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Fix conda environment yaml parsing errors #4078

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merged 2 commits into from
Jan 15, 2025
Merged

Fix conda environment yaml parsing errors #4078

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c9c023e
Fix conda environment yaml parsing errors
AyanSinhaMahapatra Jan 7, 2025
2de7396
Merge branch 'develop' into fix-package-scan-bugs
AyanSinhaMahapatra Jan 15, 2025
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3 changes: 3 additions & 0 deletions src/packagedcode/conda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -378,6 +378,7 @@ def parse(cls, location, package_only=False):
primary_language=cls.default_primary_language,
dependencies=dependencies,
extra_data=extra_data,
is_private=True,
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Why private?

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Conda environment YAMLs are ostly used to export a particular conda environment (this is like a lockfile used in projects) and to import the environment from them to replicate the conda environment. See https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file and https://docs.conda.io/projects/conda/en/stable/user-guide/concepts/environments.html
This is not a manifest that you can publish a conda package, for that you need build recipes in meta.yaml files, since this manifest is not used to publish packages at all, and only publish environments, I've marked the packages created as private.

)
yield models.PackageData.from_data(package_data, package_only)

Expand Down Expand Up @@ -536,6 +537,8 @@ def get_conda_yaml_dependencies(conda_data):

if "::" in dep:
namespace, dep = dep.split("::")
if "/" in namespace or ":" in namespace:
namespace = None

req = parse_requirement_line(dep)
if req:
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2 changes: 1 addition & 1 deletion tests/packagedcode/data/conda/conda-yaml/phc-gnn/environment_gpu.yml-expected.json
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Expand Up @@ -33,7 +33,7 @@
"notice_text": null,
"source_packages": [],
"file_references": [],
"is_private": false,
"is_private": true,
"is_virtual": false,
"extra_data": {
"channels": [
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2 changes: 1 addition & 1 deletion tests/packagedcode/data/conda/conda-yaml/ringer/environment.yaml-expected.json
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Expand Up @@ -33,7 +33,7 @@
"notice_text": null,
"source_packages": [],
"file_references": [],
"is_private": false,
"is_private": true,
"is_virtual": false,
"extra_data": {
"channels": [
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3 changes: 3 additions & 0 deletions tests/packagedcode/data/conda/conda-yaml/test/environment_host_port.yml
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@@ -0,0 +1,3 @@
name: test
dependencies:
- https://104.17.92.24:443::flask=1.0.2
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Is the URL a namespace, or is is rather a repository_url qualifier?

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It is a repository URL qualifier allright, there are common ones like conda-forge, anaconda, bioconda and the URL is usually not specified fully, but denoted by just a reference word.

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Actually I am not sure, this probably requires a bit more research, there are examples which seem more like a namespace, less like a repository URL:

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#4094

58 changes: 58 additions & 0 deletions tests/packagedcode/data/conda/conda-yaml/test/environment_host_port.yml-expected.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,58 @@
[
{
"type": "conda",
"namespace": null,
"name": "test",
"version": null,
"qualifiers": {},
"subpath": null,
"primary_language": "Python",
"description": null,
"release_date": null,
"parties": [],
"keywords": [],
"homepage_url": null,
"download_url": null,
"size": null,
"sha1": null,
"md5": null,
"sha256": null,
"sha512": null,
"bug_tracking_url": null,
"code_view_url": null,
"vcs_url": null,
"copyright": null,
"holder": null,
"declared_license_expression": null,
"declared_license_expression_spdx": null,
"license_detections": [],
"other_license_expression": null,
"other_license_expression_spdx": null,
"other_license_detections": [],
"extracted_license_statement": null,
"notice_text": null,
"source_packages": [],
"file_references": [],
"is_private": true,
"is_virtual": false,
"extra_data": {},
"dependencies": [
{
"purl": "pkg:conda/[email protected]",
"extracted_requirement": "=1.0.2",
"scope": "dependencies",
"is_runtime": true,
"is_optional": false,
"is_pinned": true,
"is_direct": true,
"resolved_package": {},
"extra_data": {}
}
],
"repository_homepage_url": null,
"repository_download_url": null,
"api_data_url": null,
"datasource_id": "conda_yaml",
"purl": "pkg:conda/test"
}
]
2 changes: 1 addition & 1 deletion tests/packagedcode/data/misc/conda/scenicplus.yaml-expected.json
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Expand Up @@ -33,7 +33,7 @@
"notice_text": null,
"source_packages": [],
"file_references": [],
"is_private": false,
"is_private": true,
"is_virtual": false,
"extra_data": {
"channels": [
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6 changes: 6 additions & 0 deletions tests/packagedcode/test_conda.py
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Expand Up @@ -115,6 +115,12 @@ def test_parse_conda_yaml_simple_dependencies(self):
expected_loc = self.get_test_loc('conda/conda-yaml/ringer/environment.yaml-expected.json')
self.check_packages_data(package, expected_loc, regen=REGEN_TEST_FIXTURES)

def test_parse_conda_yaml_does_not_fail_on_test_files_with_port(self):
test_file = self.get_test_loc('conda/conda-yaml/test/environment_host_port.yml')
package = conda.CondaYamlHandler.parse(test_file)
expected_loc = self.get_test_loc('conda/conda-yaml/test/environment_host_port.yml-expected.json')
self.check_packages_data(package, expected_loc, regen=REGEN_TEST_FIXTURES)

def test_conda_get_conda_meta_json(self):
meta_yaml_path = 'conda/pkgs/requests-2.32.3-py312h06a4308_1/info/recipe/meta.yaml'
conda_meta_json_path = 'conda/conda-meta/requests-2.32.3-py312h06a4308_1.json'
Expand Down