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 <[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
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