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semgrep / semgrep-action

This project is deprecated. Use https://github.com/returntocorp/semgrep instead
https://semgrep.dev/docs/semgrep-ci/
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internal error #477

Closed ryanking closed 2 years ago

ryanking commented 2 years ago

We got an error in CI and it said to file an issue:

/usr/bin/docker run --name returntocorpsemgrepagentv1_77b64c --label 6a6825 --workdir /github/workspace --rm -e INPUT_PUBLISHTOKEN -e INPUT_CONFIG -e INPUT_GENERATESARIF -e INPUT_AUDITON -e HOME -e GITHUB_JOB -e GITHUB_REF -e GITHUB_SHA -e GITHUB_REPOSITORY -e GITHUB_REPOSITORY_OWNER -e GITHUB_RUN_ID -e GITHUB_RUN_NUMBER -e GITHUB_RETENTION_DAYS -e GITHUB_RUN_ATTEMPT -e GITHUB_ACTOR -e GITHUB_WORKFLOW -e GITHUB_HEAD_REF -e GITHUB_BASE_REF -e GITHUB_EVENT_NAME -e GITHUB_SERVER_URL -e GITHUB_API_URL -e GITHUB_GRAPHQL_URL -e GITHUB_REF_NAME -e GITHUB_REF_PROTECTED -e GITHUB_REF_TYPE -e GITHUB_WORKSPACE -e GITHUB_ACTION -e GITHUB_EVENT_PATH -e GITHUB_ACTION_REPOSITORY -e GITHUB_ACTION_REF -e GITHUB_PATH -e GITHUB_ENV -e RUNNER_OS -e RUNNER_ARCH -e RUNNER_NAME -e RUNNER_TOOL_CACHE -e RUNNER_TEMP -e RUNNER_WORKSPACE -e ACTIONS_RUNTIME_URL -e ACTIONS_RUNTIME_TOKEN -e ACTIONS_CACHE_URL -e GITHUB_ACTIONS=true -e CI=true -v "/var/run/docker.sock":"/var/run/docker.sock" -v "/home/runner/work/_temp/_github_home":"/github/home" -v "/home/runner/work/_temp/_github_workflow":"/github/workflow" -v "/home/runner/work/_temp/_runner_file_commands":"/github/file_commands" -v "/home/runner/work/color/color":"/github/workspace" returntocorp/semgrep-agent:v1
| versions          - semgrep 0.77.0 on Python 3.9.7
| environment       - running in environment github-actions, triggering event is 'push'
| manage            - authenticated as the organization 'color'
| policy            - using Rule Board - Block column, Rule Board - Audit column
=== setting up agent configuration
| using 296 semgrep rules configured on the web UI
| using 0 code asset inventory rules
| using default path ignore rules of common test and dependency directories
| found 16199 files in the paths to be scanned
| skipping 112 files based on path ignore rules
=== looking for current issues in 16087 files

=== failed command's STDOUT:

=== failed command's STDERR:

Error: ROR] `/root/.local/bin/semgrep --skip-unknown-extensions --disable-nosem --json --autofix --dryrun --time --timeout-threshold 3 --config .semgrep_logs/semgrep_app_rules.yaml --enable-metrics --no-rewrite-rule-ids --debug -o /tmp/tmpg88w667_ src/util/log_config.py src/util/files.py src/util/text_mailer.py src/util/py.py src/util/bedtools.py src/util/json_proto.py src/util/fax.py src/util/integrations_bot.py src/util/iterables.py src/util/bcftools.py src/util/async_task.py src/util/testfiles.py src/util/pipeline_automation.py src/util/cnv_compare.py src/util/__init__.py src/util/amazon_mws.py src/util/etcfiles.py src/util/tasks.py src/util/salesforce_soap_client.py src/util/csv.py src/util/hubspot.py src/util/aldy_config_parser.py src/util/celery.py src/util/rdict.py src/util/aws.py src/util/pdf.py src/util/timeout.py src/util/mathutil.py src/util/sentry.py src/util/tokens.py src/util/testutil.py src/util/waffle.py src/util/s3_checksums.py src/util/identifier.py src/util/usps.py src/util/git.py src/util/payment_processor.py src/util/constants.py src/util/date.py src/util/google_cloud.py src/util/url.py src/util/aldy_parser.py src/util/tee.py src/util/ec2.py src/util/iter.py src/util/jira.py src/util/requests.py src/util/paypal.py src/util/commandline.py src/util/salesforce.py src/util/bigquery.py src/util/mailchimp.py src/util/network.py src/util/common.py src/util/datadog.py src/util/symmetric_encryption.py src/bioinf/validation/cnvkit/cnvkit_call.py src/bioinf/validation/cnvkit/BUILD.pants src/bioinf/validation/cnvkit/compare.py src/bioinf/validation/README.md src/bioinf/sv_calling.py src/bioinf/proto/usd_proto_validation_util.py src/bioinf/proto/usd_proto_util.py src/bioinf/proto/BUILD.pants src/bioinf/proto/__init__.py src/bioinf/proto/usd.proto src/bioinf/clinical.py src/bioinf/BUILD.pants src/bioinf/working_directory.py src/bioinf/risk/BUILD.pants src/bioinf/risk/__init__.py src/bioinf/risk/gail_score.R src/bioinf/risk/gail_score.py src/bioinf/regions_util.py src/bioinf/resources.py src/bioinf/pseudogenes.py src/bioinf/bam_calculators.py src/bioinf/__init__.py src/bioinf/ancestry/fastngsadmix.py src/bioinf/ancestry/BUILD.pants src/bioinf/ancestry/__init__.py src/bioinf/ancestry/laser_pca.py src/bioinf/ancestry/ancestry_util.py src/bioinf/ancestry/admixture_project_utils.py src/bioinf/prod.py src/bioinf/sanger_plots/BUILD.pants src/bioinf/sanger_plots/__init__.py src/bioinf/sanger_plots/sanger_plot_generator.py src/bioinf/sanger_plots/r/sanger_ab1_to_chromatogram.R src/bioinf/sanger_plots/r/sanger_ab1_breakpoint_analysis.R src/bioinf/tenX_images/tenXviz.R src/bioinf/quality_control.py src/bioinf/cnvkit/cnvkit.py src/bioinf/cnvkit/BUILD.pants src/bioinf/cnvkit/util.py src/bioinf/cnvkit/__init__.py src/bioinf/cnvkit/segmenters/BUILD.pants src/bioinf/cnvkit/segmenters/cusum.py src/bioinf/cnvkit/segmenters/__init__.py src/bioinf/cnvkit/README.md src/bioinf/elasticsearch/config.yaml src/bioinf/elasticsearch/BUILD.pants src/bioinf/elasticsearch/applications.py src/bioinf/elasticsearch/__init__.py src/bioinf/elasticsearch/indexer.py src/bioinf/elasticsearch/searcher.py src/bioinf/elasticsearch/document.py src/bioinf/diplotype/BUILD.pants src/bioinf/diplotype/config_parser.py src/bioinf/diplotype/__init__.py src/bioinf/diplotype/matcher.py src/bioinf/diplotype/strings.py src/bioinf/diplotype/diplo.py src/bioinf/constants.py src/bioinf/kinship/BUILD.pants src/bioinf/kinship/__init__.py src/bioinf/kinship/lc_pc_relate.py src/bioinf/common.py src/bioinf/plots.py src/infra/validation/etc/BUILD.pants src/infra/validation/etc/known_variants.tsv src/infra/validation/etc/sample_run_manifest.csv src/infra/validation/etc/known_mnvs.tsv src/infra/validation/etc/mnv_manifest.tsv src/infra/validation/etc/known_cnvs.tsv src/infra/validation/etc/validation_batches.tsv src/infra/validation/etc/known_metrics.tsv src/infra/validation/etc/tg_sample_run_manifest.csv src/infra/validation/etc/vcf_manifest.tsv src/infra/validation/etc/known_split_reads.tsv src/infra/validation/etc/cnv_manifest.tsv src/infra/validation/cross_batch_validator.py src/infra/validation/BUILD.pants src/infra/validation/__init__.py src/infra/validation/single_batch_validator.py src/infra/validation/common.py src/infra/prs/BUILD.pants src/infra/prs/additive_prs.py src/infra/prs/__init__.py src/infra/BUILD.pants src/infra/imputation/BUILD.pants src/infra/imputation/__init__.py src/infra/imputation/bamfile_identity.py src/infra/imputation/glimpse.py src/infra/imputation/low_cov_imputation.py src/infra/imputation/imputation_utils.py src/infra/enterprise_billing/BUILD.pants src/infra/enterprise_billing/report.py src/infra/enterprise_billing/__init__.py src/infra/enterprise_billing/tribune_script.py src/infra/etl/grandparent_ancestry.py src/infra/etl/celery_heartbeat.py src/infra/etl/covid/covid_dump.py src/infra/etl/covid/covid_eligibility_quiz.py src/infra/etl/covid/BUILD.pants src/infra/etl/covid/covid_results.py src/infra/etl/covid/covid_vaccine_eligibility_quiz.py src/infra/etl/covid/__init__.py src/infra/etl/covid/covid_repeat_testing.py src/infra/etl/covid/covid_questions_cdph.py src/infra/etl/covid/upload_pki_insurance.py src/infra/etl/covid/covid_pooled_samples.py src/infra/etl/covid/covid_samples_fast.py src/infra/etl/covid/covid_registered_participants.py src/infra/etl/covid/covid_samples.py src/infra/etl/covid/self_reported_vaccination_status.py src/infra/etl/covid/covid_vaccine_availability.py src/infra/etl/covid/covid_runs.py src/infra/etl/covid/covid_insurance.py src/infra/etl/io_locks.py src/infra/etl/filters/health_history_horizontal.yaml src/infra/etl/filters/covid_samples.yaml src/infra/etl/filters/health_history.yaml src/infra/etl/amazon_to_bigquery.py src/infra/etl/dbt/macros/select_star_rename.sql src/infra/etl/dbt/macros/star.sql src/infra/etl/dbt/macros/select_first_row.sql src/infra/etl/dbt/macros/get_extractionrun_methods.sql src/infra/etl/dbt/data/.gitkeep src/infra/etl/dbt/dbt_project.yml src/infra/etl/dbt/BUILD.pants src/infra/etl/dbt/models/marts/lims/libraryprep_details.sql src/infra/etl/dbt/models/marts/lims/sequencing_details.sql src/infra/etl/dbt/models/marts/lims/pipeline_details.sql src/infra/etl/dbt/models/marts/lims/confirmation_details.sql src/infra/etl/dbt/models/marts/lims/ssr_details.sql src/infra/etl/dbt/models/marts/lims/schema.yml src/infra/etl/dbt/models/marts/lims/intermediate/sample_level_libraryprep_details.sql src/infra/etl/dbt/models/marts/lims/intermediate/user_samples.sql src/infra/etl/dbt/models/marts/lims/intermediate/lims_sequencingrun.sql src/infra/etl/dbt/models/marts/lims/intermediate/lims_extractionruns.sql src/infra/etl/dbt/models/marts/lims/intermediate/sample_level_extraction_details.sql src/infra/etl/dbt/models/marts/lims/intermediate/sample_level_samplerun_details.sql src/infra/etl/dbt/models/marts/lims/intermediate/lims_librarypreparationrunv2.sql src/infra/etl/dbt/models/marts/lims/intermediate/pipeline.sql src/infra/etl/dbt/models/marts/lims/intermediate/sample_level_sequencing_details.sql src/infra/etl/dbt/models/marts/lims/intermediate/pipeline_level_confirmation_details.sql src/infra/etl/dbt/models/marts/lims/intermediate/lims_samples.sql src/infra/etl/dbt/models/marts/lims/intermediate/kitorders.sql src/infra/etl/dbt/models/marts/lims/samplesdiplotype_details.sql src/infra/etl/dbt/models/marts/lims/cnv_details.sql src/infra/etl/dbt/models/marts/lims/variantclassification_details.sql src/infra/etl/dbt/models/marts/lims/physician_details.sql src/infra/etl/dbt/models/marts/lims/extraction_details.sql src/infra/etl/dbt/models/marts/django/intermediate/schema.yml src/infra/etl/dbt/models/marts/django/intermediate/user_addresses.sql src/infra/etl/dbt/models/marts/django/intermediate/promocodes.sql src/infra/etl/dbt/models/lims/stg_lims__sampleevententry.sql src/infra/etl/dbt/models/lims/stg_lims__sequencingpoolingentry.sql src/infra/etl/dbt/models/lims/stg_lims__samples.sql src/infra/etl/dbt/models/lims/stg_lims__sequencingrun.sql src/infra/etl/dbt/models/lims/stg_lims__collapsed_consumables.sql src/infra/etl/dbt/models/lims/stg_lims__extractionruns.sql src/infra/etl/dbt/models/lims/stg_lims__dnasequencingentry.sql src/infra/etl/dbt/models/lims/stg_lims__collapsed_equipment.sql src/infra/etl/dbt/models/lims/schema.yml src/infra/etl/dbt/models/lims/stg_lims__dnaextractionentries.sql src/infra/etl/dbt/models/lims/stg_lims__dnaquantificationentry.sql src/infra/etl/dbt/models/lims/sources.yml src/infra/etl/dbt/models/lims/stg_lims__dropsenserunentries.sql src/infra/etl/dbt/models/lims/stg_lims__librarypreparationrunv2.sql src/infra/etl/dbt/models/django/sources.yml src/infra/etl/dbt/analysis/.gitkeep src/infra/etl/dbt/deploy.sh src/infra/etl/dbt/packages.yml src/infra/etl/counselor_availabilities.py src/infra/etl/BUILD.pants src/infra/etl/census_data.py src/infra/etl/kinship_to_bigquery.py 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src/infra/etl/merge_imputed_vcfs.py src/infra/etl/pg.py src/infra/__init__.py src/infra/read_generation/BUILD.pants src/infra/read_generation/__init__.py src/infra/read_generation/conversion_util.py src/infra/read_generation/fastq_check.py src/infra/read_generation/bcl_conversion.py src/infra/all_of_us/BUILD.pants src/infra/all_of_us/__init__.py src/infra/all_of_us/gem.py src/infra/pants/BUILD.pants src/infra/pants/macros.py src/infra/annotation/BUILD.pants src/infra/annotation/__init__.py src/infra/lims_daemons/BUILD.pants src/infra/lims_daemons/__init__.py src/infra/lims_daemons/lims_uploader.py src/infra/lims_daemons/find_new_robot_files.py src/infra/bioinformatics/rd/aegea/rootfs.skel/etc/update-motd.d/99-bioinfrd src/infra/bioinformatics/rd/aegea/config.yml src/infra/ml/census_prediction.py src/infra/ml/BUILD.pants src/infra/ml/__init__.py src/infra/ml/client/BUILD.pants src/infra/ml/client/confirmation.py src/infra/ml/lumpy.py src/infra/ml/confirmation.py src/infra/ml/census_prediction.R src/infra/ml/sagemaker/confirmation/entrypoint.py src/infra/ml/sagemaker/confirmation/BUILD.pants src/infra/ml/sagemaker/confirmation/train.py src/infra/ml/sagemaker/confirmation/Dockerfile src/infra/ml/sagemaker/confirmation/inference.py src/infra/ml/sagemaker/BUILD.pants src/infra/ml/sagemaker/inference_utils.py src/infra/ml/sagemaker/train_utils.py src/infra/ml/sagemaker/__init__.py src/infra/ml/sagemaker/package_and_push_images_to_ecr.sh src/infra/ml/sagemaker/Dockerfile src/infra/ml/sagemaker/main.py src/infra/ml/sagemaker/deploy_models_to_sagemaker.py src/infra/ml/insertions.py src/infra/pipeline/variant_calling.py src/infra/pipeline/qc_email.py src/infra/pipeline/etc/BUILD.pants src/infra/pipeline/etc/email_templates/pipeline_qc_report.txt src/infra/pipeline/vcf_calculator.py src/infra/pipeline/ancestry.py src/infra/pipeline/cwl.py src/infra/pipeline/elasticsearch.py src/infra/pipeline/ctk/file_ops.py src/infra/pipeline/ctk/pgx.py 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src/infra/pipeline/annotator/annotator.py src/infra/pipeline/usd/filter_and_annotate.py src/infra/pipeline/usd/BUILD.pants src/infra/pipeline/usd/usd_pipeline_util.py src/infra/pipeline/usd/__init__.py src/infra/pipeline/usd/usd_vcf.py src/infra/pipeline/usd/gen.py src/infra/pipeline/usd/search.py src/infra/pipeline/qc_import.py src/infra/pipeline/pipeline_rerun.py src/infra/pipeline/insertions.py src/infra/pipeline/risk_scores.py src/infra/pipeline/dashboard/templates/scheduler_info.html src/infra/pipeline/dashboard/dashboard.py src/infra/pipeline/dashboard/BUILD.pants src/infra/pipeline/dashboard/__init__.py src/infra/pipeline/dashboard/static/style.css src/infra/pipeline/automatic_annotation.py setenv.sh .github/dependabot.yml .github/workflows/check-conflicting-paths.yaml .github/workflows/test-db-ci.yaml .github/workflows/translate.yml .github/workflows/etl-ci.yaml .github/workflows/stale.yml .github/workflows/projects-common-frontend-ci.yml .github/workflows/swagger-ci-check.yaml .github/workflows/ci.yaml .github/workflows/semgrep.yml .github/workflows/ci-cwltool.yaml .github/workflows/migrations-comment.yaml .github/workflows/pulumi.yml .github/workflows/ownd.yml .github/workflows/storybook.yml .github/workflows/update-readme-prod.yaml .github/workflows/pants.yml .github/workflows/gp-ci.yml .github/workflows/rhp-ci.yml .github/workflows/circleci-docker.yaml .github/workflows/lokalise-push.yml .github/workflows/pr-size-labeler.yml .github/workflows/lokalise-pull.yml .github/CODEOWNERS .github/auto-merge.yml .github/ownd.yml .gitattributes pants.toml .tool-versions config/BUILD.pants config/apple-developer-merchantid-domain-association config/ssh/aws-ssm-proxy config/ssh/aws-ssm-proxy-toil config/wisdom_wsdl.xml config/salesforce_wsdl.xml config/ipython/profile_default/startup/01_django.py config/ipython/profile_default/startup/BUILD.pants config/ipython/profile_default/startup/05_pipeline.py config/ipython/profile_default/startup/02_disable_writes.py config/ipython/profile_default/startup/03_logger.py config/ipython/profile_default/startup/04_reset_email_cache.py config/ipython/profile_default/startup/06_etl.py config/cdph_soap/ca_impl_wsdl.xml config/cdph_soap/ca_prod_wsdl.xml config/geographical_area.yaml config/cair_soap/cair_prod_soap_service.wsdl config/cair_soap/cair_staging_soap_service.wsdl config/pipeline/pipeline_job.yaml config/pipeline/pipeline_rerun_batches.yaml config/pipeline/pipeline_job_inputs_example.txt config/miis_soap/miis_prod_cdc_service.wsdl config/miis_soap/miis_staging_cdc_service.wsdl` failed with exit code 2
brendongo commented 2 years ago

Hi @ryanking. Apologies this fell through the cracks during the holidays. Was this working before 0.77.0 and is it still not working on 0.80.0?

ryanking commented 2 years ago

Seems to be working for now.