fix: Deduplicate deps while amending (#1266)

* fix: Deduplicate deps while amending

* Add comment

* Remove unnecessary code

* Add test case

MODULE.bazel

@@ -558,6 +558,8 @@ dev_maven.install(
         "build.buf:protovalidate:0.1.9",
         # https://github.com/bazelbuild/rules_jvm_external/issues/1250
         "com.github.spotbugs:spotbugs:4.7.0",
+        # https://github.com/bazelbuild/rules_jvm_external/issues/1267
+        "org.mockito:mockito-core:pom:3.3.3",
     ],
     fail_if_repin_required = True,
     generate_compat_repositories = True,

WORKSPACE

@@ -278,6 +278,8 @@ maven_install(
         "build.buf:protovalidate:0.1.9",
         # https://github.com/bazelbuild/rules_jvm_external/issues/1250
         "com.github.spotbugs:spotbugs:4.7.0",
+        # https://github.com/bazelbuild/rules_jvm_external/issues/1267
+        "org.mockito:mockito-core:pom:3.3.3",
     ],
     fail_if_repin_required = True,
     generate_compat_repositories = True,

private/rules/coursier.bzl

@@ -956,6 +956,13 @@ def rewrite_files_attribute_if_necessary(repository_ctx, dep_tree):
         # `pinned_maven_install`. Oh well, let's just do this the manual way.
         if dep["file"].endswith(".pom"):
             jar_path = dep["file"].removesuffix(".pom") + ".jar"
+
+            # The same artifact can being depended on via pom and jar at different
+            # places in the tree. In such case, we deduplicate it so that 2
+            # entries do not reference the same file, which will otherwise lead
+            # in symlink error because of existing file down the road.
+            if is_dep(jar_path, amended_deps):
+                continue
             if repository_ctx.path(jar_path).exists:
                 dep["file"] = jar_path
 
@@ -965,6 +972,12 @@ def rewrite_files_attribute_if_necessary(repository_ctx, dep_tree):
 
     return dep_tree
 
+def is_dep(jar_path, deps):
+    for dep in deps:
+        if jar_path == dep.get("file", None):
+            return True
+    return False
+
 def remove_prefix(s, prefix):
     if s.startswith(prefix):
         return s[len(prefix):]

tests/bazel_run_tests.sh

@@ -259,7 +259,7 @@ function test_transitive_dependency_with_type_of_pom {
   bazel query @transitive_dependency_with_type_of_pom//:org_javamoney_moneta_moneta_core >> "$TEST_LOG" 2>&1
 }
 
-function test_when_both_pom_and_artifact_are_available_jar_artifact_is_present {
+function test_when_both_pom_and_jar_artifact_are_available_jar_artifact_is_present {
   # The `maven_coordinates` of the target should be set to the coordinates of the jar
   # If the `pom` classifier is asked for, something has gone wrong and no results will
   # match
@@ -268,6 +268,16 @@ function test_when_both_pom_and_artifact_are_available_jar_artifact_is_present {
   expect_log "@regression_testing_coursier//:com_github_spotbugs_spotbugs"
 }
 
+function test_when_both_pom_and_jar_artifact_are_dependencies_jar_artifact_is_present {
+  # The `maven_coordinates` of the target should be set to the coordinates of the jar
+  # If both the `jar` and `pom` classifiers are asked for, something has gone wrong and no results
+  # will match
+  bazel query 'attr(tags, "org.mockito:mockito-core:3.3.3", @regression_testing_coursier//:org_mockito_mockito_core)' >> "$TEST_LOG" 2>&1
+
+  expect_log "@regression_testing_coursier//:org_mockito_mockito_core"
+}
+
+
 TESTS=(
   "test_maven_resolution"
   "test_dependency_aggregation"
@@ -286,7 +296,8 @@ TESTS=(
   "test_v1_lock_file_format"
   "test_dependency_pom_exclusion"
   "test_transitive_dependency_with_type_of_pom"
-  "test_when_both_pom_and_artifact_are_available_jar_artifact_is_present"
+  "test_when_both_pom_and_jar_artifact_are_available_jar_artifact_is_present"
+  "test_when_both_pom_and_jar_artifact_are_dependencies_jar_artifact_is_present"
 )
 
 function run_tests() {

tests/custom_maven_install/regression_testing_coursier_install.json

@@ -1,7 +1,7 @@
 {
   "__AUTOGENERATED_FILE_DO_NOT_MODIFY_THIS_FILE_MANUALLY": "THERE_IS_NO_DATA_ONLY_ZUUL",
-  "__INPUT_ARTIFACTS_HASH": 1906932742,
-  "__RESOLVED_ARTIFACTS_HASH": 1555926687,
+  "__INPUT_ARTIFACTS_HASH": -1504192575,
+  "__RESOLVED_ARTIFACTS_HASH": 2071728921,
   "artifacts": {
     "android.arch.core:common": {
       "shasums": {
@@ -618,9 +618,9 @@
     },
     "com.nimbusds:nimbus-jose-jwt": {
       "shasums": {
-        "jar": "978cc75ee13ef021e288bf1aa78d8ad9f69cee558119a09a5a64e7fc92085000"
+        "jar": "388f3fcec4f7ce41557b0271033c978c30f386cc302a6783be181edd599e9dff"
       },
-      "version": "9.41.1"
+      "version": "9.45"
     },
     "com.nimbusds:oauth2-oidc-sdk": {
       "shasums": {