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)
>
>
>
>
>
>
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>
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>
>
>
>
>
>
> 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
>>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [email protected]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>
>>>
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>>
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