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 <[email protected]> escribió:
>>>>>
>>>>>
>>>>>
>>>>>> De: Arek Kasprzyk <[email protected]>
>>>>>> Asunto: Re: [BioMart Users] test scripts for biomart 0.8
>>>>>> Para: "Syed Haider" <[email protected]>
>>>>>> CC: "Jorge Zamora Berna" <[email protected]>, "[email protected]"
>>>>>> <[email protected]>
>>>>>> 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" <[email protected]>
>>>>>> 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
>>>>>>>> [email protected]
>>>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>> _______________________________________________
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>
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> 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
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