chore(deps): update dependency pathling to v9 #403
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✅
|
| Descriptor | Linter | Files | Fixed | Errors | Warnings | Elapsed time |
|---|---|---|---|---|---|---|
| ✅ ACTION | actionlint | 6 | 0 | 0 | 0.05s | |
| ✅ DOCKERFILE | hadolint | 8 | 0 | 0 | 0.63s | |
| ✅ EDITORCONFIG | editorconfig-checker | 51 | 0 | 0 | 0.05s | |
| ✅ JSON | jsonlint | 6 | 0 | 0 | 0.17s | |
| ✅ JSON | prettier | 6 | 0 | 0 | 0.7s | |
| ✅ JSON | v8r | 6 | 0 | 0 | 7.13s | |
| markdownlint | 9 | 6 | 0 | 0.95s | ||
| ✅ REPOSITORY | checkov | yes | no | no | 22.05s | |
| ✅ REPOSITORY | gitleaks | yes | no | no | 0.56s | |
| ✅ REPOSITORY | git_diff | yes | no | no | 0.03s | |
| kics | yes | no | 2 | 3.77s | ||
| ✅ REPOSITORY | secretlint | yes | no | no | 1.92s | |
| ✅ REPOSITORY | syft | yes | no | no | 8.15s | |
| trivy | yes | 11 | 5 | 11.19s | ||
| ✅ REPOSITORY | trivy-sbom | yes | no | no | 1.74s | |
| ✅ REPOSITORY | trufflehog | yes | no | no | 13.83s | |
| ✅ YAML | prettier | 9 | 0 | 0 | 0.57s | |
| ✅ YAML | v8r | 9 | 0 | 0 | 7.36s | |
| ✅ YAML | yamllint | 9 | 0 | 0 | 0.5s |
Detailed Issues
⚠️ REPOSITORY / kics - 2 warnings
warning: The 'Dockerfile' contains the 'chown' flag
┌─ images/ml-on-fhir/Dockerfile:43:1
│
43 │ COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
│ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
│
= Chown Flag Exists
= It is considered a best practice for every executable in a container to be owned by the root user even if it is executed by a non-root user, only execution permissions are required on the file, not ownership
warning: The 'Dockerfile' contains the 'chown' flag
┌─ images/hive-metastore/Dockerfile:30:1
│
30 │ COPY --from=downloader --chown=0:0 /tmp/libs/*.jar /opt/hive/lib/
│ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
│
= Chown Flag Exists
= It is considered a best practice for every executable in a container to be owned by the root user even if it is executed by a non-root user, only execution permissions are required on the file, not ownership
warning: 2 warnings emitted
⚠️ MARKDOWN / markdownlint - 6 errors
images/dsf-bpe-full/CHANGELOG.md:141 MD022/blanks-around-headings Headings should be surrounded by blank lines [Expected: 1; Actual: 0; Below] [Context: "### Description"]
images/dsf-bpe-full/CHANGELOG.md:144 MD022/blanks-around-headings Headings should be surrounded by blank lines [Expected: 1; Actual: 0; Below] [Context: "### Versions:"]
images/dsf-bpe-full/CHANGELOG.md:144:13 MD026/no-trailing-punctuation Trailing punctuation in heading [Punctuation: ':']
images/dsf-bpe-full/CHANGELOG.md:145 MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "* DFN CA certificate chain fro..."]
images/dsf-bpe-full/CHANGELOG.md:151:31 MD039/no-space-in-links Spaces inside link text [Context: "["MII Data Transfer" process ]"]
images/dsf-bpe-full/CHANGELOG.md:152:30 MD039/no-space-in-links Spaces inside link text [Context: "["MII Data Sharing" process ]"]
⚠️ REPOSITORY / trivy - 11 errors
error: Package: @isaacs/brace-expansion
Installed Version: 5.0.0
Vulnerability CVE-2026-25547
Severity: HIGH
Fixed Version: 5.0.1
Link: [CVE-2026-25547](https://avd.aquasec.com/nvd/cve-2026-25547)
┌─ images/semantic-release/package-lock.json:3443:1
│
3443 │ ╭ "node_modules/npm/node_modules/@isaacs/brace-expansion": {
3444 │ │ "version": "5.0.0",
3445 │ │ "inBundle": true,
3446 │ │ "license": "MIT",
· │
3452 │ │ }
3453 │ │ },
│ ╰^
│
= brace-expansion: brace-expansion: Denial of Service via unbounded brace range expansion
= @isaacs/brace-expansion is a hybrid CJS/ESM TypeScript fork of brace-expansion. Prior to version 5.0.1, @isaacs/brace-expansion is vulnerable to a denial of service (DoS) issue caused by unbounded brace range expansion. When an attacker provides a pattern containing repeated numeric brace ranges, the library attempts to eagerly generate every possible combination synchronously. Because the expansion grows exponentially, even a small input can consume excessive CPU and memory and may crash the Node.js process. This issue has been patched in version 5.0.1.
error: Package: glob
Installed Version: 10.4.5
Vulnerability CVE-2025-64756
Severity: HIGH
Fixed Version: 11.1.0, 10.5.0
Link: [CVE-2025-64756](https://avd.aquasec.com/nvd/cve-2025-64756)
┌─ images/semantic-release/package-lock.json:4800:1
│
4800 │ ╭ "node_modules/npm/node_modules/node-gyp/node_modules/glob": {
4801 │ │ "version": "10.4.5",
4802 │ │ "inBundle": true,
4803 │ │ "license": "ISC",
· │
4817 │ │ }
4818 │ │ },
│ ╰^
│
= glob: glob: Command Injection Vulnerability via Malicious Filenames
= Glob matches files using patterns the shell uses. Starting in version 10.2.0 and prior to versions 10.5.0 and 11.1.0, the glob CLI contains a command injection vulnerability in its -c/--cmd option that allows arbitrary command execution when processing files with malicious names. When glob -c <command> <patterns> are used, matched filenames are passed to a shell with shell: true, enabling shell metacharacters in filenames to trigger command injection and achieve arbitrary code execution under the user or CI account privileges. This issue has been patched in versions 10.5.0 and 11.1.0.
error: Package: glob
Installed Version: 11.0.3
Vulnerability CVE-2025-64756
Severity: HIGH
Fixed Version: 11.1.0, 10.5.0
Link: [CVE-2025-64756](https://avd.aquasec.com/nvd/cve-2025-64756)
┌─ images/semantic-release/package-lock.json:4202:1
│
4202 │ ╭ "node_modules/npm/node_modules/glob": {
4203 │ │ "version": "11.0.3",
4204 │ │ "inBundle": true,
4205 │ │ "license": "ISC",
· │
4222 │ │ }
4223 │ │ },
│ ╰^
│
= glob: glob: Command Injection Vulnerability via Malicious Filenames
= Glob matches files using patterns the shell uses. Starting in version 10.2.0 and prior to versions 10.5.0 and 11.1.0, the glob CLI contains a command injection vulnerability in its -c/--cmd option that allows arbitrary command execution when processing files with malicious names. When glob -c <command> <patterns> are used, matched filenames are passed to a shell with shell: true, enabling shell metacharacters in filenames to trigger command injection and achieve arbitrary code execution under the user or CI account privileges. This issue has been patched in versions 10.5.0 and 11.1.0.
warning: Package: js-yaml
Installed Version: 4.1.0
Vulnerability CVE-2025-64718
Severity: MEDIUM
Fixed Version: 4.1.1, 3.14.2
Link: [CVE-2025-64718](https://avd.aquasec.com/nvd/cve-2025-64718)
┌─ images/semantic-release/package-lock.json:2874:1
│
2874 │ ╭ "node_modules/js-yaml": {
2875 │ │ "version": "4.1.0",
2876 │ │ "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz",
2877 │ │ "integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==",
· │
2884 │ │ }
2885 │ │ },
│ ╰^
│
= js-yaml: js-yaml prototype pollution in merge
= js-yaml is a JavaScript YAML parser and dumper. In js-yaml before 4.1.1 and 3.14.2, it's possible for an attacker to modify the prototype of the result of a parsed yaml document via prototype pollution (`__proto__`). All users who parse untrusted yaml documents may be impacted. The problem is patched in js-yaml 4.1.1 and 3.14.2. Users can protect against this kind of attack on the server by using `node --disable-proto=delete` or `deno` (in Deno, pollution protection is on by default).
warning: Package: lodash
Installed Version: 4.17.21
Vulnerability CVE-2025-13465
Severity: MEDIUM
Fixed Version: 4.17.23
Link: [CVE-2025-13465](https://avd.aquasec.com/nvd/cve-2025-13465)
┌─ images/semantic-release/package-lock.json:2972:1
│
2972 │ ╭ "node_modules/lodash": {
2973 │ │ "version": "4.17.21",
2974 │ │ "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
2975 │ │ "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==",
2976 │ │ "license": "MIT"
2977 │ │ },
│ ╰^
│
= lodash: prototype pollution in _.unset and _.omit functions
= Lodash versions 4.0.0 through 4.17.22 are vulnerable to prototype pollution in the _.unset and _.omit functions. An attacker can pass crafted paths which cause Lodash to delete methods from global prototypes.
The issue permits deletion of properties but does not allow overwriting their original behavior.
This issue is patched on 4.17.23
warning: Package: lodash-es
Installed Version: 4.17.21
Vulnerability CVE-2025-13465
Severity: MEDIUM
Fixed Version: 4.17.23
Link: [CVE-2025-13465](https://avd.aquasec.com/nvd/cve-2025-13465)
┌─ images/semantic-release/package-lock.json:2978:1
│
2978 │ ╭ "node_modules/lodash-es": {
2979 │ │ "version": "4.17.21",
2980 │ │ "resolved": "https://registry.npmjs.org/lodash-es/-/lodash-es-4.17.21.tgz",
2981 │ │ "integrity": "sha512-mKnC+QJ9pWVzv+C4/U3rRsHapFfHvQFoFB92e52xeyGMcX6/OlIl78je1u8vePzYZSkkogMPJ2yjxxsb89cxyw==",
2982 │ │ "license": "MIT"
2983 │ │ },
│ ╰^
│
= lodash: prototype pollution in _.unset and _.omit functions
= Lodash versions 4.0.0 through 4.17.22 are vulnerable to prototype pollution in the _.unset and _.omit functions. An attacker can pass crafted paths which cause Lodash to delete methods from global prototypes.
The issue permits deletion of properties but does not allow overwriting their original behavior.
This issue is patched on 4.17.23
error: Package: tar
Installed Version: 7.5.1
Vulnerability CVE-2026-23745
Severity: HIGH
Fixed Version: 7.5.3
Link: [CVE-2026-23745](https://avd.aquasec.com/nvd/cve-2026-23745)
┌─ images/semantic-release/package-lock.json:5408:1
│
5408 │ ╭ "node_modules/npm/node_modules/tar": {
5409 │ │ "version": "7.5.1",
5410 │ │ "inBundle": true,
5411 │ │ "license": "ISC",
· │
5421 │ │ }
5422 │ │ },
│ ╰^
│
= node-tar: tar: node-tar: Arbitrary file overwrite and symlink poisoning via unsanitized linkpaths in archives
= node-tar is a Tar for Node.js. The node-tar library (<= 7.5.2) fails to sanitize the linkpath of Link (hardlink) and SymbolicLink entries when preservePaths is false (the default secure behavior). This allows malicious archives to bypass the extraction root restriction, leading to Arbitrary File Overwrite via hardlinks and Symlink Poisoning via absolute symlink targets. This vulnerability is fixed in 7.5.3.
error: Package: tar
Installed Version: 7.5.1
Vulnerability CVE-2026-23950
Severity: HIGH
Fixed Version: 7.5.4
Link: [CVE-2026-23950](https://avd.aquasec.com/nvd/cve-2026-23950)
┌─ images/semantic-release/package-lock.json:5408:1
│
5408 │ ╭ "node_modules/npm/node_modules/tar": {
5409 │ │ "version": "7.5.1",
5410 │ │ "inBundle": true,
5411 │ │ "license": "ISC",
· │
5421 │ │ }
5422 │ │ },
│ ╰^
│
= node-tar: tar: node-tar: Arbitrary file overwrite via Unicode path collision race condition
= node-tar,a Tar for Node.js, has a race condition vulnerability in versions up to and including 7.5.3. This is due to an incomplete handling of Unicode path collisions in the `path-reservations` system. On case-insensitive or normalization-insensitive filesystems (such as macOS APFS, In which it has been tested), the library fails to lock colliding paths (e.g., `ß` and `ss`), allowing them to be processed in parallel. This bypasses the library's internal concurrency safeguards and permits Symlink Poisoning attacks via race conditions. The library uses a `PathReservations` system to ensure that metadata checks and file operations for the same path are serialized. This prevents race conditions where one entry might clobber another concurrently. This is a Race Condition which enables Arbitrary File Overwrite. This vulnerability affects users and systems using node-tar on macOS (APFS/HFS+). Because of using `NFD` Unicode normalization (in which `ß` and `ss` are different), conflicting paths do not have their order properly preserved under filesystems that ignore Unicode normalization (e.g., APFS (in which `ß` causes an inode collision with `ss`)). This enables an attacker to circumvent internal parallelization locks (`PathReservations`) using conflicting filenames within a malicious tar archive. The patch in version 7.5.4 updates `path-reservations.js` to use a normalization form that matches the target filesystem's behavior (e.g., `NFKD`), followed by first `toLocaleLowerCase('en')` and then `toLocaleUpperCase('en')`. As a workaround, users who cannot upgrade promptly, and who are programmatically using `node-tar` to extract arbitrary tarball data should filter out all `SymbolicLink` entries (as npm does) to defend against arbitrary file writes via this file system entry name collision issue.
error: Package: tar
Installed Version: 7.5.1
Vulnerability CVE-2026-24842
Severity: HIGH
Fixed Version: 7.5.7
Link: [CVE-2026-24842](https://avd.aquasec.com/nvd/cve-2026-24842)
┌─ images/semantic-release/package-lock.json:5408:1
│
5408 │ ╭ "node_modules/npm/node_modules/tar": {
5409 │ │ "version": "7.5.1",
5410 │ │ "inBundle": true,
5411 │ │ "license": "ISC",
· │
5421 │ │ }
5422 │ │ },
│ ╰^
│
= node-tar: tar: node-tar: Arbitrary file creation via path traversal bypass in hardlink security check
= node-tar,a Tar for Node.js, contains a vulnerability in versions prior to 7.5.7 where the security check for hardlink entries uses different path resolution semantics than the actual hardlink creation logic. This mismatch allows an attacker to craft a malicious TAR archive that bypasses path traversal protections and creates hardlinks to arbitrary files outside the extraction directory. Version 7.5.7 contains a fix for the issue.
warning: Package: tar
Installed Version: 7.5.1
Vulnerability CVE-2025-64118
Severity: MEDIUM
Fixed Version: 7.5.2
Link: [CVE-2025-64118](https://avd.aquasec.com/nvd/cve-2025-64118)
┌─ images/semantic-release/package-lock.json:5408:1
│
5408 │ ╭ "node_modules/npm/node_modules/tar": {
5409 │ │ "version": "7.5.1",
5410 │ │ "inBundle": true,
5411 │ │ "license": "ISC",
· │
5421 │ │ }
5422 │ │ },
│ ╰^
│
= node-tar: tar: node-tar: Information disclosure via reading a truncated tar file
= node-tar is a Tar for Node.js. In 7.5.1, using .t (aka .list) with { sync: true } to read tar entry contents returns uninitialized memory contents if tar file was changed on disk to a smaller size while being read. This vulnerability is fixed in 7.5.2.
warning: Package: undici
Installed Version: 5.29.0
Vulnerability CVE-2026-22036
Severity: MEDIUM
Fixed Version: 7.18.2, 6.23.0
Link: [CVE-2026-22036](https://avd.aquasec.com/nvd/cve-2026-22036)
┌─ images/semantic-release/package-lock.json:7375:1
│
7375 │ ╭ "node_modules/undici": {
7376 │ │ "version": "5.29.0",
7377 │ │ "resolved": "https://registry.npmjs.org/undici/-/undici-5.29.0.tgz",
7378 │ │ "integrity": "sha512-raqeBD6NQK4SkWhQzeYKd1KmIG6dllBOTt55Rmkt4HtI9mwdWtJljnrXjAFUBLTSN67HWrOIZ3EPF4kjUw80Bg==",
· │
7385 │ │ }
7386 │ │ },
│ ╰^
│
= undici: Undici: Denial of Service via excessive decompression steps
= Undici is an HTTP/1.1 client for Node.js. Prior to 7.18.0 and 6.23.0, the number of links in the decompression chain is unbounded and the default maxHeaderSize allows a malicious server to insert thousands compression steps leading to high CPU usage and excessive memory allocation. This vulnerability is fixed in 7.18.0 and 6.23.0.
error: Artifact: images/apache-superset/Dockerfile
Type: dockerfile
Vulnerability DS017
Severity: HIGH
Message: The instruction 'RUN <package-manager> update' should always be followed by '<package-manager> install' in the same RUN statement.
Link: [DS017](https://avd.aquasec.com/misconfig/ds017)
┌─ images/apache-superset/Dockerfile:8:1
│
8 │ ╭ RUN <<EOF
9 │
(Truncated to 13333 characters out of 16764)
See detailed reports in MegaLinter artifacts
You could have the same capabilities but better runtime performances if you use a MegaLinter flavor:
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Your project could benefit from a custom flavor, which would allow you to run only the linters you need, and thus improve runtime performances. (Skip this info by defining FLAVOR_SUGGESTIONS: false)
- Documentation: Custom Flavors
- Command:
npx [email protected] --custom-flavor-setup --custom-flavor-linters ACTION_ACTIONLINT,DOCKERFILE_HADOLINT,EDITORCONFIG_EDITORCONFIG_CHECKER,JSON_JSONLINT,JSON_V8R,JSON_PRETTIER,MARKDOWN_MARKDOWNLINT,REPOSITORY_CHECKOV,REPOSITORY_GIT_DIFF,REPOSITORY_GITLEAKS,REPOSITORY_KICS,REPOSITORY_SECRETLINT,REPOSITORY_SYFT,REPOSITORY_TRIVY,REPOSITORY_TRIVY_SBOM,REPOSITORY_TRUFFLEHOG,YAML_PRETTIER,YAML_YAMLLINT,YAML_V8R
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This PR contains the following updates:
==7.2.0→==9.2.0Release Notes
aehrc/pathling (pathling)
v9.2.0Compare Source
What's changed
ViewDefinition resource support
The encoders module now supports ViewDefinition as a custom resource type from the SQL on FHIR specification. This includes:
ResourceTypesutility class for resource type validation that supports custom resource typesWrite operation details
All data sink write methods (
ndjson(),parquet(),delta(),tables()) now return aWriteDetailsobject containing information about the files that were written. This is usefulfor downstream processing and logging.
This change affects both the Java library API and the Python library.
Authentication library
The terminology module now includes the
fhir-authlibrary (1.0.0) for enhanced authentication capabilities when connecting to terminology servers.Code quality infrastructure
New tooling has been added to enforce consistent code formatting:
pyproject.toml.lintrconfiguration for R code lintingDependency updates
bulk-exportversion from 1.0.3 to 1.0.4fhir-authdependency (1.0.0)New contributors
Full changelog: aehrc/pathling@v9.1.0...v9.2.0
v9.1.0Compare Source
What's Changed
New features
repeatdirective for recursive traversal of nested structures by @piotrszul in #2516toQuantity()andconvertsToQuantity()FHIRPath functions with UCUM unit conversion support by @piotrszul in #2514Bug fixes
getResourceKey()returning versioned IDs that don't matchgetReferenceKey()(#2519) by @johngrimes in #2520Security updates
Other changes
Full Changelog: aehrc/pathling@v9.0.0...v9.1.0
v9.0.0Compare Source
This major release includes significant infrastructure upgrades, new FHIRPath functionality, and important bug fixes.
Major changes
Infrastructure upgrades (#2496)
FHIRPath enhancements
Delta Lake improvements (#2499 by @MartinBernstorff)
whenNotMatchedBySourceDelete()to allow Delta Lake state to reflect current FHIR server statewrite.delta()method to control deletion behaviourBug fixes
ofType(Quantity).valuewithcollection: trueBreaking changes
This release includes breaking changes due to the infrastructure upgrades:
v8.1.0Compare Source
This release includes the following changes:
✨ Features
🐛 Bug Fixes
ofType()🔧 Dependencies
v8.0.2Compare Source
This release fixes a problem with the
library-runtimepackage, where the version of Gson being used gets overridden by the version in Spark.Full Changelog: aehrc/pathling@v8.0.1...v8.0.2
v8.0.1Compare Source
What's Changed
Security updates
Full Changelog: aehrc/pathling@v8.0.0...v8.0.1
v8.0.0Compare Source
This release features our new SQL on FHIR view runner, a completely reworked and more performant query engine, and many other changes.
As part of this release, we took the decision to significantly change the focus and scope of Pathling with the purpose of rebuilding it around the SQL on FHIR specification.
This will mean that the server implementation will be temporarily removed. It will also mean that the scope of FHIRPath functions will be temporarily reduced to the minimal FHIRPath subset defined within the SQL on FHIR Shareable View Definition specification (with the exception of the terminology functions).
We have released this functionality as version 8, and we have spawned three work streams to build upon this new foundation:
on FHIR server API. This server will not include the aggregate or extract operations.
We think that this is the best way to align Pathling to user needs, and also to make sure that the code base is sustainable going forwards.
If you are a current user of the server, aggregate or extract operations, please continue using the v7.x series. We are happy to continue maintaining and accepting contributions to this series as
requested by users, but will be focusing our enhancement efforts on v8.
Major dependency updates
Full Changelog: aehrc/pathling@v7.2.0...v8.0.0
Configuration
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