Don't throw exceptions if dependencies can't be pre-calculated (#475)

We observed this issue:

```
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - Problem scanning file /tmp/codemodder-project6927415874030968841/app/src/main/java/org/apache/roller/weblogger/util/PasswordUtility.java
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - io.codemodder.plugins.maven.MavenProvider$DependencyUpdateException: Failure when retrieving dependencies
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - at io.codemodder.plugins.maven.MavenProvider.getAllDependencies(MavenProvider.java:146)
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - at io.codemodder.DefaultCodemodExecutor.lambda$execute$0(DefaultCodemodExecutor.java:187)
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - at java.base/java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:273)
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
INFO - 4abaf6cf-c5e6-4f48-b198-edc124aedf71 - at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
...
io.codemodder.DefaultCodemodExecutor.lambda$execute$1(DefaultCodemodExecutor.java:188)
edc124aedf71 - Caused by: org.dom4j.DocumentException: Error on line 781 of document  : The element type "sequential" must be terminated by the matching end-tag "</sequential>".
```

This error is preventing _analysis_ from occurring, not the updating of
Maven dependencies. We should still run our codemods, even if
dependencies can't be pre-calculated.

Author: nahsra

framework/codemodder-base/src/main/java/io/codemodder/DefaultCodemodExecutor.java

@@ -15,6 +15,7 @@
 import java.util.*;
 import java.util.concurrent.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.VisibleForTesting;
 import org.slf4j.Logger;
@@ -184,7 +185,14 @@ public CodeTFResult execute(final List<Path> filePaths) {
               Collection<DependencyGAV> deps =
                   projectProviders.stream()
                       .flatMap(
-                          provider -> provider.getAllDependencies(projectDir, filePath).stream())
+                          provider -> {
+                            try {
+                              return provider.getAllDependencies(projectDir, filePath).stream();
+                            } catch (Exception e) {
+                              log.error("Problem getting dependencies for file {}", filePath, e);
+                              return Stream.empty();
+                            }
+                          })
                       .toList();
 
               CodemodInvocationContext context =

framework/codemodder-base/src/test/java/io/codemodder/DefaultCodemodExecutorTest.java

@@ -146,7 +146,7 @@ public DependencyUpdateResult updateDependencies(
     }
 
     @Override
-    public Collection<DependencyGAV> getAllDependencies(Path projectDir, Path file) {
+    public Collection<DependencyGAV> getAllDependencies(final Path projectDir, final Path file) {
       return List.of();
     }
   }
@@ -158,7 +158,41 @@ void it_generates_single_codemod_codetf() {
 
     // should have just 1 entry because we only scanned javaFile1
     List<CodeTFChangesetEntry> changeset = result.getChangeset();
-    assertThat(changeset.size()).isEqualTo(1);
+    assertThat(changeset).hasSize(1);
+    assertThat(changeset.get(0)).satisfies(DefaultCodemodExecutorTest::isJavaFile1ChangedCorrectly);
+  }
+
+  @Test
+  void it_works_despite_fail_prefetching_all_deps() {
+    FakeDepsProvider depsProvider =
+        new FakeDepsProvider() {
+          @Override
+          public Collection<DependencyGAV> getAllDependencies(
+              final Path projectDir, final Path file) {
+            throw new RuntimeException("failed to prefetch deps");
+          }
+        };
+
+    executor =
+        new DefaultCodemodExecutor(
+            repoDir,
+            includesEverything,
+            beforeAfterCodemod,
+            List.of(depsProvider),
+            List.of(),
+            fileCache,
+            javaParserFacade,
+            encodingDetector,
+            -1,
+            -1,
+            -1);
+
+    CodeTFResult result = executor.execute(List.of(javaFile1));
+    assertThat(result).satisfies(DefaultCodemodExecutorTest::hasBeforeAfterCodemodMetadata);
+
+    // should have just 1 entry because we only scanned javaFile1
+    List<CodeTFChangesetEntry> changeset = result.getChangeset();
+    assertThat(changeset).hasSize(1);
     assertThat(changeset.get(0)).satisfies(DefaultCodemodExecutorTest::isJavaFile1ChangedCorrectly);
   }
 
@@ -241,7 +275,7 @@ public CodeTFChange onChangeCreated(
 
     // confirm the change was updated by the provider
     List<CodeTFChangesetEntry> changeset = result.getChangeset();
-    assertThat(changeset.size()).isEqualTo(1);
+    assertThat(changeset).hasSize(1);
     CodeTFChangesetEntry entry = changeset.get(0);
     assertThat(entry.getChanges().get(0).getDescription()).isEqualTo("hi " + javaFile1.toString());
     assertThat(entry.getChanges().get(0).getProperties()).hasSize(1);
@@ -256,7 +290,7 @@ void it_generates_all_files_codemod_codetf() {
 
     // should have 2 entries for both javaFile1 and javaFile3
     List<CodeTFChangesetEntry> changeset = result.getChangeset();
-    assertThat(changeset.size()).isEqualTo(2);
+    assertThat(changeset).hasSize(2);
     assertThat(changeset.get(0)).satisfies(DefaultCodemodExecutorTest::isJavaFile1ChangedCorrectly);
     assertThat(changeset.get(1)).satisfies(DefaultCodemodExecutorTest::isJavaFile3ChangedCorrectly);
   }

plugins/codemodder-plugin-maven/src/main/java/io/codemodder/plugins/maven/MavenProvider.java

@@ -143,8 +143,9 @@ public Collection<DependencyGAV> getAllDependencies(final Path projectDir, final
 
       return pomOperator.getAllFoundDependencies();
     } catch (Exception e) {
-      throw new DependencyUpdateException("Failure when retrieving dependencies", e);
+      LOG.warn("Not all Maven dependencies could be found", e);
     }
+    return Collections.emptyList();
   }
 
   private static final Logger LOG = LoggerFactory.getLogger(MavenProvider.class);