>  ^^^^^^^
>>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>>  Element subAttribute = (Element) subAttributesIterator.next();
>>>>>                          ^^^^^^^
>>>>> 54 problems (40 errors, 14 warnings)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Jonathan Guberman wrote:
>>>>>
>>>>>
>>>>>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>>>>>
>>>>>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>>>>>
>>>>>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>>>>>
>>>>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>>>>
>>>>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>>>>
>>>>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>>>>
>>>>>> I hope that helps!
>>>>>>
>>>>>> Jonathan
>>>>>>
>>>>>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Arek,
>>>>>>>
>>>>>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>> Jorge
>>>>>>>
>>>>>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>>>>>> SoakTest.java
>>>>>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>>>>>> Diff.java
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> De: Arek Kasprzyk <[hidden email]>
>>>>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>>>>> Para: "Syed Haider" <[hidden email]>
>>>>>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>>>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>>>>>> I believe that there is a soak script
>>>>>>>> that the guys here use routinely
>>>>>>>> to check for working filters and atts. Is that what you are
>>>>>>>> after?
>>>>>>>>
>>>>>>>> a
>>>>>>>>
>>>>>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Jorge,
>>>>>>>>>
>>>>>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> rc6, we should be
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> add
>>>>>>>>> these scripts
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Syed
>>>>>>>>>
>>>>>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> I mean scripts
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>> that automatically query the mart and report the
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> queries that failed.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Jorge
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Users mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Users mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Users mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Users mailing list
>>>>>> [hidden email]
>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>
>>>>>>
>>>>>>
>>>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>>>>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>>>>
>>>>>
>>>>>
>>>>
>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>>
>>>
>>
>>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>

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Re: [BioMart Users] test scripts for biomart 0.8

Jorge Zamora-2
Hello Jonathan,

Just to check if the open ID was responsible for not getting the logs  I
deployed the mart  in  my local machine so all the data is diplayed
under the 'anonymous' user group (without Open ID) and then got a very
long log!!

Thanks,
Jorge


Jonathan Guberman wrote:

> There is more comprehensive logging: it should be outputting the status for each filter and attribute to STDERR as it goes. The two possibilities are the your STDERR isn't displaying for some reason, or that, because of the openID authentication, it can't see any filters and attributes and therefore can't test it (and therefore passes by default, because nothing goes wrong).
>
> The simplest way to check if that is the case is to manually look at the martService URLs to see if they return results.
>
> On 2011-02-22, at 12:15 PM, Jorge Zamora wrote:
>
>  
>> Hi Jonathan,
>>
>> Yes, I meant -1. Actually what I'm testing in our ICGC mart, that is one
>> mart. However is it possible to have more comprehensive log? I just say
>> this since our mart is using open ID and wouldn't expect the test script
>> access the mart from the url without authentication.
>>
>> Thanks,
>> Jorge
>>
>>
>>
>>
>> Jonathan Guberman wrote:
>>    
>>> It appears that you've only tested one Mart, not all of them. To test all of them, testCounter must be set to -1 (minus 1), not 1.
>>>
>>> On 2011-02-22, at 12:02 PM, Jorge Zamora wrote:
>>>
>>>
>>>      
>>>> Hi Jonathan,
>>>>
>>>> Thanks for the clarification.
>>>>
>>>> Now I set my mart url, set the testCounter to 1 and the testValues to
>>>> 'true', then compiled, executed and this I what I got :
>>>>
>>>> Success! 1
>>>>
>>>> doest it means that all filters and attributes in the marts available
>>>> from my url are OK?
>>>>
>>>> Thanks a lot,
>>>>
>>>> Jorge
>>>>
>>>>
>>>>
>>>>
>>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>>
>>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>>
>>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Jonathan Guberman wrote:
>>>>
>>>>        
>>>>> Jorge,
>>>>>
>>>>> You need to specify the classpath. From the root directory of my RC4 install, I use the following command:
>>>>> javac test/org/biomart/soak/SoakTest.java -classpath ./test/org/biomart/soak:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar
>>>>>
>>>>> Then, to execute it, you also need to specify the classpath. Again from the root directory I run:
>>>>> java -classpath ./test:./lib/jdom-1.0.jar:./lib/commons-codec-1.3.jar org.biomart.soak.SoakTest
>>>>>
>>>>> On 2011-02-22, at 10:38 AM, Jorge Zamora wrote:
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>> Hi Jonathan,
>>>>>>
>>>>>> I'm trying the soak test but it fails when I try to compile  (javac -g
>>>>>> SoakTest.java) I get the following errors. any idea why it fails?
>>>>>>
>>>>>> Thanks,
>>>>>> Jorge
>>>>>>
>>>>>> SoakTest.java:13: error: The import org.apache cannot be resolved
>>>>>>  import org.apache.commons.codec.EncoderException;
>>>>>>         ^^^^^^^^^^
>>>>>> SoakTest.java:14: error: The import org.apache cannot be resolved
>>>>>>  import org.apache.commons.codec.net.URLCodec;
>>>>>>         ^^^^^^^^^^
>>>>>> SoakTest.java:15: error: The import org.jdom cannot be resolved
>>>>>>  import org.jdom.Document;
>>>>>>         ^^^^^^^^
>>>>>> SoakTest.java:16: error: The import org.jdom cannot be resolved
>>>>>>  import org.jdom.Element;
>>>>>>         ^^^^^^^^
>>>>>> SoakTest.java:17: error: The import org.jdom cannot be resolved
>>>>>>  import org.jdom.JDOMException;
>>>>>>         ^^^^^^^^
>>>>>> SoakTest.java:18: error: The import org.jdom cannot be resolved
>>>>>>  import org.jdom.input.SAXBuilder;
>>>>>>         ^^^^^^^^
>>>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>>>  URLCodec safeURL = new URLCodec();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:27: error: URLCodec cannot be resolved to a type
>>>>>>  URLCodec safeURL = new URLCodec();
>>>>>>                         ^^^^^^^^
>>>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>>>  SAXBuilder builder = new SAXBuilder();
>>>>>>  ^^^^^^^^^^
>>>>>> SoakTest.java:34: error: SAXBuilder cannot be resolved to a type
>>>>>>  SAXBuilder builder = new SAXBuilder();
>>>>>>                           ^^^^^^^^^^
>>>>>> SoakTest.java:35: error: Document cannot be resolved to a type
>>>>>>  Document martDoc = builder.build(martsURL);
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:37: error: Element cannot be resolved to a type
>>>>>>  Element martRoot = martDoc.getRootElement();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:39: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List martPointers = martRoot.getChildren("mart");
>>>>>>  ^^^^
>>>>>> SoakTest.java:40: warning: Iterator is a raw type. References to generic
>>>>>> type Iterator<E> should be parameterized
>>>>>>  Iterator mpIterator = martPointers.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>>>  Element martPointer = (Element) mpIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:47: error: Element cannot be resolved to a type
>>>>>>  Element martPointer = (Element) mpIterator.next();
>>>>>>                         ^^^^^^^
>>>>>> SoakTest.java:63: error: Document cannot be resolved to a type
>>>>>>  Document datasetsDoc = builder.build(datasetsURL);
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:65: error: Element cannot be resolved to a type
>>>>>>  Element datasetsRoot = datasetsDoc.getRootElement();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:67: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List datasets = datasetsRoot.getChildren("dataset");
>>>>>>  ^^^^
>>>>>> SoakTest.java:68: warning: Iterator is a raw type. References to generic
>>>>>> type Iterator<E> should be parameterized
>>>>>>  Iterator datasetsIterator = datasets.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>>>  Element dataset = (Element) datasetsIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:70: error: Element cannot be resolved to a type
>>>>>>  Element dataset = (Element) datasetsIterator.next();
>>>>>>                     ^^^^^^^
>>>>>> SoakTest.java:78: error: Document cannot be resolved to a type
>>>>>>  Document attributeDoc = builder.build(attributeURL);
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:80: error: Element cannot be resolved to a type
>>>>>>  Element attributeRoot = attributeDoc.getRootElement();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:82: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List attributes = attributeRoot.getChildren("attribute");
>>>>>>  ^^^^
>>>>>> SoakTest.java:83: warning: Iterator is a raw type. References to generic
>>>>>> type Iterator<E> should be parameterized
>>>>>>  Iterator attributeIterator = attributes.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>>>  Element attribute = (Element) attributeIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:86: error: Element cannot be resolved to a type
>>>>>>  Element attribute = (Element) attributeIterator.next();
>>>>>>                       ^^^^^^^
>>>>>> SoakTest.java:94: error: Document cannot be resolved to a type
>>>>>>  Document filterDoc = builder.build(filterURL);
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:96: error: Element cannot be resolved to a type
>>>>>>  Element filterRoot = filterDoc.getRootElement();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:98: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List filters = filterRoot.getChildren("filter");
>>>>>>  ^^^^
>>>>>> SoakTest.java:99: warning: Iterator is a raw type. References to generic
>>>>>> type Iterator<E> should be parameterized
>>>>>>  Iterator filterIterator = filters.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>>>  Element filter = (Element) filterIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:101: error: Element cannot be resolved to a type
>>>>>>  Element filter = (Element) filterIterator.next();
>>>>>>                    ^^^^^^^
>>>>>> SoakTest.java:113: error: JDOMException cannot be resolved to a type
>>>>>>  } catch (JDOMException e) {
>>>>>>           ^^^^^^^^^^^^^
>>>>>> SoakTest.java:116: error: EncoderException cannot be resolved to a type
>>>>>>  } catch (EncoderException e) {
>>>>>>           ^^^^^^^^^^^^^^^^
>>>>>> SoakTest.java:132: error: URLCodec cannot be resolved to a type
>>>>>>  HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>>>                            ^^^^^^^^
>>>>>> SoakTest.java:134: error: Element cannot be resolved to a type
>>>>>>  Element filter) throws MalformedURLException, EncoderException {
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:134: error: EncoderException cannot be resolved to a type
>>>>>>  Element filter) throws MalformedURLException, EncoderException {
>>>>>>                                                ^^^^^^^^^^^^^^^^
>>>>>> SoakTest.java:141: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List subFilters = filter.getChildren("filter");
>>>>>>  ^^^^
>>>>>> SoakTest.java:142: warning: Iterator is a raw type. References to
>>>>>> generic type Iterator<E> should be parameterized
>>>>>>  Iterator subFiltersIterator = subFilters.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>>>  Element subFilter = (Element) subFiltersIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:144: error: Element cannot be resolved to a type
>>>>>>  Element subFilter = (Element) subFiltersIterator.next();
>>>>>>                       ^^^^^^^
>>>>>> SoakTest.java:193: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List values = filter.getChildren("value");
>>>>>>  ^^^^
>>>>>> SoakTest.java:194: warning: Iterator is a raw type. References to
>>>>>> generic type Iterator<E> should be parameterized
>>>>>>  Iterator valueIterator = values.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>>>  Element value = (Element) valueIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:196: error: Element cannot be resolved to a type
>>>>>>  Element value = (Element) valueIterator.next();
>>>>>>                   ^^^^^^^
>>>>>> SoakTest.java:244: error: URLCodec cannot be resolved to a type
>>>>>>  HashSet<String> failInfo, URLCodec safeURL, String martName,
>>>>>>                            ^^^^^^^^
>>>>>> SoakTest.java:246: error: Element cannot be resolved to a type
>>>>>>  Element attribute) throws MalformedURLException, EncoderException {
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:246: error: EncoderException cannot be resolved to a type
>>>>>>  Element attribute) throws MalformedURLException, EncoderException {
>>>>>>                                                   ^^^^^^^^^^^^^^^^
>>>>>> SoakTest.java:247: warning: List is a raw type. References to generic
>>>>>> type List<E> should be parameterized
>>>>>>  List subAttributes = attribute.getChildren("attribute");
>>>>>>  ^^^^
>>>>>> SoakTest.java:293: warning: Iterator is a raw type. References to
>>>>>> generic type Iterator<E> should be parameterized
>>>>>>  Iterator subAttributesIterator = subAttributes.iterator();
>>>>>>  ^^^^^^^^
>>>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>>>  Element subAttribute = (Element) subAttributesIterator.next();
>>>>>>  ^^^^^^^
>>>>>> SoakTest.java:295: error: Element cannot be resolved to a type
>>>>>>  Element subAttribute = (Element) subAttributesIterator.next();
>>>>>>                          ^^^^^^^
>>>>>> 54 problems (40 errors, 14 warnings)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Jonathan Guberman wrote:
>>>>>>
>>>>>>
>>>>>>            
>>>>>>> Diff.java is outdated and will not work with the current version of Biomart. SoakTest.java is functional, but it was made as an internal testing tool, so it's not particularly user-friendly right now.
>>>>>>>
>>>>>>> To use it, set the URL on line 25 (default: "http://localhost:8888/rest/") to point to your server, with "/rest/" appended (e.g. "http://youserver:1234/rest/").
>>>>>>>
>>>>>>> To test a single mart, change the variable martNumber on line 29 and run the program. To find the number of the mart you're interested in, go to http://yourserver:1234/rest/xml/marts and count from the top (like I said, it's not very user-friendly!).
>>>>>>>
>>>>>>> To test all marts, change the variable testCounter on line 42 to equal -1, and then run the program. In this scenario, the martNumber variable doesn't matter.
>>>>>>>
>>>>>>> Status messages during testing will go to STDERR. At the end of testing a list of failed attributes and filters, along with their URLs, will be output to STDOUT. If there are no problems, "PASSED" will be output to STDOUT.
>>>>>>>
>>>>>>> There is one further user-settable parameter on line 22. If the testValues variable is set to "true," then all values of singleSelect filters will be tested, rather than just the first. This can add a significant amount of time to testing, so by default it is set to false.
>>>>>>>
>>>>>>> I hope that helps!
>>>>>>>
>>>>>>> Jonathan
>>>>>>>
>>>>>>> On 2011-02-22, at 3:14 AM, Jorge Zamora Berna wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>> Hi Arek,
>>>>>>>>
>>>>>>>> Yes, actually I found the folders where I believe the scripts are located (SoakTest.java, Diff.java). Could you please give us some help on how to use them?
>>>>>>>>
>>>>>>>> Thanks a lot,
>>>>>>>> Jorge
>>>>>>>>
>>>>>>>> /release-0_8-candidate_4/test/org/biomart/soak$ ls
>>>>>>>> SoakTest.java
>>>>>>>> /release-0_8-candidate_4/test/org/biomart/diff$ ls
>>>>>>>> Diff.java
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --- El mar, 22/2/11, Arek Kasprzyk <[hidden email]> escribió:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>>>> De: Arek Kasprzyk <[hidden email]>
>>>>>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>>>>>> Para: "Syed Haider" <[hidden email]>
>>>>>>>>> CC: "Jorge Zamora Berna" <[hidden email]>, "[hidden email]" <[hidden email]>
>>>>>>>>> Fecha: martes, 22 de febrero, 2011 07:18
>>>>>>>>> I believe that there is a soak script
>>>>>>>>> that the guys here use routinely
>>>>>>>>> to check for working filters and atts. Is that what you are
>>>>>>>>> after?
>>>>>>>>>
>>>>>>>>> a
>>>>>>>>>
>>>>>>>>> On 2011-02-22, at 5:36, "Syed Haider" <[hidden email]>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>> Hi Jorge,
>>>>>>>>>>
>>>>>>>>>> With rc4, unfortunately there are'nt any yet. With
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>> rc6, we should be
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>> add
>>>>>>>>>> these scripts
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> Syed
>>>>>>>>>>
>>>>>>>>>> On 21/02/2011 19:10, Jorge Zamora Berna wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> are the any scripts to test marts built with 0.8?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>> I mean scripts
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>>> that automatically query the mart and report the
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>> queries that failed.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Jorge
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Users mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                      
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Users mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>> _______________________________________________
>>>>>>>> Users mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>> _______________________________________________
>>>>>>> Users mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>>>>>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>>>>>>
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>>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>>>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
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>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
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**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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