Java: Model more of Apache Commons Collections by owen-mc · Pull Request #6370 · github/codeql

owen-mc · 2021-07-27T09:58:51Z

Model everything that is not in a subpackage

github-actions · 2021-07-27T10:01:05Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,762,,,,,,,,
-    Totals,,84,2465,296,13,6,6,107,33,1,66
+    Totals,,84,3029,296,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,381,,,,,,,,,,,,,,,10,371
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,381,,,,,,,,,,,,,,,10,371

java/ql/test/library-tests/frameworks/apache-collections/Test.java

java/ql/test/library-tests/frameworks/apache-collections/test.ql

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

java/ql/test/library-tests/frameworks/apache-collections/Test.java

aschackmull · 2021-08-04T07:58:21Z

There are btw. also a number of casts that could probably be removed from the generated test.

github-actions · 2021-08-04T13:49:49Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,762,,,,,,,,
-    Totals,,84,2705,360,13,6,6,107,33,1,66
+    Totals,,84,3269,360,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,381,,,,,,,,,,,,,,,,,,10,371
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,381,,,,,,,,,,,,,,,,,,10,371

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

github-actions · 2021-08-04T14:59:31Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,760,,,,,,,,
-    Totals,,84,2705,398,13,6,6,107,33,1,66
+    Totals,,84,3267,398,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,380,,,,,,,,,,,,,,,,,,,10,370
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,380,,,,,,,,,,,,,,,,,,,10,370

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

aschackmull · 2021-08-05T07:32:53Z

@atorralba Feel free to take the review from here and merge when you're happy.

atorralba · 2021-08-05T08:03:02Z

Were .class files committed by accident? e.g. https://github.com/github/codeql/blob/7862d4a222850cfb59e99cec6aaffed2f93a0359/java/ql/test/stubs/apache-commons-collections4-4.4/org/apache/commons/collections4/trie/PatriciaTrie.class

atorralba

I added some inline comments (some may be dismissible because of my lack of knowledge), otherwise LGTM.

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

The package name was org.apache.commons.collection until release 4.0.

github-actions · 2021-08-08T13:07:28Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,784,,,,,,,,
-    Totals,,84,2705,398,13,6,6,107,33,1,66
+    Totals,,84,3291,398,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,392,,,,,,,,,,,,,,,,,,,16,376
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,392,,,,,,,,,,,,,,,,,,,16,376

smowton

Reviewed the collections themselves; various Utils classes to do.

smowton · 2021-08-09T10:08:15Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+        // Note that when lambdas are supported we should model things relating to Closure, Factory, Transformer, FluentIterable.forEach, FluentIterable.transform
+        "org.apache.commons.collections4;ArrayStack;true;peek;;;Element of Argument[-1];ReturnValue;value",
+        "org.apache.commons.collections4;ArrayStack;true;pop;;;Element of Argument[-1];ReturnValue;value",
+        "org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];Element of Argument[-1];value",


Suggested change

"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];Element of Argument[-1];value",

"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];Element of Argument[-1];value",

"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];ReturnValue;value",

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

smowton · 2021-08-09T10:22:17Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+        "org.apache.commons.collections4;FluentIterable;true;skip;;;Element of Argument[-1];Element of ReturnValue;value",
+        "org.apache.commons.collections4;FluentIterable;true;toArray;;;Element of Argument[-1];ArrayElement of ReturnValue;value",
+        "org.apache.commons.collections4;FluentIterable;true;toList;;;Element of Argument[-1];Element of ReturnValue;value",
+        "org.apache.commons.collections4;FluentIterable;true;toString;;;Element of Argument[-1];ReturnValue;taint",


Might have missed a discussion on this, but I think we're still not routinely propagating taint across stringification

smowton · 2021-08-09T10:29:02Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+        "org.apache.commons.collections4;MapIterator;true;setValue;;;Argument[0];MapValue of Argument[-1];value",
+        "org.apache.commons.collections4;MultiMap;true;get;;;Element of MapValue of Argument[-1];Element of ReturnValue;value",
+        "org.apache.commons.collections4;MultiMap;true;put;;;Argument[0];MapKey of Argument[-1];value",
+        "org.apache.commons.collections4;MultiMap;true;put;;;Argument[1];Element of MapValue of Argument[-1];value",


Suggested change

"org.apache.commons.collections4;MultiMap;true;put;;;Argument[1];Element of MapValue of Argument[-1];value",

"org.apache.commons.collections4;MultiMap;true;put;;;Argument[1];Element of MapValue of Argument[-1];value",

"org.apache.commons.collections4;MultiMap;true;remove;;;Element of MapValue of Argument[-1];Element of ReturnValue;value",

This is inherited from Get and Map. Or do you think that the extra Element of components are needed?

I see, no problem then. I don't think the extra Element of is needed (though check -- no need to use the test generator, just add a little test method that adds something to a MultiMap and then removes it and see if taint is tracked)

I checked and it worked.

smowton · 2021-08-09T10:34:42Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+        "org.apache.commons.collections4;MultiSet;true;uniqueSet;;;Element of Argument[-1];Element of ReturnValue;value",
+        "org.apache.commons.collections4;MultiSet;true;entrySet;;;Element of Argument[-1];Element of Element of ReturnValue;value",
+        "org.apache.commons.collections4;MultiValuedMap;true;asMap;;;MapKey of Argument[-1];MapKey of ReturnValue;value",
+        "org.apache.commons.collections4;MultiValuedMap;true;asMap;;;Element of MapValue of Argument[-1];Element of MapValue of ReturnValue;value",


MultiValuedMap.entries?

smowton · 2021-08-09T10:42:31Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+        "org.apache.commons.collections4;SortedBag;true;last;;;Element of Argument[-1];ReturnValue;value",
+        "org.apache.commons.collections4;Trie;true;prefixMap;;;MapKey of Argument[-1];MapKey of ReturnValue;value",
+        "org.apache.commons.collections4;Trie;true;prefixMap;;;MapValue of Argument[-1];MapValue of ReturnValue;value",
+        "org.apache.commons.collections;ArrayStack;true;peek;;;Element of Argument[-1];ReturnValue;value",


Only reviewed the collections4 models. Are the two sets of models identical or supposed to be? If so use something like "org.apache.commons.collections" + ["", "4"] + ";" + ["ArrayStack;true;peek;;;Element of Argument[-1];ReturnValue;value", ...]

This way we can at least guard against the models drifting apart by accident.

My review assumed both sets were identical too. +1 to this suggestion.

We do not do this for other overrides of toString

And corresponding tests

github-actions · 2021-08-10T11:01:06Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,776,,,,,,,,
-    Totals,,84,2711,398,13,6,6,107,33,1,66
+    Totals,,84,3289,398,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,388,,,,,,,,,,,,,,,,,,,9,379
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,388,,,,,,,,,,,,,,,,,,,9,379

owen-mc · 2021-08-10T14:15:47Z

@smowton I've addressed all review comments.
@atorralba Your review was dismissed 😞 .

smowton

Comments on CollectionUtils

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

smowton · 2021-08-11T09:21:13Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[2];value",
+          ";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[3];value",


Note these two also return their Argument[2] (distinct from the element-transfer to return value case which only applies to the one-arg overload)

I don't understand your comment in parentheses. Are you saying L293 should be limited to the (Iterable,Predicate)?

Yes, the Iterable, Predicate version should be modelled elem-of-arg0 -> elem-of-ret, whereas the Iterable, Predicate, Collection[, Collection] overloads should be modelled elem-of-arg0 -> elem-of-arg2 and arg2 -> ret (cf elem of arg(0 or 2) -> elem of ret which would obscure the fact that arg2 and ret are the same object)

I was worried that we wouldn't get elem-of-arg0 -> elem-of-ret because "arg2 -> ret" would consider "arg2" from before this line is executed. But I just tested it and it works fine 😄 .

Yeah, this works for similar reasons to fluent methods, where we might have elem-of-arg -> elem-of-qualifier and also qualifier -> ret.

smowton · 2021-08-11T09:22:55Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[2];value",
+          ";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[3];value",
+          ";CollectionUtils;true;selectRejected;;;Element of Argument[0];Element of ReturnValue;value",
+          ";CollectionUtils;true;selectRejected;;;Element of Argument[0];Element of Argument[2];value",


Similarly, model the overload that takes an existing container as propagating elements to it and returning arg2 by value.

smowton · 2021-08-11T09:23:59Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";CollectionUtils;true;selectRejected;;;Element of Argument[0];Element of Argument[2];value",
+          ";CollectionUtils;true;subtract;;;Element of Argument[0];Element of ReturnValue;value",
+          ";CollectionUtils;true;synchronizedCollection;;;Element of Argument[0];Element of ReturnValue;value",
+          ";CollectionUtils;true;transformingCollection;;;Element of Argument[0];Element of ReturnValue;value",


We haven't modelled other collection operations that apply some lambda; for consistency we probably shouldn't model this one either

But the lambda isn't applied by this function: Existing entries in the specified collection will not be transformed.

I'll add a comment like you ask for below.

Ah yes, comment will do the trick

smowton

Comments on CollectionUtils and ListUtils

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

smowton · 2021-08-11T09:35:51Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";ListUtils;true;sum;;;Element of Argument[0];Element of ReturnValue;value",
+          ";ListUtils;true;sum;;;Element of Argument[1];Element of ReturnValue;value",
+          ";ListUtils;true;synchronizedList;;;Element of Argument[0];Element of ReturnValue;value",
+          ";ListUtils;true;transformedList;;;Element of Argument[0];Element of ReturnValue;value",


Probably worth a comment on this and lazyList that these models represent the perhaps-surprising behaviour that existing list elements are retained unaltered by both methods

smowton

Reviewed IteratorUtils

smowton · 2021-08-11T09:42:10Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";IteratorUtils;true;filteredListIterator;;;Element of Argument[0];Element of ReturnValue;value",
+          ";IteratorUtils;true;find;;;Element of Argument[0];ReturnValue;value",
+          ";IteratorUtils;true;first;;;Element of Argument[0];ReturnValue;value",
+          ";IteratorUtils;true;get;;;Element of Argument[0];ReturnValue;value",


forEachButLast gets the last element in an iterator by value

smowton

Reviewed IterableUtils

smowton · 2021-08-11T09:58:35Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+          ";IterableUtils;true;filteredIterable;;;Element of Argument[0];Element of ReturnValue;value",
+          ";IterableUtils;true;find;;;Element of Argument[0];ReturnValue;value",
+          ";IterableUtils;true;first;;;Element of Argument[0];ReturnValue;value",
+          ";IterableUtils;true;get;;;Element of Argument[0];ReturnValue;value",


forEachButLast exists here too

smowton

Done reviewing; this looks good to me with the given minor adjustments

smowton · 2021-08-11T10:13:42Z

java/ql/src/semmle/code/java/frameworks/apache/Collections.qll

+      ["org.apache.commons.collections4", "org.apache.commons.collections"] +
+        [
+          ";MultiMapUtils;true;emptyIfNull;;;Argument[0];ReturnValue;value",
+          ";MultiMapUtils;true;getCollection;;;MapValue of Argument[0];ReturnValue;value",


I think these need an Element of on both sides, because it's creating a new Collection/Bag/List/Set to hold whatever values the MultiValuedMap holds for the key

I don't think so. The source code is literally map.get(key) behind a null check.

Ah ok, I thought it stored them internally as something different.

You are however right about getValuesAsBag and its friends, so 75% right.

smowton · 2021-08-11T10:26:17Z

java/ql/test/library-tests/frameworks/apache-collections/test.ql

    row =
      [
        //"package;type;overrides;name;signature;ext;inputspec;outputspec;kind",
+        "org.apache.commons.collections4.iterators;IteratorEnumeration;true;IteratorEnumeration;;;Element of Argument[0];Element of Argument[-1];value",


Add a comment indicating why the test models this

github-actions · 2021-08-12T13:54:19Z

⚠️ The head of this PR and the base branch were compared for differences in the framework coverage reports. The generated reports are available in the artifacts of this workflow run. The differences will be picked up by the nightly job after the PR gets merged. The following differences were found:

java

Generated file changes for java

Changes to framework-coverage-java.rst:

-    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,198,,,,,,,,
+    `Apache Commons Collections <https://commons.apache.org/proper/commons-collections/>`_,"``org.apache.commons.collections``, ``org.apache.commons.collections4``",,788,,,,,,,,
-    Totals,,84,2711,398,13,6,6,107,33,1,66
+    Totals,,84,3301,398,13,6,6,107,33,1,66

Changes to framework-coverage-java.csv:

- org.apache.commons.collections,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections,,,394,,,,,,,,,,,,,,,,,,,9,385
- org.apache.commons.collections4,,,99,,,,,,,,,,,,,,,,,,,4,95
+ org.apache.commons.collections4,,,394,,,,,,,,,,,,,,,,,,,9,385

smowton

A heroic epic

owen-mc · 2021-08-16T15:13:26Z

I have pushed a commit fixing two small mistakes from #6138 which were caught by @atorralba after it was merged.

As this adds so many models we will do a performance analysis before merging it. I believe that is the last thing left.

smowton

Performance evaluation finished, using Apache Flink and Apache Hive (both heavy Collections users) on top of several existing light users in our dist-compare suite. No noticeable performance impact.

owen-mc requested a review from a team as a code owner July 27, 2021 09:58

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aschackmull reviewed Aug 4, 2021

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owen-mc added 4 commits August 4, 2021 14:26

Model *Utils classes

39ea0a9

Model interfaces in Apache Commons Collections main package

b823890

Add automatically generated tests

a538699

Manually improve tests

2e04319

owen-mc force-pushed the java/model/apache-collections branch from af0dab9 to 0a39995 Compare August 4, 2021 13:47

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owen-mc force-pushed the java/model/apache-collections branch from 0a39995 to 7862d4a Compare August 4, 2021 14:57

atorralba reviewed Aug 4, 2021

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owen-mc changed the title ~~Model more of Apache Commons Collections~~ Java: Model more of Apache Commons Collections Aug 5, 2021

owen-mc added 3 commits August 6, 2021 07:06

Add stubs

51a7018

Duplicate models for old package name

b922d7c

The package name was org.apache.commons.collection until release 4.0.

Add change note

26f5ac9

Remove unnecessary casts

1997dfb

owen-mc force-pushed the java/model/apache-collections branch from 7862d4a to 1997dfb Compare August 8, 2021 13:05

atorralba previously approved these changes Aug 9, 2021

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smowton reviewed Aug 9, 2021

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owen-mc added 5 commits August 9, 2021 16:25

Improve treatment of new and old package name

487a46a

Remove toString taint propagation

2d31bb8

We do not do this for other overrides of toString

Make helper functions more consistent

54fdfe3

Add more missing models

a55a32f

And corresponding tests

Remove duplicate test

2000985

owen-mc dismissed atorralba’s stale review via 2000985 August 10, 2021 10:58

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owen-mc added 2 commits August 12, 2021 14:51

Fix more models based on review comments

fe477ff

Add explanatory comments

1c2476c

smowton previously approved these changes Aug 12, 2021

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Fix errors from previous PR

b23fabe

owen-mc dismissed smowton’s stale review via b23fabe August 16, 2021 15:11

owen-mc mentioned this pull request Aug 16, 2021

Java: Model Apache commons collections MapUtils class and keyvalue package #6138

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atorralba approved these changes Aug 19, 2021

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owen-mc merged commit 714e126 into github:main Aug 19, 2021

owen-mc deleted the java/model/apache-collections branch August 19, 2021 14:09

	"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];Element of Argument[-1];value",
	"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];Element of Argument[-1];value",
	"org.apache.commons.collections4;ArrayStack;true;push;;;Argument[0];ReturnValue;value",

	"org.apache.commons.collections4;MultiMap;true;put;;;Argument[1];Element of MapValue of Argument[-1];value",
	"org.apache.commons.collections4;MultiMap;true;put;;;Argument[1];Element of MapValue of Argument[-1];value",
	"org.apache.commons.collections4;MultiMap;true;remove;;;Element of MapValue of Argument[-1];Element of ReturnValue;value",

		";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[2];value",
		";CollectionUtils;true;select;;;Element of Argument[0];Element of Argument[3];value",

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owen-mc commented Jul 27, 2021

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