diff --git a/.gitignore b/.gitignore index a61f254..c94ff9c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,10 +1,18 @@ -.venv .vscode biocypher-* *__pycache__* neo4j.pass backup -data *.DS_Store notebooks -tmp.sh \ No newline at end of file +tmp.sh + +import.report + +data + +.venv +poetry.lock +uv.lock +*.egg-info +build \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..74a0f1a --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,33 @@ +repos: +- repo: local + hooks: + - id: patient_id + name: Check for patient ids starting with "D", "H" or "M". + always_run: true + args: [--multiline] + entry: '[DHM][0-9]{3}' + language: pygrep + # - id: M-code-patient_id + # name: Check for patient ids starting with an "M". + # always_run: true + # args: [--multiline] + # entry: 'M[0-9]{3}' + # language: pygrep + # - id: D-code-patient_id + # name: Check for patient ids starting with an "D". + # always_run: true + # args: [--multiline] + # entry: 'D[0-9]{3}' + # language: pygrep + - id: OC-code-patient_id + name: Check for patient ids starting with "OC". + always_run: true + args: [--multiline] + entry: 'OC[0-9]{3}' + language: pygrep + - id: EOC-patient_code + name: Check for EOC patient codes. + always_run: true + args: [--multiline] + entry: 'EOC[0-9]{3}' + language: pygrep \ No newline at end of file diff --git a/README.md b/README.md index bf4f7c3..d176d1a 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,16 @@ shell` inside the project directory. If you have a problem with the poetry install command, it may be that the 'poetry lock' command has not been ran after changing dependencies modification in '$ONCODASHKB_HOME/pyproject.toml'. Try running 'poetry lock' to fix the issue. +### Requirements for preventing publishing patient ids + +Please, install [pre-commit](https://pre-commit.com/) hooks before committing or pushing anything new: + +``` +pre-commit install +pre-commit install --hook-type pre-push +pre-commit install --hook-type commit-msg +``` + ### Database Theoretically, any graph database supported by Biocypher may be used. diff --git a/config/biocypher_config.yaml b/config/biocypher_config.yaml index 42d5f85..9aff276 100644 --- a/config/biocypher_config.yaml +++ b/config/biocypher_config.yaml @@ -8,15 +8,15 @@ biocypher: url: https://github.com/biolink/biolink-model/raw/v3.2.1/biolink-model.owl.ttl root_node: entity - tail_ontologies: - so_variant: - url: http://purl.obolibrary.org/obo/so.owl - head_join_node: sequence variant - tail_join_node: sequence_variant - so_feature: - url: http://purl.obolibrary.org/obo/so.owl - head_join_node: attribute - tail_join_node: sequence_feature + # tail_ontologies: + # so_variant: + # url: http://purl.obolibrary.org/obo/so.owl + # head_join_node: sequence variant + # tail_join_node: sequence_variant + # so_feature: + # url: http://purl.obolibrary.org/obo/so.owl + # head_join_node: attribute + # tail_join_node: sequence_feature # go_biological_process: # url: http://purl.obolibrary.org/obo/go.owl # head_join_node: biological process diff --git a/config/schema_config.yaml b/config/schema_config.yaml index a039544..7ae9ca0 100644 --- a/config/schema_config.yaml +++ b/config/schema_config.yaml @@ -11,14 +11,15 @@ alteration: properties: citation_PM_ids: str consequence: str + homogenous: str level_of_evidence: str mutation_effect_description: str + name: str oncogenic: str reference_genome: str tumor_type: str tumor_type_summary: str variant_summary: str - name: str disease: represented_as: node @@ -33,7 +34,7 @@ drug: name: str gene status: - is_a: outcome + is_a: phenomenon represented_as: node label_in_input: gene_status properties: @@ -43,6 +44,7 @@ gene: represented_as: node label_in_input: gene properties: + gene_summary: str name: str # protein: @@ -112,7 +114,7 @@ sample carries alteration: # A gene is linked to its gene status (gain or loss of function), # which are represented as nodes, so as to allow a causal path # to go through alteration -> gene status -> transcript activity. -# Hence, outcomes have at least two instances: +# Hence, phenomenons have at least two instances: # - Gene:GoF, and # - Gene:LoF. @@ -155,15 +157,6 @@ patient has chronic illness: ### AFFECTS -alteration affects gene: - is_a: affects - represented_as: edge - label_in_input: alteration_affects_gene - source: alteration - taregt: gene - properties: - name: str - gene status affects gene: is_a: affects represented_as: edge diff --git a/hooks/install_hooks.sh b/hooks/install_hooks.sh deleted file mode 100755 index dc78607..0000000 --- a/hooks/install_hooks.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/sh - -cd $(git rev-parse --show-toplevel)/.git/hooks -ln -s ../../hooks/pre-commit -ln -s ../../hooks/pre-push - diff --git a/hooks/leaking-data b/hooks/leaking-data deleted file mode 100755 index 3d37cca..0000000 --- a/hooks/leaking-data +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/sh -# -# An example hook script to verify what is about to be committed. -# Called by "git commit" with no arguments. The hook should -# exit with non-zero status after issuing an appropriate message if -# it wants to stop the commit. -# -# To enable this hook, rename this file to "pre-commit". - -if git rev-parse --verify HEAD >/dev/null 2>&1 -then - against=HEAD -else - # Initial commit: diff against an empty tree object - against=$(git hash-object -t tree /dev/null) -fi - - - -# Check if the diff contains patient code-like strings. -test=$(GIT_CONFIG_GLOBAL='' git diff --cached HEAD | grep -e '\<[A-Z][0-9]\{3\}\>') -if [ "$test" != "" ] ; then - cat <<\EOF -ERROR: I detected patient H-code-like strings in the diff of this commit. -I will forbid any such commit. -Please double check for strings matching '\<[A-Z][0-9]\{3\}\>'. -If you're sure there's no leaking data, you may commit with: SKIP=leaking-data git commit … -EOF - exit 1 -fi diff --git a/hooks/pre-commit b/hooks/pre-commit deleted file mode 100755 index aa34c92..0000000 --- a/hooks/pre-commit +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/sh -# -# An example hook script to verify what is about to be committed. -# Called by "git commit" with no arguments. The hook should -# exit with non-zero status after issuing an appropriate message if -# it wants to stop the commit. -# -# To enable this hook, rename this file to "pre-commit". - -if git rev-parse --verify HEAD >/dev/null 2>&1 -then - against=HEAD -else - # Initial commit: diff against an empty tree object - against=$(git hash-object -t tree /dev/null) -fi - - - -# Check if the diff contains patient code-like strings. -test=$(GIT_CONFIG_GLOBAL='' git diff --cached HEAD | grep -e '\<[A-Z][0-9]\{3\}\>') -if [ "$test" != "" ] ; then - cat <<\EOF -ERROR: I detected patient H-code-like strings in the diff of this commit. -I will forbid any such commit. -Please double check for strings matching '\<[A-Z][0-9]\{3\}\>'. -If you're sure there's no leaking data, you may commit with: git --no-verify commit … -EOF - exit 1 -fi diff --git a/hooks/pre-push b/hooks/pre-push deleted file mode 100755 index 25bae28..0000000 --- a/hooks/pre-push +++ /dev/null @@ -1,64 +0,0 @@ -#!/bin/sh - -# An example hook script to verify what is about to be pushed. Called by "git -# push" after it has checked the remote status, but before anything has been -# pushed. If this script exits with a non-zero status nothing will be pushed. -# -# This hook is called with the following parameters: -# -# $1 -- Name of the remote to which the push is being done -# $2 -- URL to which the push is being done -# -# If pushing without using a named remote those arguments will be equal. -# -# Information about the commits which are being pushed is supplied as lines to -# the standard input in the form: -# -# -# -# This sample shows how to prevent push of commits where the log message starts -# with "WIP" (work in progress). - -remote="$1" -url="$2" - -zero=$(git hash-object --stdin &2 "Found WIP commit in $local_ref, not pushing" - exit 1 - fi - - test=$(GIT_CONFIG_GLOBAL='' git diff $range | grep -e '\<[A-Z][0-9]\{3\}\>') - if [ "$test" != "" ] ; then - echo "ERROR: I detected patient H-code-like strings in the diff of this push: $range" - cat <<\EOF -I will forbid any such commit. -Please double check for strings matching '\<[A-Z][0-9]\{3\}\>'. -If you're sure there's no leaking data, you may commit with: git --no-verify commit … -EOF - exit 1 - fi - fi -done - -exit 0 diff --git a/make_macos.sh b/make_macos.sh index dfaa243..39927d8 100755 --- a/make_macos.sh +++ b/make_macos.sh @@ -1,12 +1,5 @@ #!/usr/bin/bash -# When using Neo4j installed on system (like Ubuntu's packaged version), -# the current directory must be writable by user "neo4j", -# and all parent directories must be executable by "other". -# Every interaction with the database must be done by user "neo4j", -# and the import will try to write reports in the current directory. -# NEO_USER="sudo -u neo4j" - # Exit on error. set -e set -o pipefail @@ -22,9 +15,6 @@ if [[ "$2" == "debug" ]] ; then weave_args="-v DEBUG" fi -# export JAVA_HOME="/usr/lib/jvm/java-21-openjdk-amd64" - - echo "Activate virtual environment..." >&2 source $(poetry env info --path)/bin/activate @@ -43,16 +33,12 @@ fi echo "Weave data..." >&2 cmd="python3 ${py_args} $(pwd)/weave.py --verbose INFO \ - --clinical $data_dir/DECIDER/$data_version/clinical_export.csv \ - --single_nucleotide_variants $data_dir/DECIDER/$data_version/snv_external.csv \ - --copy_number_alterations $data_dir/DECIDER/$data_version/cna_external.csv \ - --gene_ontology_genes $data_dir/DECIDER/$data_version/OncoKB_gene_symbols.conf \ - --oncokb $data_dir/DECIDER/$data_version/treatments.csv \ - --gene_ontology $data_dir/GO/goa_human.gaf.gz \ - --gene_ontology_owl $data_dir/GO/go.owl \ - --gene_ontology_reverse + --clinical $data_dir/DECIDER/$data_version/clinical_export.csv \ + --short-mutations-local $data_dir/DECIDER/$data_version/snv_local.csv \ + --short-mutations-external $data_dir/DECIDER/$data_version/snv_external.csv \ + --copy-number-amplifications-local $data_dir/DECIDER/$data_version/cna_local.csv \ + --copy-number-amplifications-external $data_dir/DECIDER/$data_version/cna_external.csv \ ${weave_args}" # \ - #--small_molecules $data_dir/omnipath_networks/omnipath_webservice_interactions__small_molecule_interactions_filtered.tsv.gz" echo "Weaving command:" >&2 echo "$cmd" >&2 @@ -63,15 +49,14 @@ $cmd > tmp.sh if [[ "$2" != "debug" ]] ; then echo "Run import script..." >&2 chmod a+x $(cat tmp.sh) - $(cat tmp.sh) | tee /dev/tty | ${NEO_USER} sh + sh $(cat tmp.sh) echo "Restart Neo4j..." >&2 $server start sleep 5 echo "Send a test query..." >&2 - sudo -u neo4j cypher-shell --username neo4j --database oncodash --password $(cat neo4j.pass) "MATCH (p:Patient) RETURN p LIMIT 20;" + cypher-shell --username neo4j --database oncodash --password $(cat neo4j.pass) "MATCH (p:Patient) RETURN p LIMIT 20;" fi -echo "Done" >&2 - +echo "Done" >&2 \ No newline at end of file diff --git a/oncodashkb/adapters/clinical.yaml b/oncodashkb/adapters/clinical.yaml index 885eb5c..f836f3c 100644 --- a/oncodashkb/adapters/clinical.yaml +++ b/oncodashkb/adapters/clinical.yaml @@ -1,11 +1,10 @@ row: map: - columns: - - cohort_code + column: cohort_code to_subject: patient transformers: - map: - columns: survival + column: survival to_property: survival for_object: patient - map: diff --git a/oncodashkb/adapters/copy_number_alterations.yaml b/oncodashkb/adapters/copy_number_alterations.yaml deleted file mode 100644 index 9d635e7..0000000 --- a/oncodashkb/adapters/copy_number_alterations.yaml +++ /dev/null @@ -1,198 +0,0 @@ -row: - map: - columns: - - patient_id - to_subject: patient -transformers: - - map: - columns: - - sample_id - to_object: sample - via_relation: patient_carries_sample - - cat_format: - columns: - - hugoSymbol - - alteration - from_subject: sample - to_object: alteration - format_string: "{hugoSymbol}:{alteration}" - via_relation: sample_carries_alteration - - map: - columns: - - hugoSymbol - from_subject: alteration - to_object: gene - via_relation: alteration_affects_gene - - cat_format: - columns: - - hugoSymbol - - gene_role - from_subject: alteration - to_object: gene_status - format_string: "{hugoSymbol}:{gene_role}" - via_relation: alteration_causes_gene_status - - map: - columns: - - hugoSymbol - from_subject: gene_status - to_object: gene - via_relation: gene_status_affects_gene - - map: - columns: - - tumorType - to_property: - - tumor_type - for_objects: - - alteration - - map: - columns: - - oncogenic - to_property: - - oncogenic - for_objects: - - alteration - - map: - columns: - - mutationEffectDescription - to_property: - - mutation_effect_description - for_objects: - - alteration - - map: - columns: - - variantSummary - to_property: - - variant_summary - for_objects: - - alteration - - map: - columns: - - tumorTypeSummary - to_property: - - tumor_type_summary - for_objects: - - alteration - - map: - columns: - - citationPMids - to_property: - - citation_PM_ids - for_objects: - - alteration - - map: - columns: - - level_of_evidence - to_property: - - level_of_evidence - for_objects: - - alteration - - string: - value: " " - to_property: edgelabel - for_objects: - - patient_carries_sample - - sample_carries_alteration - - alteration_causes_gene_status - - gene_status_affects_gene - -metadata: - - name: copy_number_alterations - -validate: # Validation for cna labeled "external.". - strict: true - columns: - patient_id: - dtype: str - description: "Cohort code from clinical data" - sample_id: - dtype: str - description: "Sample id of biopsy (origin OVCA database)" - referenceGenome: - dtype: str - description: "Standard human reference genome used in WGS read alignment" - checks: - isin: - value: - - GRCh38 - alteration: - dtype: str - description: "Genomic alteration type" - checks: - isin: - value: - - AMPLIFICATION - hugoSymbol: - dtype: str - description: "Gene name in Hugo nomenclature" - checks: - str_matches: ^[a-zA-Z0-9-]+$ - tumorType: - dtype: str - description: "Tumor type abbreviation (OncoTree based)" - checks: - isin: - value: - - HGSOC - oncogenic: - dtype: str - description: "Indication of alteration oncogenecity" - nullable: true - checks: - isin: - value: - - Inconclusive - - known - - Likely Neutral - - Likely Oncogenic - - Oncogenic - - Unknown - mutationEffectDescription: - dtype: str - description: "Brief overview of the biological effect of the alteration with references" - nullable: true - gene_role: - dtype: str - description: "The biological effect of a mutation/alteration on the gene function" - nullable: true - checks: - isin: - value: - - Unknown - - Likely Gain-of-function - - Gain-of-function - - LoF - - Inconclusive - - Act - - ambiguous - citationPMids: - dtype: str - description: "Citations related to the biological effect separated by semicolon" - nullable: true - checks: - str_matches: ^[0-9]{7,}(,[0-9]{7,})*$ - level_of_evidence: - dtype: str - description: "The highest level of evidence for therapeutic implications based on OncoKB (CGI levels are mapped to this)" - nullable: true - checks: - isin: - value: - - LEVEL_1 - - LEVEL_2 - - LEVEL_3A - - LEVEL_3B - - LEVEL_4 - - LEVEL_R1 - - LEVEL_R2 - geneSummary: - dtype: str - description: "Brief overview of the gene and its role in cancer" - nullable: true - variantSummary: - dtype: str - description: "Brief description of the variant oncogenicity" - nullable: true - tumorTypeSummary: - dtype: str - description: "Describes the therapeutic implication that applies to the drug indication in discovered cancer" - nullable: true \ No newline at end of file diff --git a/oncodashkb/adapters/copy_number_amplifications_external.yaml b/oncodashkb/adapters/copy_number_amplifications_external.yaml new file mode 100644 index 0000000..9bd3455 --- /dev/null +++ b/oncodashkb/adapters/copy_number_amplifications_external.yaml @@ -0,0 +1,73 @@ +row: + map: + column: patient_id + to_subject: patient +transformers: + - map: + column: sample_id + to_object: sample + via_relation: patient_carries_sample + - cat_format: + columns: + - hugoSymbol + - alteration + from_subject: sample + to_object: alteration + format_string: "{hugoSymbol}:{alteration}" + via_relation: sample_carries_alteration + - cat_format: + columns: + - hugoSymbol + - gene_role + from_subject: alteration + to_object: gene_status + format_string: "{hugoSymbol}:{gene_role}" + via_relation: alteration_causes_gene_status + - map: + column: hugoSymbol + from_subject: gene_status + to_object: gene + via_relation: gene_status_affects_gene + - map: + column: tumorType + to_property: tumor_type + for_object: alteration + - map: + column: oncogenic + to_property: oncogenic + for_object: alteration + - map: + column: mutationEffectDescription + to_property: mutation_effect_description + for_object: alteration + - map: + column: citationPMids + to_property: citation_PM_ids + for_object: alteration + - map: + column: level_of_evidence + to_property: level_of_evidence + for_object: alteration + - map: + column: geneSummary + to_property: gene_summary + for_object: gene + - map: + column: variantSummary + to_property: variant_summary + for_object: alteration + - map: + column: tumorTypeSummary + to_property: tumor_type_summary + for_object: alteration + - string: + value: " " + to_property: edgelabel + for_objects: + - patient_carries_sample + - sample_carries_alteration + - alteration_causes_gene_status + - gene_status_affects_gene + +metadata: + - data_source: copy_number_amplifications_external \ No newline at end of file diff --git a/oncodashkb/adapters/copy_number_amplifications_local.yaml b/oncodashkb/adapters/copy_number_amplifications_local.yaml new file mode 100644 index 0000000..dfd4396 --- /dev/null +++ b/oncodashkb/adapters/copy_number_amplifications_local.yaml @@ -0,0 +1,27 @@ +row: + map: + column: patient_id + to_subject: patient +transformers: + - map: + column: sample_id + to_object: sample + via_relation: patient_carries_sample + - cat_format: + columns: + - hugoSymbol + - alteration + from_subject: sample + to_object: alteration + format_string: "{hugoSymbol}:{alteration}" + via_relation: sample_carries_alteration + - map: + column: referenceGenome + to_property: reference_genome + for_object: alteration + - map: + column: tumorType + to_property: tumor_type + for_object: alteration +metadata: + - data_source: copy_number_amplifications_local \ No newline at end of file diff --git a/oncodashkb/adapters/gene_ontology.py b/oncodashkb/adapters/gene_ontology.py index 3ac5ad0..4b6b7af 100644 --- a/oncodashkb/adapters/gene_ontology.py +++ b/oncodashkb/adapters/gene_ontology.py @@ -17,7 +17,7 @@ def __init__(self, ontology: str, genes_list: str, config: dict, - type_affix=ontoweaver.tabular.TypeAffixes.none + type_affix=ontoweaver.base.TypeAffixes.none ): # logging.info(" | | In Gene_ontology adapter init") diff --git a/oncodashkb/adapters/gene_ontology.yaml b/oncodashkb/adapters/gene_ontology.yaml index 8910d05..d8d4184 100644 --- a/oncodashkb/adapters/gene_ontology.yaml +++ b/oncodashkb/adapters/gene_ontology.yaml @@ -29,8 +29,8 @@ transformers: # to_object: molecular_function # via_relation: gene_to_molecular_function - string: - value: "." + value: " " to_property: edgelabel for_objects: gene_to_biological_process metadata: - - name: . + - data_source: gene_ontology diff --git a/oncodashkb/adapters/gene_ontology_reverse.yaml b/oncodashkb/adapters/gene_ontology_reverse.yaml index 8ad43f7..1c72430 100644 --- a/oncodashkb/adapters/gene_ontology_reverse.yaml +++ b/oncodashkb/adapters/gene_ontology_reverse.yaml @@ -28,9 +28,9 @@ transformers: # from_subject: gene # to_object: molecular_function # via_relation: gene_to_molecular_function - # - string: - # value: "." - # to_property: edgelabel - # for_objects: gene_to_biological_process + - string: + value: " " + to_property: edgelabel + for_objects: biological_process_to_gene metadata: - - name: . + - data_source: gene_ontology diff --git a/oncodashkb/adapters/oncokb.yaml b/oncodashkb/adapters/oncokb.yaml index b589b4e..81323e0 100644 --- a/oncodashkb/adapters/oncokb.yaml +++ b/oncodashkb/adapters/oncokb.yaml @@ -16,7 +16,7 @@ transformers: for_objects: - alteration_biomarker_for_drug metadata: - - name: . + - data_source: . validate: columns: diff --git a/oncodashkb/adapters/short_mutations_external.yaml b/oncodashkb/adapters/short_mutations_external.yaml new file mode 100644 index 0000000..c79e85a --- /dev/null +++ b/oncodashkb/adapters/short_mutations_external.yaml @@ -0,0 +1,73 @@ +row: + map: + column: patient_id + to_subject: patient +transformers: + - map: + column: sample_id + to_object: sample + via_relation: patient_carries_sample + - map: + column: alteration + from_subject: sample + to_object: alteration + via_relation: sample_carries_alteration + - cat_format: + columns: + - hugoSymbol + - gene_role + from_subject: alteration + to_object: gene_status + format_string: "{hugoSymbol}:{gene_role}" + via_relation: alteration_causes_gene_status + - map: + column: hugoSymbol + from_subject: gene_status + to_object: gene + via_relation: gene_status_affects_gene + - map: + column: tumorType + to_property: tumor_type + for_object: alteration + - map: + column: consequence + to_property: consequence + for_object: alteration + - map: + column: oncogenic + to_property: oncogenic + for_object: alteration + - map: + column: mutationEffectDescription + to_property: mutation_effect_description + for_object: alteration + - map: + column: citationPMids + to_property: citation_PM_ids + for_object: alteration + - map: + column: level_of_evidence + to_property: level_of_evidence + for_object: alteration + - map: + column: geneSummary + to_property: gene_summary + for_object: gene + - map: + column: variantSummary + to_property: variant_summary + for_object: alteration + - map: + column: tumorTypeSummary + to_property: tumor_type_summary + for_object: alteration + - string: + value: " " + to_property: edgelabel + for_objects: + - patient_carries_sample + - sample_carries_alteration + - alteration_causes_gene_status + - gene_status_affects_gene +metadata: + - data_source: short_mutations_external \ No newline at end of file diff --git a/oncodashkb/adapters/short_mutations_local.yaml b/oncodashkb/adapters/short_mutations_local.yaml new file mode 100644 index 0000000..67bc745 --- /dev/null +++ b/oncodashkb/adapters/short_mutations_local.yaml @@ -0,0 +1,39 @@ +row: + map: + column: patient_id + to_subject: patient +transformers: + - map: + column: sample_id + to_object: sample + via_relation: patient_carries_sample + - map: + column: alteration + from_subject: sample + to_object: alteration + via_relation: sample_carries_alteration + - map: + column: referenceGenome + to_property: reference_genome + for_object: alteration + - map: + column: tumorType + to_property: tumor_type + for_object: alteration + - map: + column: consequence + to_property: consequence + for_object: alteration + - map: + column: homogenous + to_property: homogenous + for_object: alteration + - string: + value: " " + to_property: edgelabel + for_objects: + - patient_carries_sample + - sample_carries_alteration + - alteration_affects_gene +metadata: + - data_source: short_mutations_local \ No newline at end of file diff --git a/oncodashkb/adapters/copy_number_alterations_local.yaml b/oncodashkb/validators/copy_number_amplification_local.yaml similarity index 53% rename from oncodashkb/adapters/copy_number_alterations_local.yaml rename to oncodashkb/validators/copy_number_amplification_local.yaml index faae5ec..7ca2dc5 100644 --- a/oncodashkb/adapters/copy_number_alterations_local.yaml +++ b/oncodashkb/validators/copy_number_amplification_local.yaml @@ -1,102 +1,3 @@ -row: - map: - columns: - - patient_id - to_subject: patient -transformers: - - map: - columns: - - sample_id - to_object: sample - via_relation: patient_carries_sample - - cat_format: - columns: - - hugoSymbol - - alteration - from_subject: sample - to_object: alteration - format_string: "{hugoSymbol}:{alteration}" - via_relation: sample_carries_alteration - - map: - columns: - - hugoSymbol - from_subject: alteration - to_object: gene - via_relation: alteration_affects_gene - - cat_format: - columns: - - hugoSymbol - - gene_role - from_subject: alteration - to_object: functional_outcome - format_string: "{hugoSymbol}:{gene_role}" - via_relation: alteration_causes_functional_outcome - - map: - columns: - - hugoSymbol - from_subject: functional_outcome - to_object: gene - via_relation: functional_outcome_affects_gene - - map: - columns: - - referenceGenome - to_property: - - reference_genome - for_objects: - - alteration - - map: - columns: - - tumorType - to_property: - - tumor_type - for_objects: - - alteration - - map: - columns: - - oncogenic - to_property: - - oncogenic - for_objects: - - alteration - - map: - columns: - - mutationEffectDescription - to_property: - - mutation_effect_description - for_objects: - - alteration - - map: - columns: - - variantSummary - to_property: - - variant_summary - for_objects: - - alteration - - map: - columns: - - tumorTypeSummary - to_property: - - tumor_type_summary - for_objects: - - alteration - - map: - columns: - - citationPMids - to_property: - - citation_PM_ids - for_objects: - - alteration - - map: - columns: - - level_of_evidence - to_property: - - level_of_evidence - for_objects: - - alteration -metadata: - - name: copy_number_alterations - - validate: # Validation for cna labeled "local.". strict: true columns: @@ -128,7 +29,7 @@ validate: # Validation for cna labeled "local.". checks: isin: value: - - HGSOC + - CANCER nMajor: dtype: int64 description: "Major allele copynumber" diff --git a/oncodashkb/validators/copy_number_amplifications_external.yaml b/oncodashkb/validators/copy_number_amplifications_external.yaml new file mode 100644 index 0000000..716fccb --- /dev/null +++ b/oncodashkb/validators/copy_number_amplifications_external.yaml @@ -0,0 +1,91 @@ +validate: # Validation for cna labeled "external.". + strict: true + columns: + patient_id: + dtype: str + description: "Cohort code from clinical data" + sample_id: + dtype: str + description: "Sample id of biopsy (origin OVCA database)" + alteration: + dtype: str + description: "Genomic alteration type" + checks: + isin: + value: + - AMPLIFICATION + hugoSymbol: + dtype: str + description: "Gene name in Hugo nomenclature" + checks: + str_matches: ^[a-zA-Z0-9-]+$ + tumorType: + dtype: str + description: "Tumor type abbreviation (OncoTree based)" + checks: + isin: + value: + - CANCER + oncogenic: + dtype: str + description: "Indication of alteration oncogenecity" + nullable: true + checks: + isin: + value: + - Inconclusive + - known + - Likely Neutral + - Likely Oncogenic + - Oncogenic + - Unknown + mutationEffectDescription: + dtype: str + description: "Brief overview of the biological effect of the alteration with references" + nullable: true + gene_role: + dtype: str + description: "The biological effect of a mutation/alteration on the gene function" + nullable: true + checks: + isin: + value: + - Unknown + - Likely Gain-of-function + - Gain-of-function + - LoF + - Inconclusive + - Act + - ambiguous + citationPMids: + dtype: str + description: "Citations related to the biological effect separated by semicolon" + nullable: true + checks: + str_matches: ^[0-9]{7,}(,[0-9]{7,})*$ + level_of_evidence: + dtype: str + description: "The highest level of evidence for therapeutic implications based on OncoKB (CGI levels are mapped to this)" + nullable: true + checks: + isin: + value: + - LEVEL_1 + - LEVEL_2 + - LEVEL_3A + - LEVEL_3B + - LEVEL_4 + - LEVEL_R1 + - LEVEL_R2 + geneSummary: + dtype: str + description: "Brief overview of the gene and its role in cancer" + nullable: true + variantSummary: + dtype: str + description: "Brief description of the variant oncogenicity" + nullable: true + tumorTypeSummary: + dtype: str + description: "Describes the therapeutic implication that applies to the drug indication in discovered cancer" + nullable: true \ No newline at end of file diff --git a/oncodashkb/adapters/single_nucleotide_variants.yaml b/oncodashkb/validators/short_mutations_external.yaml similarity index 50% rename from oncodashkb/adapters/single_nucleotide_variants.yaml rename to oncodashkb/validators/short_mutations_external.yaml index 82ea212..39c8f1a 100644 --- a/oncodashkb/adapters/single_nucleotide_variants.yaml +++ b/oncodashkb/validators/short_mutations_external.yaml @@ -1,115 +1,4 @@ -row: - map: - columns: - - patient_id - to_subject: patient -transformers: - - map: - columns: - - sample_id - to_object: sample - via_relation: patient_carries_sample - - map: - columns: - - alteration - from_subject: sample - to_object: alteration - via_relation: sample_carries_alteration - # - map: - # columns: - # - hugoSymbol - # from_subject: alteration - # to_object: gene - # via_relation: alteration_affects_gene - - cat_format: - columns: - - hugoSymbol - - gene_role - from_subject: alteration - to_object: gene_status - format_string: "{hugoSymbol}:{gene_role}" - via_relation: alteration_causes_gene_status - - map: - columns: - - hugoSymbol - from_subject: gene_status - to_object: gene - via_relation: gene_status_affects_gene - # - map: - # columns: - # - referenceGenome - # to_property: - # - reference_genome - # for_objects: - # - alteration - - map: - columns: - - tumorType - to_property: - - tumor_type - for_objects: - - alteration - - map: - columns: - - oncogenic - to_property: - - oncogenic - for_objects: - - alteration - - map: - columns: - - mutationEffectDescription - to_property: - - mutation_effect_description - for_objects: - - alteration - - map: - columns: - - variantSummary - to_property: - - variant_summary - for_objects: - - alteration - - map: - columns: - - tumorTypeSummary - to_property: - - tumor_type_summary - for_objects: - - alteration - - map: - columns: - - citationPMids - to_property: - - citation_PM_ids - for_objects: - - alteration - - map: - columns: - - consequence - to_property: - - consequence - for_objects: - - alteration - - map: - columns: - - level_of_evidence - to_property: - - level_of_evidence - for_objects: - - alteration - - string: - value: " " - to_property: edgelabel - for_objects: - - patient_carries_sample - - sample_carries_alteration - - alteration_causes_gene_status - - gene_status_affects_gene -metadata: - - name: . - -validate: # SNV table labeled as "external". +validate: # Short mutations table labeled as "external". strict: true columns: patient_id: @@ -122,12 +11,14 @@ validate: # SNV table labeled as "external". dtype: str description: "Genomic alteration in format hugoSymbol:chromosome:position:reference_allele:sample_allele" checks: - str_matches: ^[a-zA-Z0-9-]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+:[ACTG]+$ + # str_matches: ^[a-zA-Z0-9-]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+:[ACTG]+$ + str_matches: ^[a-zA-Z0-9-,]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+:[ACTG]+$ hugoSymbol: dtype: str description: "Gene name in Hugo nomenclature" checks: - str_matches: ^[a-zA-Z0-9-]+$ + # str_matches: ^[a-zA-Z0-9-]+$ + str_matches: ^[a-zA-Z0-9-,]+$ tumorType: dtype: str description: "Tumor type abbreviation (OncoTree based)" @@ -161,7 +52,6 @@ validate: # SNV table labeled as "external". isin: value: - Inconclusive # Not present in source documentation description. - - Likely Neutral # Not present in source documentation description. - Likely Oncogenic - Oncogenic - Unknown @@ -190,7 +80,8 @@ validate: # SNV table labeled as "external". description: "Citations related to the biological effect separated by semicolon" nullable: true checks: - str_matches: ^[0-9]{7,}(,[0-9]{7,})*$ + # str_matches: ^[0-9]{7,}(,\s[0-9]{7,})*$ + str_matches: ^[0-9]{7,}(?:,(?:[0-9]{6,}|\s[0-9]{6,}))*$ level_of_evidence: dtype: str description: "Level of evidence for the alteration" @@ -216,4 +107,4 @@ validate: # SNV table labeled as "external". tumorTypeSummary: dtype: str description: "Describes the therapeutic implication that applies to the indication in cancer" - nullable: true + nullable: true \ No newline at end of file diff --git a/oncodashkb/adapters/single_nucleotide_variants_local.yaml b/oncodashkb/validators/short_mutations_local.yaml similarity index 74% rename from oncodashkb/adapters/single_nucleotide_variants_local.yaml rename to oncodashkb/validators/short_mutations_local.yaml index 7d85650..61b2dc0 100644 --- a/oncodashkb/adapters/single_nucleotide_variants_local.yaml +++ b/oncodashkb/validators/short_mutations_local.yaml @@ -1,107 +1,4 @@ -row: - map: - columns: - - patient_id - to_subject: patient -transformers: - - map: - columns: - - sample_id - to_object: sample - via_relation: patient_carries_sample - - map: - columns: - - alteration - from_subject: sample - to_object: alteration - via_relation: sample_carries_alteration - - map: - columns: - - hugoSymbol - from_subject: alteration - to_object: gene - via_relation: alteration_affects_gene - - cat_format: - columns: - - hugoSymbol - - gene_role - from_subject: alteration - to_object: functional_outcome - format_string: "{hugoSymbol}:{gene_role}" - via_relation: alteration_causes_functional_outcome - - map: - columns: - - hugoSymbol - from_subject: functional_outcome - to_object: gene - via_relation: functional_outcome_affects_gene - - map: - columns: - - referenceGenome - to_property: - - reference_genome - for_objects: - - alteration - - map: - columns: - - tumorType - to_property: - - tumor_type - for_objects: - - alteration - - map: - columns: - - oncogenic - to_property: - - oncogenic - for_objects: - - alteration - - map: - columns: - - mutationEffectDescription - to_property: - - mutation_effect_description - for_objects: - - alteration - - map: - columns: - - variantSummary - to_property: - - variant_summary - for_objects: - - alteration - - map: - columns: - - tumorTypeSummary - to_property: - - tumor_type_summary - for_objects: - - alteration - - map: - columns: - - citationPMids - to_property: - - citation_PM_ids - for_objects: - - alteration - - map: - columns: - - consequence - to_property: - - consequence - for_objects: - - alteration - - map: - columns: - - level_of_evidence - to_property: - - level_of_evidence - for_objects: - - alteration -metadata: - - name: single_nucleotide_variants - -validate: # SNV table labeled as "local". +validate: # Short mutations table labeled as "local". columns: patient_id: dtype: str @@ -142,12 +39,14 @@ validate: # SNV table labeled as "local". dtype: str description: "Gene name in Hugo nomenclature" checks: - str_matches: ^[a-zA-Z0-9-]+$ + str_matches: ^[a-zA-Z0-9-,]+$ + # str_matches: ^[a-zA-Z0-9-]÷$ alteration: dtype: str description: "Genomic alteration in format hugoSymbol:chromosome:position:reference_allele:sample_allele" checks: - str_matches: ^[a-zA-Z0-9-]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+>[ACTG]+$ + # str_matches: ^[a-zA-Z0-9-]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+>[ACTG]+$ + str_matches: ^[a-zA-Z0-9-,]+:chr[\d|X|Y]{1,2}:\d+:[ACTG]+>[ACTG]+$ tumorType: dtype: str description: "Tumor type abbreviation (OncoTree based)" @@ -162,14 +61,16 @@ validate: # SNV table labeled as "local". checks: isin: value: - - stopgain - - nonsynonymous_SNV + - UTR3 # new + - UTR5 # new - frameshift_deletion - frameshift_insertion - intergenic - intron - intronic + - nonsynonymous_SNV - splicing + - stopgain - upstream cytoBand: dtype: str @@ -197,13 +98,15 @@ validate: # SNV table labeled as "local". checks: isin: value: + - UTR3 # new + - UTR5 # new - exonic + - exonic;splicing - intergenic - intron - intronic - splicing - upstream - - exonic;splicing AAChangeMANE: dtype: str description: "Protein change by MANE" @@ -215,17 +118,19 @@ validate: # SNV table labeled as "local". checks: isin: value: - - UTR3 + - UTR3 # Not in data + - UTR5 # new + - downstream - exonic + - exonic;splicing - intergenic - intron - intronic - ncRNA_exonic + - ncRNA_exonic;splicing - ncRNA_intronic - splicing - upstream - - exonic;splicing - - ncRNA_exonic;splicing exonicFuncRefGene: dtype: str description: "Genomic consequence of variant (from RefGene)" @@ -246,11 +151,11 @@ validate: # SNV table labeled as "local". description: "Protein change by RefGene" nullable: true nMinor: - dtype: int64 + dtype: float64 description: "Minor allele copynumber (from CNAs if available)" nullable: true nMajor: - dtype: int64 + dtype: float64 description: "Major allele copynumber (from CNAs if available)" nullable: true ad0: @@ -275,10 +180,10 @@ validate: # SNV table labeled as "local". - HET - LOH hom_lo: - dtype: int64 + dtype: float64 description: "Lower bound for expected homogeneity confidence interval" hom_hi: - dtype: int64 + dtype: float64 description: "Higher bound for expected homogeneity confidence interval" hom_pbinom_lo: dtype: float64 @@ -311,13 +216,12 @@ validate: # SNV table labeled as "local". checks: isin: value: - - pathogenic - - likely_pathogenic - - benign - - likely_benign - - ambiguous + - deleterious + - deleterious,NA + - tolerated + - tolerated,NA sift_score: - dtype: float64 + dtype: str description: "SIFT score from WGS annotations (not yet available in WGS annotations)" nullable: true polyphen_category: @@ -327,32 +231,39 @@ validate: # SNV table labeled as "local". checks: isin: value: - - pathogenic - - likely_pathogenic - benign + - benign,NA # New + - possibly_damaging + - possibly_damaging,NA + - probably_damaging + - probably_damaging,NA + - unknown + - unknown,NA + - likely_pathogenic # Not in - likely_benign - ambiguous polyphen_score: - dtype: float64 + dtype: str description: "Polyphen score from WGS annotations (not yet available in WGS annotations)" nullable: true - amis_category: + AM_class: dtype: str description: "Alphamissense category from WGS annotations" nullable: true checks: isin: value: - - pathogenic - - likely_pathogenic - - benign - likely_benign + - likely_pathogenic - ambiguous - ambiguous,likely_pathogenic - ambiguous,likely_benign - likely_benign,ambiguous - likely_pathogenic,ambiguous - amis_score: + - pathogenic + - benign + - ambiguous,likely_pathogenic,likely_pathogenic #TO_CHECK + AM_score: dtype: str description: "Alphamissense score from WGS annotations. 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parser.add_argument("-i", "--clinical", metavar="CSV", nargs="+", - help="Extract from a clinical CSV file.") - - parser.add_argument("-snv", "--single_nucleotide_variants", metavar="CSV",nargs="+", - help="Extract from a CSV file with single nucleotide variants (SNV) annotations.") - - parser.add_argument("-cna", "--copy_number_alterations", metavar="CSV",nargs="+", - help="Extract from a CSV file with copy number alterations (CNA) annotations.") - - - parser.add_argument("-g", "--gene_ontology", metavar="CSV", nargs="+", + parser.add_argument("-g", "--gene-ontology", metavar="CSV", nargs="+", help="Extract from a Gene_Ontology_Annotation GAF file.") - parser.add_argument("-n", "--gene_ontology_owl", metavar="OWL", + parser.add_argument("-n", "--gene-ontology-owl", metavar="OWL", help="Download Gene_Ontology owl file.") - parser.add_argument("-G", "--gene_ontology_genes", metavar="TXT", + parser.add_argument("-G", "--gene-ontology-genes", metavar="TXT", help="List of genes for which we integrate Gene Ontology annotations (by default genes from OncoKB).") - parser.add_argument("-r", "--gene_ontology_reverse", action='store_true', + parser.add_argument("-r", "--gene-ontology-reverse", action='store_true', help="Extract from a Gene_Ontology_Annotation GAF file.") - parser.add_argument("-e", "--open_targets_evidences", metavar="PARQUET", nargs="+", + parser.add_argument("-e", "--open-targets-evidences", metavar="PARQUET", nargs="+", help="Extract parquet files from the directory evidences CHEMBL.") - parser.add_argument("-t", "--open_targets", metavar="PARQUET", nargs="+", + parser.add_argument("-t", "--open-targets", metavar="PARQUET", nargs="+", help="Extract parquet files from the directory targets.") - parser.add_argument("-d", "--open_targets_drugs", metavar="PARQUET", nargs="+", + parser.add_argument("-d", "--open-targets-drugs", metavar="PARQUET", nargs="+", help="Extract parquet files from the directory molecule.") parser.add_argument("-p", "--open_targets_diseases", metavar="PARQUET", nargs="+", help="Extract parquet files from the directory diseases.") @@ -193,6 +198,83 @@ def progress_read(filename, hint=None, steps=100, estimate_lines=10, **kwargs): data_mappings = {} + # DECIDER Patient Clinical Data + + if asked.clinical: + data_file = asked.clinical[0] + mapping_file = "./oncodashkb/adapters/clinical.yaml" + + # logging.info(f"Weave Clinical data...") + logging.info(f"Weave `{data_file}:{mapping_file}`...") + logging.info(f" | Load data `{data_file}`...") + table = progress_read(data_file, sep=",", hint=673) + + with open(mapping_file) as fd: + ymapping = yaml.full_load(fd) + # logging.info("test") + + # n, e = ontoweaver.extract_table( + # # df=networks_df, config=mapping, separator=":", affix="suffix" + # df=clinical_df, + # config=mapping, + # type_affix_sep=":", + # affix="suffix", + # raise_errors = True + # ) + + # nodes += n + # edges += e + + # logging.info(f"OK, wove Clinical data: {len(nodes)} nodes, {len(edges)} edges.") + + logging.info(f" | Process {mapping_file}...") + + yparser = ontoweaver.mapping.YamlParser(ymapping) + mapping = yparser() + + adapter = ontoweaver.tabular.PandasAdapter( + table, + *mapping, + type_affix="suffix", + type_affix_sep=":", + raise_errors = True + ) + + local_nodes = [] + local_edges = [] + with alive_bar(len(table), file=sys.stderr) as progress: + for n,e in adapter(): + # NOTE: here, n & e are ontoweaver.base.Element, not BioCypher tuples. + local_nodes += n + local_edges += e + progress() + + + logging.info(f"OK, wove: {len(local_nodes)} nodes, {len(local_edges)} edges.") + nodes += local_nodes + edges += local_edges + + # DECIDER Patient molecular Data + + ## Short mutations + + if asked.short_mutations_local: + for file_path in asked.short_mutations_local: + data_mappings[file_path] = "./oncodashkb/adapters/short_mutations_local.yaml" + + if asked.short_mutations_external: + for file_path in asked.short_mutations_external: + data_mappings[file_path] = "./oncodashkb/adapters/short_mutations_external.yaml" + + ## Copy number amplifications + + if asked.copy_number_amplifications_local: + for file_path in asked.copy_number_amplifications_local: + data_mappings[file_path] = "./oncodashkb/adapters/copy_number_amplifications_local.yaml" + + if asked.copy_number_amplifications_external: + for file_path in asked.copy_number_amplifications_external: + data_mappings[file_path] = "./oncodashkb/adapters/copy_number_amplifications_external.yaml" # Extract from databases requiring specialized preprocessing adapters. if asked.open_targets: @@ -378,37 +460,6 @@ def progress_read(filename, hint=None, steps=100, estimate_lines=10, **kwargs): for file_path in asked.cgi: data_mappings[file_path] = "./oncodashkb/adapters/cgi.yaml" - if asked.clinical: - logging.info(f"Weave Clinical data...") - - clinical_df = progress_read(asked.clinical[0], sep=",", hint=673) - - mapping_file = "./oncodashkb/adapters/clinical.yaml" - with open(mapping_file) as fd: - mapping = yaml.full_load(fd) - - n, e = ontoweaver.extract_table( - # df=networks_df, config=mapping, separator=":", affix="suffix" - df=clinical_df, - config=mapping, - type_affix_sep=":", - affix="suffix", - raise_errors = True - ) - - nodes += n - edges += e - - logging.info(f"OK, wove Clinical data: {len(nodes)} nodes, {len(edges)} edges.") - - if asked.single_nucleotide_variants: - for file_path in asked.single_nucleotide_variants: - data_mappings[file_path] = "./oncodashkb/adapters/single_nucleotide_variants.yaml" - - if asked.copy_number_alterations: - for file_path in asked.copy_number_alterations: - data_mappings[file_path] = "./oncodashkb/adapters/copy_number_alterations.yaml" - ################################################### # Map the data that were declared the simple way. # @@ -424,7 +475,7 @@ def progress_read(filename, hint=None, steps=100, estimate_lines=10, **kwargs): logging.info(f" | Process {mapping_file}...") - yparser = ontoweaver.tabular.YamlParser(ymapping) + yparser = ontoweaver.mapping.YamlParser(ymapping) mapping = yparser() adapter = ontoweaver.tabular.PandasAdapter(