From b2380c4cd492ac2fa06dc0dd610350b065551e5f Mon Sep 17 00:00:00 2001 From: Justin Reese Date: Sat, 26 Sep 2020 17:48:30 -0700 Subject: [PATCH 1/3] Merge yaml file for Jenkins --- merge_jenkins.yaml | 134 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 merge_jenkins.yaml diff --git a/merge_jenkins.yaml b/merge_jenkins.yaml new file mode 100644 index 00000000..8f9a6774 --- /dev/null +++ b/merge_jenkins.yaml @@ -0,0 +1,134 @@ +--- +configuration: + output_directory: data/merged + checkpoint: false + property_types: + # define the type for non-canonical node/edge properties + combined_score: 'xsd:float' + confidence_score: 'xsd:float' + neighborhood: 'xsd:float' + neighborhood_transferred: 'xsd:float' + fusion: 'xsd:float' + cooccurence: 'xsd:float' + homology: 'xsd:float' + coexpression: 'xsd:float' + coexpression_transferred: 'xsd:float' + experiments: 'xsd:float' + experiments_transferred: 'xsd:float' + database: 'xsd:float' + database_transferred: 'xsd:float' + textmining: 'xsd:float' + textmining_transferred: 'xsd:float' + +merged_graph: + name: KG-COVID-19 Graph + targets: + drug-central: + type: tsv + filename: + - data/transformed/drug_central/nodes.tsv + - data/transformed/drug_central/edges.tsv + pharmgkb: + type: tsv + filename: + - data/transformed/pharmgkb/nodes.tsv + - data/transformed/pharmgkb/edges.tsv + STRING: + type: tsv + filename: + - data/transformed/STRING/nodes.tsv + - data/transformed/STRING/edges.tsv + filters: + node_filters: + category: + - biolink:Gene + - biolink:Protein + edge_filters: + subject_category: + - biolink:Gene + - biolink:Protein + object_category: + - biolink:Gene + - biolink:Protein + edge_label: + - biolink:interacts_with + - biolink:has_gene_product + operations: + - name: kgx.utils.graph_utils.remap_node_identifier + args: + category: biolink:Protein + alternative_property: xrefs + prefix: UniProtKB + ttd: + type: tsv + filename: + - data/transformed/ttd/nodes.tsv + - data/transformed/ttd/edges.tsv + zhou-host-proteins: + type: tsv + filename: + - data/transformed/zhou_host_proteins/nodes.tsv + - data/transformed/zhou_host_proteins/edges.tsv + SciBite-CORD-19: + type: tsv + filename: + - data/transformed/SciBite-CORD-19/nodes.tsv + - data/transformed/SciBite-CORD-19/edges.tsv + sars-cov-2-gene-annot: + type: tsv + filename: + - data/transformed/sars_cov_2_gene_annot/nodes.tsv + - data/transformed/sars_cov_2_gene_annot/edges.tsv + intact: + type: tsv + filename: + - data/transformed/intact/nodes.tsv + - data/transformed/intact/edges.tsv + chembl: + type: tsv + filename: + - data/transformed/ChEMBL/nodes.tsv + - data/transformed/ChEMBL/edges.tsv + gene-ontology: + type: tsv + filename: + - data/transformed/ontologies/go-plus_nodes.tsv + - data/transformed/ontologies/go-plus_edges.tsv + mondo-ontology: + type: tsv + filename: + - data/transformed/ontologies/mondo_nodes.tsv + - data/transformed/ontologies/mondo_edges.tsv + hp-ontology: + type: tsv + filename: + - data/transformed/ontologies/hp_nodes.tsv + - data/transformed/ontologies/hp_edges.tsv + go-cams: + type: tsv + filename: + - data/transformed/GOCAMs/GOCAMs_nodes.tsv + - data/transformed/GOCAMs/GOCAMs_edges.tsv + operations: + - name: kgx.operations.summarize_graph.generate_graph_stats + args: + graph_name: KG-COVID-19 Graph + filename: merged_graph_stats.yaml + node_facet_properties: + - provided_by + edge_facet_properties: + - provided_by + destination: + merged-kg-tsv: + type: tsv + compression: tar.gz + filename: merged-kg + merged-kg-nt: + type: nt + compression: gz + filename: merged-kg.nt.gz +# merged-kg-neo4j: +# type: neo4j +# uri: http://localhost:8484 +# username: neo4j +# password: admin From 8544ad5fcec98da9a483899e739cab55982b6d5c Mon Sep 17 00:00:00 2001 From: Justin Reese Date: Sat, 26 Sep 2020 17:50:53 -0700 Subject: [PATCH 2/3] Remove nt output from default merge.yaml --- merge.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/merge.yaml b/merge.yaml index 8f9a6774..503fe262 100644 --- a/merge.yaml +++ b/merge.yaml @@ -123,10 +123,10 @@ merged_graph: type: tsv compression: tar.gz filename: merged-kg - merged-kg-nt: - type: nt - compression: gz - filename: merged-kg.nt.gz +# merged-kg-nt: +# type: nt +# compression: gz +# filename: merged-kg.nt.gz # merged-kg-neo4j: # type: neo4j # uri: http://localhost:8484 From cc0f76546ebb659419c64a5f7a9384bfccab597d Mon Sep 17 00:00:00 2001 From: Justin Reese Date: Sat, 26 Sep 2020 17:51:25 -0700 Subject: [PATCH 3/3] Point Jenkins at updated (merge_jenkins.yaml) file --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index cbd00260..09f197a2 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -98,7 +98,7 @@ pipeline { stage('Merge') { steps { dir('./gitrepo') { - sh '. venv/bin/activate && python3.7 run.py merge' + sh '. venv/bin/activate && python3.7 run.py merge -y merge_jenkins.yaml' sh 'env' sh 'cp merged_graph_stats.yaml merged_graph_stats_$BUILDSTARTDATE.yaml' sh 'tar -rvf data/merged/merged-kg.tar merged_graph_stats_$BUILDSTARTDATE.yaml'