@cubis/foundry 0.3.10

package/Ai Agent Workflow/skills/static-analysis/workflows/create-data-extensions.md

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+# Create Data Extensions Workflow
+
+Generate data extension YAML files to improve CodeQL's data flow coverage for project-specific APIs. Runs after database build and before analysis.
+
+## Task System
+
+Create these tasks on workflow start:
+
+```
+TaskCreate: "Check for existing data extensions" (Step 1)
+TaskCreate: "Query known sources and sinks" (Step 2) - blockedBy: Step 1
+TaskCreate: "Identify missing sources and sinks" (Step 3) - blockedBy: Step 2
+TaskCreate: "Create data extension files" (Step 4) - blockedBy: Step 3
+TaskCreate: "Validate with re-analysis" (Step 5) - blockedBy: Step 4
+```
+
+### Early Exit Points
+
+| After Step | Condition | Action |
+|------------|-----------|--------|
+| Step 1 | Extensions already exist | Return found packs/files to run-analysis workflow, finish |
+| Step 3 | No missing models identified | Report coverage is adequate, finish |
+
+---
+
+## Steps
+
+### Step 1: Check for Existing Data Extensions
+
+Search the project for existing data extensions and model packs.
+
+**1. In-repo model packs** — `qlpack.yml` or `codeql-pack.yml` with `dataExtensions`:
+
+```bash
+fd '(qlpack|codeql-pack)\.yml$' . --exclude codeql_*.db | while read -r f; do
+  if grep -q 'dataExtensions' "$f"; then
+    echo "MODEL PACK: $(dirname "$f") - $(grep '^name:' "$f")"
+  fi
+done
+```
+
+**2. Standalone data extension files** — `.yml` files with `extensions:` key:
+
+```bash
+rg -l '^extensions:' --glob '*.yml' --glob '!codeql_*.db/**' | head -20
+```
+
+**3. Installed model packs:**
+
+```bash
+codeql resolve qlpacks 2>/dev/null | grep -iE 'model|extension'
+```
+
+**If any found:** Report to user what was found and finish. These will be picked up by the run-analysis workflow's model pack detection (Step 2b).
+
+**If none found:** Proceed to Step 2.
+
+---
+
+### Step 2: Query Known Sources and Sinks
+
+Run custom QL queries against the database to enumerate all sources and sinks CodeQL currently recognizes. This gives a direct inventory of what is modeled vs. what is not.
+
+#### 2a: Select Database and Language
+
+```bash
+DB_NAME=$(ls -dt codeql_*.db 2>/dev/null | head -1)
+LANG=$(codeql resolve database --format=json -- "$DB_NAME" | jq -r '.languages[0]')
+echo "Database: $DB_NAME, Language: $LANG"
+
+DIAG_DIR="${DB_NAME%.db}-diagnostics"
+mkdir -p "$DIAG_DIR"
+```
+
+#### 2b: Write Source Enumeration Query
+
+Use the `Write` tool to create `$DIAG_DIR/list-sources.ql` using the source template from [diagnostic-query-templates.md](../references/diagnostic-query-templates.md#source-enumeration-query). Pick the correct import block for `$LANG`.
+
+#### 2c: Write Sink Enumeration Query
+
+Use the `Write` tool to create `$DIAG_DIR/list-sinks.ql` using the language-specific sink template from [diagnostic-query-templates.md](../references/diagnostic-query-templates.md#sink-enumeration-queries). The Concepts API differs significantly across languages — use the exact template for the detected language.
+
+**For Java:** Also create `$DIAG_DIR/qlpack.yml` with a `codeql/java-all` dependency and run `codeql pack install` before executing queries. See the Java section in the templates reference.
+
+#### 2d: Run Queries
+
+```bash
+# Run sources query
+codeql query run \
+  --database="$DB_NAME" \
+  --output="$DIAG_DIR/sources.bqrs" \
+  -- "$DIAG_DIR/list-sources.ql"
+
+codeql bqrs decode \
+  --format=csv \
+  --output="$DIAG_DIR/sources.csv" \
+  -- "$DIAG_DIR/sources.bqrs"
+
+# Run sinks query
+codeql query run \
+  --database="$DB_NAME" \
+  --output="$DIAG_DIR/sinks.bqrs" \
+  -- "$DIAG_DIR/list-sinks.ql"
+
+codeql bqrs decode \
+  --format=csv \
+  --output="$DIAG_DIR/sinks.csv" \
+  -- "$DIAG_DIR/sinks.bqrs"
+```
+
+#### 2e: Summarize Results
+
+```bash
+echo "=== Known Sources ==="
+wc -l < "$DIAG_DIR/sources.csv"
+# Show unique source types
+cut -d',' -f2 "$DIAG_DIR/sources.csv" | sort -u
+
+echo "=== Known Sinks ==="
+wc -l < "$DIAG_DIR/sinks.csv"
+# Show unique sink kinds
+cut -d',' -f2 "$DIAG_DIR/sinks.csv" | sort -u
+```
+
+Read both CSV files and present a summary to the user:
+
+```
+## CodeQL Known Models
+
+### Sources (<N> total):
+- remote: <count> (HTTP handlers, request parsing)
+- local: <count> (CLI args, file reads)
+- ...
+
+### Sinks (<N> total):
+- sql-execution: <count>
+- command-execution: <count>
+- file-access: <count>
+- ...
+```
+
+---
+
+### Step 3: Identify Missing Sources and Sinks
+
+This is the core analysis step. Cross-reference the project's API surface against CodeQL's known models.
+
+#### 3a: Map the Project's API Surface
+
+Read source code to identify security-relevant patterns. Look for:
+
+| Pattern | What To Find | Likely Model Type |
+|---------|-------------|-------------------|
+| HTTP/request handlers | Custom request parsing, parameter access | `sourceModel` (kind: `remote`) |
+| Database layers | Custom ORM methods, raw query wrappers | `sinkModel` (kind: `sql-injection`) |
+| Command execution | Shell wrappers, process spawners | `sinkModel` (kind: `command-injection`) |
+| File operations | Custom file read/write, path construction | `sinkModel` (kind: `path-injection`) |
+| Template rendering | HTML output, response builders | `sinkModel` (kind: `xss`) |
+| Deserialization | Custom deserializers, data loaders | `sinkModel` (kind: `unsafe-deserialization`) |
+| HTTP clients | URL construction, request builders | `sinkModel` (kind: `ssrf`) |
+| Sanitizers | Input validation, escaping functions | `neutralModel` |
+| Pass-through wrappers | Logging, caching, encoding | `summaryModel` (kind: `taint`) |
+
+Use `Grep` to search for these patterns in source code:
+
+```bash
+# Examples for Python - adapt patterns per language
+rg -n 'def (get_param|get_header|get_body|parse_request)' --type py
+rg -n '(execute|query|raw_sql|cursor\.)' --type py
+rg -n '(subprocess|os\.system|popen|exec)' --type py
+rg -n '(open|read_file|write_file|path\.join)' --type py
+rg -n '(render|template|html)' --type py
+rg -n '(requests\.|urlopen|fetch|http_client)' --type py
+```
+
+#### 3b: Cross-Reference Against Known Sources and Sinks
+
+For each API pattern found in 3a, check if it appears in the source/sink CSVs from Step 2:
+
+```bash
+# Check if a specific file/function appears in known sources
+grep -i "<function_or_file>" "$DIAG_DIR/sources.csv"
+
+# Check if a specific file/function appears in known sinks
+grep -i "<function_or_file>" "$DIAG_DIR/sinks.csv"
+```
+
+**An API is "missing" if:**
+- It handles user input but does not appear in `sources.csv`
+- It performs a dangerous operation but does not appear in `sinks.csv`
+- It wraps/transforms tainted data but CodeQL has no summary model for it (these won't appear in either CSV — identify by reading the code for wrapper patterns around known sources/sinks)
+
+#### 3c: Report Gaps
+
+Present findings to user:
+
+```
+## Data Flow Coverage Gaps
+
+### Missing Sources (user input not tracked):
+- `myapp.http.Request.get_param()` — custom parameter access
+- `myapp.auth.Token.decode()` — untrusted token data
+
+### Missing Sinks (dangerous operations not checked):
+- `myapp.db.Connection.raw_query()` — SQL execution wrapper
+- `myapp.shell.Runner.execute()` — command execution
+
+### Missing Summaries (taint lost through wrappers):
+- `myapp.cache.Cache.get()` — taint not propagated through cache
+- `myapp.utils.encode_json()` — taint lost in serialization
+
+Proceed to create data extension files?
+```
+
+Use `AskUserQuestion`:
+
+```
+header: "Extensions"
+question: "Create data extension files for the identified gaps?"
+options:
+  - label: "Create all (Recommended)"
+    description: "Generate extensions for all identified gaps"
+  - label: "Select individually"
+    description: "Choose which gaps to model"
+  - label: "Skip"
+    description: "No extensions needed, proceed to analysis"
+```
+
+**If "Skip":** Finish workflow.
+
+**If "Select individually":** Use `AskUserQuestion` with `multiSelect: true` listing each gap.
+
+---
+
+### Step 4: Create Data Extension Files
+
+Generate YAML data extension files for the gaps confirmed by the user.
+
+#### File Structure
+
+Create files in a `codeql-extensions/` directory at project root:
+
+```
+codeql-extensions/
+  sources.yml       # sourceModel entries
+  sinks.yml         # sinkModel entries
+  summaries.yml     # summaryModel and neutralModel entries
+```
+
+#### YAML Format
+
+All extension files follow this structure:
+
+```yaml
+extensions:
+  - addsTo:
+      pack: codeql/<language>-all  # Target library pack
+      extensible: <model-type>      # sourceModel, sinkModel, summaryModel, neutralModel
+    data:
+      - [<columns>]
+```
+
+#### Source Models
+
+Columns: `[package, type, subtypes, name, signature, ext, output, kind, provenance]`
+
+| Column | Description | Example |
+|--------|-------------|---------|
+| package | Module/package path | `myapp.auth` |
+| type | Class or module name | `AuthManager` |
+| subtypes | Include subclasses | `True` (Java: capitalized) / `true` (Python/JS/Go) |
+| name | Method name | `get_token` |
+| signature | Method signature (optional) | `""` (Python/JS), `"(String,int)"` (Java) |
+| ext | Extension (optional) | `""` |
+| output | What is tainted | `ReturnValue`, `Parameter[0]` (Java) / `Argument[0]` (Python/JS/Go) |
+| kind | Source category | `remote`, `local`, `file`, `environment`, `database` |
+| provenance | How model was created | `manual` |
+
+**Java-specific format differences:**
+- **subtypes**: Use `True` / `False` (capitalized, Python-style), not `true` / `false`
+- **output for parameters**: Use `Parameter[N]` (not `Argument[N]`) to mark method parameters as sources
+- **signature**: Required for disambiguation — use Java type syntax: `"(String)"`, `"(String,int)"`
+- **Parameter ranges**: Use `Parameter[0..2]` to mark multiple consecutive parameters
+
+Example (Python):
+
+```yaml
+# codeql-extensions/sources.yml
+extensions:
+  - addsTo:
+      pack: codeql/python-all
+      extensible: sourceModel
+    data:
+      - ["myapp.http", "Request", true, "get_param", "", "", "ReturnValue", "remote", "manual"]
+      - ["myapp.http", "Request", true, "get_header", "", "", "ReturnValue", "remote", "manual"]
+```
+
+Example (Java — note `True`, `Parameter[N]`, and signature):
+
+```yaml
+# codeql-extensions/sources.yml
+extensions:
+  - addsTo:
+      pack: codeql/java-all
+      extensible: sourceModel
+    data:
+      - ["com.myapp.controller", "ApiController", True, "search", "(String)", "", "Parameter[0]", "remote", "manual"]
+      - ["com.myapp.service", "FileService", True, "upload", "(String,String)", "", "Parameter[0..1]", "remote", "manual"]
+```
+
+#### Sink Models
+
+Columns: `[package, type, subtypes, name, signature, ext, input, kind, provenance]`
+
+Note: column 7 is `input` (which argument receives tainted data), not `output`.
+
+| Kind | Vulnerability |
+|------|---------------|
+| `sql-injection` | SQL injection |
+| `command-injection` | Command injection |
+| `path-injection` | Path traversal |
+| `xss` | Cross-site scripting |
+| `code-injection` | Code injection |
+| `ssrf` | Server-side request forgery |
+| `unsafe-deserialization` | Insecure deserialization |
+
+Example (Python):
+
+```yaml
+# codeql-extensions/sinks.yml
+extensions:
+  - addsTo:
+      pack: codeql/python-all
+      extensible: sinkModel
+    data:
+      - ["myapp.db", "Connection", true, "raw_query", "", "", "Argument[0]", "sql-injection", "manual"]
+      - ["myapp.shell", "Runner", false, "execute", "", "", "Argument[0]", "command-injection", "manual"]
+```
+
+Example (Java — note `True` and `Argument[N]` for sink input):
+
+```yaml
+extensions:
+  - addsTo:
+      pack: codeql/java-all
+      extensible: sinkModel
+    data:
+      - ["com.myapp.db", "QueryRunner", True, "execute", "(String)", "", "Argument[0]", "sql-injection", "manual"]
+```
+
+#### Summary Models
+
+Columns: `[package, type, subtypes, name, signature, ext, input, output, kind, provenance]`
+
+| Kind | Description |
+|------|-------------|
+| `taint` | Data flows through, still tainted |
+| `value` | Data flows through, exact value preserved |
+
+Example:
+
+```yaml
+# codeql-extensions/summaries.yml
+extensions:
+  # Pass-through: taint propagates
+  - addsTo:
+      pack: codeql/python-all
+      extensible: summaryModel
+    data:
+      - ["myapp.cache", "Cache", true, "get", "", "", "Argument[0]", "ReturnValue", "taint", "manual"]
+      - ["myapp.utils", "JSON", false, "parse", "", "", "Argument[0]", "ReturnValue", "taint", "manual"]
+
+  # Sanitizer: taint blocked
+  - addsTo:
+      pack: codeql/python-all
+      extensible: neutralModel
+    data:
+      - ["myapp.security", "Sanitizer", "escape_html", "", "summary", "manual"]
+```
+
+**`neutralModel` vs no model:** If a function has no model at all, CodeQL may still infer flow through it. Use `neutralModel` to explicitly block taint propagation through known-safe functions.
+
+#### Language-Specific Notes
+
+**Python:** Use dotted module paths for `package` (e.g., `myapp.db`).
+
+**JavaScript:** `package` is often `""` for project-local code. Use the import path for npm packages.
+
+**Go:** Use full import paths (e.g., `myapp/internal/db`). `type` is often `""` for package-level functions.
+
+**Java:** Use fully qualified package names (e.g., `com.myapp.db`).
+
+**C/C++:** Use `""` for package, put the namespace in `type`.
+
+#### Write the Files
+
+Use the `Write` tool to create each file. Only create files that have entries — skip empty categories.
+
+#### Deploy the Extensions
+
+**Known limitation:** `--additional-packs` and `--model-packs` flags do not work with pre-compiled query packs (bundled CodeQL distributions that cache `java-all` inside `.codeql/libraries/`). Extensions placed in a standalone model pack directory will be resolved by `codeql resolve qlpacks` but silently ignored during `codeql database analyze`.
+
+**Workaround — copy extensions into the library pack's `ext/` directory:**
+
+> **Warning:** Files copied into the `ext/` directory live inside CodeQL's managed pack cache. They will be **lost** when packs are updated via `codeql pack download` or version upgrades. After any pack update, re-run this deployment step to restore the extensions.
+
+```bash
+# Find the java-all ext directory used by the query pack
+JAVA_ALL_EXT=$(find "$(codeql resolve qlpacks 2>/dev/null | grep 'java-queries' | awk '{print $NF}' | tr -d '()')" \
+  -path '*/.codeql/libraries/codeql/java-all/*/ext' -type d 2>/dev/null | head -1)
+
+if [ -n "$JAVA_ALL_EXT" ]; then
+  PROJECT_NAME=$(basename "$(pwd)")
+  cp codeql-extensions/sources.yml "$JAVA_ALL_EXT/${PROJECT_NAME}.sources.model.yml"
+  [ -f codeql-extensions/sinks.yml ] && cp codeql-extensions/sinks.yml "$JAVA_ALL_EXT/${PROJECT_NAME}.sinks.model.yml"
+  [ -f codeql-extensions/summaries.yml ] && cp codeql-extensions/summaries.yml "$JAVA_ALL_EXT/${PROJECT_NAME}.summaries.model.yml"
+
+  # Verify deployment — confirm files landed correctly
+  DEPLOYED=$(ls "$JAVA_ALL_EXT/${PROJECT_NAME}".*.model.yml 2>/dev/null | wc -l)
+  if [ "$DEPLOYED" -gt 0 ]; then
+    echo "Extensions deployed to $JAVA_ALL_EXT ($DEPLOYED files):"
+    ls -la "$JAVA_ALL_EXT/${PROJECT_NAME}".*.model.yml
+  else
+    echo "ERROR: Files were copied but verification failed. Check path: $JAVA_ALL_EXT"
+  fi
+else
+  echo "WARNING: Could not find java-all ext directory. Extensions may not load."
+  echo "Attempted path lookup from: codeql resolve qlpacks | grep java-queries"
+  echo "Run 'codeql resolve qlpacks' manually to debug."
+fi
+```
+
+**For Python/JS/Go:** The same limitation may apply. Locate the `<lang>-all` pack's `ext/` directory and copy extensions there.
+
+**Alternative (if query packs are NOT pre-compiled):** Use `--additional-packs=./codeql-extensions` with a proper model pack `qlpack.yml`:
+
+```yaml
+# codeql-extensions/qlpack.yml
+name: custom/<project>-extensions
+version: 0.0.1
+library: true
+extensionTargets:
+  codeql/<lang>-all: "*"
+dataExtensions:
+  - sources.yml
+  - sinks.yml
+  - summaries.yml
+```
+
+---
+
+### Step 5: Validate with Re-Analysis
+
+Run a full security analysis with and without extensions to measure the finding delta. This is more reliable than re-running source/sink enumeration queries, which may not reflect the `sourceModel` extensible being used by taint-tracking queries.
+
+#### 5a: Run Baseline Analysis (without extensions)
+
+```bash
+RESULTS_DIR="${DB_NAME%.db}-results"
+mkdir -p "$RESULTS_DIR"
+
+# Baseline run (or skip if already run in a previous step)
+codeql database analyze "$DB_NAME" \
+  --format=sarif-latest \
+  --output="$RESULTS_DIR/baseline.sarif" \
+  --threads=0 \
+  -- codeql/<lang>-queries:codeql-suites/<lang>-security-extended.qls
+```
+
+#### 5b: Run Analysis with Extensions
+
+```bash
+# Clean cache to force re-evaluation
+codeql database cleanup "$DB_NAME"
+
+codeql database analyze "$DB_NAME" \
+  --format=sarif-latest \
+  --output="$RESULTS_DIR/with-extensions.sarif" \
+  --threads=0 \
+  --rerun \
+  -- codeql/<lang>-queries:codeql-suites/<lang>-security-extended.qls
+```
+
+Use `-vvv` flag to verify extensions are being loaded — look for `Loading data extensions in ... <your-extension-file>.yml` in stderr.
+
+#### 5c: Compare Findings
+
+```bash
+BASELINE=$(python3 -c "import json; print(sum(len(r.get('results',[])) for r in json.load(open('$RESULTS_DIR/baseline.sarif')).get('runs',[])))")
+WITH_EXT=$(python3 -c "import json; print(sum(len(r.get('results',[])) for r in json.load(open('$RESULTS_DIR/with-extensions.sarif')).get('runs',[])))")
+echo "Findings: $BASELINE → $WITH_EXT (+$((WITH_EXT - BASELINE)))"
+```
+
+**If counts did not increase:** The extension YAML may have syntax errors or column values that don't match the code. Check:
+
+| Issue | Solution |
+|-------|----------|
+| Extension not loaded | Run with `-vvv` and grep for your extension filename in output |
+| Pre-compiled pack ignores extensions | Use the `ext/` directory workaround above |
+| Java: No new findings | Verify `True`/`False` (capitalized) for subtypes, `Parameter[N]` for sources |
+| No new sources/sinks | Verify column values match actual code signatures exactly |
+| Type not found | Use exact type name as it appears in CodeQL database |
+| Wrong argument index | Arguments are 0-indexed; `self` is `Argument[self]` (Python), `Parameter[0]` (Java) |
+
+Fix the extension files, re-deploy to `ext/`, and re-run 5b until counts increase.
+
+---
+
+## Final Output
+
+```
+## Data Extensions Created
+
+**Database:** $DB_NAME
+**Language:** <LANG>
+
+### Files Created:
+- codeql-extensions/sources.yml — <N> source models
+- codeql-extensions/sinks.yml — <N> sink models
+- codeql-extensions/summaries.yml — <N> summary/neutral models
+
+### Model Coverage:
+- Sources: <BEFORE> → <AFTER> (+<DELTA>)
+- Sinks: <BEFORE> → <AFTER> (+<DELTA>)
+
+### Usage:
+Extensions deployed to `<lang>-all` ext/ directory (auto-loaded).
+Source files in `codeql-extensions/` for version control.
+Run the run-analysis workflow to use them.
+```
+
+## References
+
+- [Threat models reference](../references/threat-models.md) — control which source categories are active during analysis
+- [CodeQL data extensions](https://codeql.github.com/docs/codeql-cli/using-custom-queries-with-the-codeql-cli/#using-extension-packs)
+- [Customizing library models](https://codeql.github.com/docs/codeql-language-guides/customizing-library-models-for-python/)