org.json jar file is old and lacks some JSON spec methods

[sammyjava]

The included org.json package is quite old and lacks some useful methods in the current JSON spec, for exampe: keySet() and toMap(). I suggest replacing it with a current version, which I can supply, compiled from here: https://github.com/stleary/JSON-java

intermine/intermine/model/main/lib/json20110106.jar
intermine/intermine/webservice/client/main/lib/json20110106.jar

[sammyjava]

json20160810.zip

[julie-sullivan]

Failed Travis tests. Seems like there is some sort of Java version compatibility problem.

[justinccdev]

fwiw, here's a version compiled for java 1.7. Name is 20161008 as this is of the last change to that repo (I suspect this is the same as sammyjava but with switched month and day).

json20161008.zip

Analysis of sammyjava's jar does show compilation for 1.8

[sammyjava]

Ahhh, sorry about that.

[justinccdev]

No worries 😊

On 21 Nov 2016 5:08 p.m., "Sam Hokin" notifications@github.com wrote:

Ahhh, sorry about that.

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[justinccdev]

This is being progressed under #1457. After sorting out various issues with actually getting the right jar in built for the right Java version, it turns out some change in JSON-java [1] is causing a couple of InterMine tests to fail. It's not obvious when this occurred so the next step will be to divide and conquer to find out which JSON-java change is causing this and then work out what to do about it.

[1] https://github.com/stleary/JSON-java

[julie-sullivan]

@justinccdev Can you update the JAR in maven's config please

[justinccdev]

This can't be done until the test failures on updating the jar have been fixed.

[julie-sullivan]

oh. okay. I'll take a look. Hopefully just reordering?

[justinccdev]

Unfortunately not, afair, it was something else caused by some subtle change in the behaviour of JSON-java (aka json-lib). When I last looked, I had come to the point of actually comparing json-lib source code to try and identify the change directly but other priorities took over. If we're really unlucky the change was a local patch by somebody in InterMine which has since been lost. A more fruitful approach may be to simply update the JAR and directly change the InterMine source code to accommodate the different behaviour but this won't be simple either. I suspect it's buried deep within JSON generation.

[julie-sullivan]

Two test failures

1. imjs -- which I am guessing is related to the test failings in Add List.ID to all end points #1683 and Json queries #1670. imjs is handling JSON weirdly.

2. JSON row iterator test

FAILURE: Class org.intermine.webservice.server.output.JSONRowIteratorTest, method testResultsWithNulls

junit.framework.ComparisonFailure: null expected:<null> but was:
<[Problem with index 0:
 [Expected the keys
 [column, id, class, value, url], 
but got these: 
[column, url], 

Problem with id: org.json.JSONException: JSONObject["id"] not found., Problem with class: org.json.JSONException: JSONObject["class"] not found., 
Problem with value: org.json.JSONException: JSONObject["value"] not found.],
 Problem with index 1: [Expected the keys [column, id, class, value, url], but got these: [column, url], Problem with id: org.json.JSONException: JSONObject["id"] not found., 
Problem with class: org.json.JSONException: JSONObject["class"] not found., Problem with value: org.json.JSONException: JSONObject["value"] not found.]]>

	at org.intermine.webservice.server.output.JSONRowIteratorTest.testResultsWithNulls(JSONRowIteratorTest.java:315)

It's weird the other tests pass though, right?

EDIT: oh i see, the JSON row formatter is ignoring / dropping NULL columns. whoops.