Add CodeQL Analysis Github Action (#809)

* Create codeql-analysis.yml

* CodeQL Fix: explicitly cast long to int

* CodeQL Fix: prevent "zip slip"

* Add comment about CodeQL action

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,73 @@
+# This file was created by CodeQL for this repository. The only change was 
+# removing 'python' and 'javascript' from the language array.
+#
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ dev ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ dev ]
+  schedule:
+    - cron: '24 12 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

src/main/java/com/conveyal/r5/streets/StreetRouter.java

@@ -35,7 +35,6 @@
 import java.util.List;
 import java.util.PriorityQueue;
 
-import static com.conveyal.r5.common.Util.isNullOrEmpty;
 import static com.conveyal.r5.common.Util.notNullOrEmpty;
 import static com.conveyal.r5.streets.LinkedPointSet.OFF_STREET_SPEED_MILLIMETERS_PER_SECOND;
 import static gnu.trove.impl.Constants.DEFAULT_CAPACITY;
@@ -968,8 +967,8 @@ public void incrementTimeInSeconds(long seconds) {
                 durationSeconds-=seconds;
                 durationFromOriginSeconds -= seconds;
             } else {
-                durationSeconds+=seconds;
-                durationFromOriginSeconds += seconds;
+                durationSeconds += (int) seconds;
+                durationFromOriginSeconds += (int) seconds;
             }
 
         }

src/main/java/com/conveyal/r5/transit/TransportNetworkCache.java

@@ -6,16 +6,15 @@
 import com.conveyal.file.FileStorageKey;
 import com.conveyal.file.FileUtils;
 import com.conveyal.gtfs.GTFSCache;
-import com.conveyal.r5.analyst.cluster.TransportNetworkConfig;
 import com.conveyal.r5.analyst.cluster.ScenarioCache;
+import com.conveyal.r5.analyst.cluster.TransportNetworkConfig;
 import com.conveyal.r5.analyst.scenario.Modification;
 import com.conveyal.r5.analyst.scenario.RasterCost;
 import com.conveyal.r5.analyst.scenario.Scenario;
 import com.conveyal.r5.analyst.scenario.ShapefileLts;
 import com.conveyal.r5.common.JsonUtilities;
 import com.conveyal.r5.kryo.KryoNetworkSerializer;
 import com.conveyal.r5.profile.StreetMode;
-import com.conveyal.r5.shapefile.ShapefileMatcher;
 import com.conveyal.r5.streets.OSMCache;
 import com.conveyal.r5.streets.StreetLayer;
 import com.github.benmanes.caffeine.cache.Caffeine;
@@ -207,6 +206,10 @@ private TransportNetwork buildNetworkFromBundleZip (String networkId) {
             ZipEntry entry;
             while ((entry = zis.getNextEntry()) != null) {
                 File entryDestination = new File(dataDirectory, entry.getName());
+                if (!entryDestination.toPath().normalize().startsWith(dataDirectory.toPath())) {
+                    throw new Exception("Bad zip entry");
+                }
+
                 // Are both these mkdirs calls necessary?
                 entryDestination.getParentFile().mkdirs();
                 if (entry.isDirectory())