diff --git a/build.sbt b/build.sbt
index 1db06f43..d4bb05a5 100644
--- a/build.sbt
+++ b/build.sbt
@@ -8,7 +8,7 @@ organization := "org.renci"
name := "cam-kp-api"
-version := "0.3-pre1"
+version := "0.3-pre2"
licenses := Seq("MIT license" -> url("https://opensource.org/licenses/MIT"))
diff --git a/src/it/resources/examples/PRCD-increases-chemical.json b/src/it/resources/examples/PRCD-increases-chemical.json
new file mode 100644
index 00000000..f0034ba3
--- /dev/null
+++ b/src/it/resources/examples/PRCD-increases-chemical.json
@@ -0,0 +1,47 @@
+{
+ "description": "PRCD increases chemical",
+ "message": {
+ "query_graph": {
+ "nodes": {
+ "gene": {
+ "categories": [
+ "biolink:Gene"
+ ],
+ "ids": [
+ "NCBIGene:768206"
+ ]
+ },
+ "chemical": {
+ "categories": [
+ "biolink:ChemicalEntity"
+ ]
+ }
+ },
+ "edges": {
+ "t_edge": {
+ "object": "gene",
+ "subject": "chemical",
+ "predicates": [
+ "biolink:affects"
+ ],
+ "knowledge_type": "inferred",
+ "qualifier_constraints": [
+ {
+ "qualifier_set": [
+ {
+ "qualifier_type_id": "biolink:object_aspect_qualifier",
+ "qualifier_value": "activity_or_abundance"
+ },
+ {
+ "qualifier_type_id": "biolink:object_direction_qualifier",
+ "qualifier_value": "increased"
+ }
+ ]
+ }
+ ]
+ }
+ }
+ }
+ },
+ "minExpectedResults": 1000
+}
\ No newline at end of file
diff --git a/src/it/resources/examples/genes-upstream-of-GPR35.json b/src/it/resources/examples/genes-upstream-of-GPR35.json
index 2d53d30c..70250497 100644
--- a/src/it/resources/examples/genes-upstream-of-GPR35.json
+++ b/src/it/resources/examples/genes-upstream-of-GPR35.json
@@ -19,7 +19,17 @@
"e0": {
"subject": "n0",
"object": "n1",
- "predicates": ["biolink:affects_activity_of"]
+ "predicates": ["biolink:affects"],
+ "qualifier_constraints": [
+ {
+ "qualifier_set": [
+ {
+ "qualifier_type_id": "biolink:object_aspect_qualifier",
+ "qualifier_value": "activity"
+ }
+ ]
+ }
+ ]
},
"e1": {
"subject": "n1",
diff --git a/src/it/resources/examples/swagger-example.json b/src/it/resources/examples/swagger-example.json
index 5ece3dde..be0d58d9 100644
--- a/src/it/resources/examples/swagger-example.json
+++ b/src/it/resources/examples/swagger-example.json
@@ -17,7 +17,17 @@
"edges": {
"e0": {
"predicates": [
- "biolink:positively_regulates"
+ "biolink:regulates"
+ ],
+ "qualifier_constraints": [
+ {
+ "qualifier_set": [
+ {
+ "qualifier_type_id": "biolink:object_direction_qualifier",
+ "qualifier_value": "upregulated"
+ }
+ ]
+ }
],
"subject": "n0",
"object": "n1"
diff --git a/src/main/resources/application.conf b/src/main/resources/application.conf
index 3a15d95c..f667d580 100644
--- a/src/main/resources/application.conf
+++ b/src/main/resources/application.conf
@@ -1,10 +1,11 @@
{
- version = "0.3-pre1"
+ version = "0.3-pre3"
host = 0.0.0.0
port = 8080
port = ${?PORT}
trapi-version = "1.3.0"
trapi-version = ${?TRAPI_VERSION}
+ biolink-version = "v3.2.3"
location = "http://localhost:8080"
location = ${?LOCATION}
sparql-endpoint = "https://cam-kp-sparql.apps.renci.org/sparql"
diff --git a/src/main/resources/biolink/README.md b/src/main/resources/biolink/README.md
new file mode 100644
index 00000000..95bdeb5c
--- /dev/null
+++ b/src/main/resources/biolink/README.md
@@ -0,0 +1,38 @@
+# Biolink mappings
+
+CAM-KP needs Biolink information in both the triplestore backend as well as the
+frontend. This is frustrating -- if only one of them needed to know about the
+Biolink model, that would greatly simplify what we need to do here.
+
+We previously generated `predicates.csv` and `mkg-nodes.csv` from the
+[CAM Pipeline](https://github.com/ExposuresProvider/cam-pipeline) and incorporated
+them in here (via the parent directory). This was relatively easy to do when
+Biolink predicates could be mapped directly to relations in the triplestore, but
+since Biolink 3 includes predicates modified with qualifiers, this mapping is more
+complicated.
+
+This directory takes all of our predicate mapping logic and puts it into one place:
+the [`predicates.json`](./predicates.json) file in this directory is intended to provide
+the definitive set of mappings between Biolink predicate/qualifier combinations and
+triplestore relations. A single relation may be mapped to several predicate/qualifier
+combinations and vice versa.
+
+Two pieces of code interact with this file:
+1. `org.renci.cam.util.GenerateBiolinkPredicateMappings` is a standalone program that
+ can be used to regenerate this file. It currently uses the
+ [Biolink predicate_mapping.yaml](https://github.com/biolink/biolink-model/blob/master/predicate_mapping.yaml),
+ mapping information from the triplestore and a list of manual mappings added during
+ development, but in the future it may be expanded to include additional files.
+2. `org.renci.cam.domain.PredicateMappings` is a module in the code that provides a
+ programmatic interface to the contents of the `predicates.json` file, and provides
+ methods to map from Biolink predicate/qualifier combinations to relations.
+
+The `predicates.json` file can be regenerated by updating the
+Biolink version in application.conf and then running:
+
+```shell
+$ SPARQL_ENDPOINT=https://cam-kp-sparql-dev.apps.renci.org/sparql sbt "runMain org.renci.cam.util.GenerateBiolinkPredicateMappings"
+```
+
+The latest `predicates.json` file should be checked into the GitHub repository so that
+changes to it can be tracked.
\ No newline at end of file
diff --git a/src/main/resources/biolink/predicates.json b/src/main/resources/biolink/predicates.json
new file mode 100644
index 00000000..90e2a161
--- /dev/null
+++ b/src/main/resources/biolink/predicates.json
@@ -0,0 +1,5082 @@
+[
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004008",
+ "label" : [
+ "has primary output"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/temporally_related_to"
+ },
+ "shorthand" : "temporally_related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002497",
+ "label" : [
+ "end stage"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/temporally_related_to"
+ },
+ "shorthand" : "temporally_related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002087",
+ "label" : [
+ "immediately_preceded_by"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.org/dc/terms/contributor",
+ "label" : [
+ "contributor"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002019",
+ "label" : [
+ "has ligand"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/acts_upstream_of"
+ },
+ "shorthand" : "acts_upstream_of"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004034",
+ "label" : [
+ "acts upstream of, positive effect"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/BFO_0000050",
+ "label" : [
+ "part_of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+ "label" : [
+ "created_by"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002162",
+ "label" : [
+ "in taxon"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002496",
+ "label" : [
+ "existence starts during or after"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002608",
+ "label" : [
+ "process has causal agent"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004034",
+ "label" : [
+ "acts upstream of, positive effect"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002215",
+ "label" : [
+ "capable_of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/participates_in"
+ },
+ "shorthand" : "participates_in"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002216",
+ "label" : [
+ "capable of part of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/IAO_0000425",
+ "label" : [
+ "expand assertion to"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002174",
+ "label" : [
+ "dubious_for_taxon"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/has_participant"
+ },
+ "shorthand" : "has_participant"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002296",
+ "label" : [
+ "results in development of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+ "label" : [
+ "has_obo_namespace"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/positively_regulates"
+ },
+ "shorthand" : "positively_regulates"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004032",
+ "label" : [
+ "acts upstream of or within, positive effect"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002597",
+ "label" : [
+ "capable of negatively regulating"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/ECO_9000002",
+ "label" : [
+ "has GO evidence code"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/UBPROP_0000015",
+ "label" : [
+ "location_notes"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002338",
+ "label" : [
+ "has target start location"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002423",
+ "label" : [
+ "logical macro assertion on an annotation property"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0011002",
+ "label" : [
+ "regulates activity of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/acts_upstream_of"
+ },
+ "shorthand" : "acts_upstream_of"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004035",
+ "label" : [
+ "acts upstream of, negative effect"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/UBPROP_0000202",
+ "label" : [
+ "fma_set_term"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0017001",
+ "label" : [
+ "device utilizes material"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004035",
+ "label" : [
+ "acts upstream of, negative effect"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002163",
+ "label" : [
+ "spatially disjoint from"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/has_output"
+ },
+ "shorthand" : "has_output"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004008",
+ "label" : [
+ "has primary output"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#inSubset",
+ "label" : [
+ "in_subset"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/temporally_related_to"
+ },
+ "shorthand" : "temporally_related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002412",
+ "label" : [
+ "immediately causally upstream of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/participates_in"
+ },
+ "shorthand" : "participates_in"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002215",
+ "label" : [
+ "capable of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/has_output"
+ },
+ "shorthand" : "has_output"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002299",
+ "label" : [
+ "results in maturation of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004046",
+ "label" : [
+ "causally upstream of or within, negative effect"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002581",
+ "label" : [
+ "is a defining property chain axiom"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/has_input"
+ },
+ "shorthand" : "has_input"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002590",
+ "label" : [
+ "results in disassembly of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002333",
+ "label" : [
+ "enabled by"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002431",
+ "label" : [
+ "involved in or involved in regulation of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/overlaps"
+ },
+ "shorthand" : "overlaps"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/BFO_0000050",
+ "label" : [
+ "part of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002087",
+ "label" : [
+ "starts_at_end_of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002454",
+ "label" : [
+ "has host"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/temporally_related_to"
+ },
+ "shorthand" : "temporally_related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002087",
+ "label" : [
+ "starts_at_end_of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002175",
+ "label" : [
+ "present in taxon"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym",
+ "label" : [
+ "has related synonym"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/temporally_related_to"
+ },
+ "shorthand" : "temporally_related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002093",
+ "label" : [
+ "ends during"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002174",
+ "label" : [
+ "dubious for taxon"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002501",
+ "label" : [
+ "causal relation between processes"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://translator.renci.org/ubergraph-axioms.ofn#acts_upstream_of_o_enabled_by",
+ "label" : [
+ "acts_upstream_of_o_enabled_by"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym",
+ "label" : [
+ "has_exact_synonym"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0012006",
+ "label" : [
+ "is small molecule inhibitor of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/related_to"
+ },
+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002298",
+ "label" : [
+ "results in morphogenesis of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+ "label" : [
+ "creation_date"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/UBPROP_0000010",
+ "label" : [
+ "structure_notes"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/regulates"
+ },
+ "shorthand" : "regulates"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002295",
+ "label" : [
+ "results in developmental progression of"
+ ]
+ }
+ },
+ {
+ "predicate" : {
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+ },
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+ "label" : [
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+ "biolinkPredicate" : {
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+ "shorthand" : "related_to"
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+ "biolinkPredicate" : {
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+ ]
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+ "biolinkPredicate" : {
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+ },
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+ },
+ "predicate" : {
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+ ]
+ }
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+ }
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+ "label" : [
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+ },
+ "predicate" : {
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+ ]
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+ },
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+ ]
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+ "predicate" : {
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+ },
+ "predicate" : {
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+ "label" : [
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+ {
+ "biolinkPredicate" : {
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+ },
+ "shorthand" : "negatively_regulates"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004035",
+ "label" : [
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+ {
+ "biolinkPredicate" : {
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+ "value" : "https://w3id.org/biolink/vocab/related_to"
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+ "shorthand" : "related_to"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0002215",
+ "label" : [
+ "capable of"
+ ]
+ }
+ },
+ {
+ "biolinkPredicate" : {
+ "iri" : {
+ "value" : "https://w3id.org/biolink/vocab/has_participant"
+ },
+ "shorthand" : "has_participant"
+ },
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0000057",
+ "label" : [
+ "has participant"
+ ]
+ }
+ },
+ {
+ "predicate" : {
+ "iri" : "http://purl.obolibrary.org/obo/RO_0004050",
+ "label" : [
+ "is negative form of"
+ ]
+ }
+ }
+]
\ No newline at end of file
diff --git a/src/main/resources/sri-testing.json b/src/main/resources/sri-testing.json
new file mode 100644
index 00000000..6f282d5d
--- /dev/null
+++ b/src/main/resources/sri-testing.json
@@ -0,0 +1,8 @@
+{
+ "edges" : [
+ ],
+ "exclude_tests" : [
+ ],
+ "infores" : "cam-kp",
+ "source_type" : "aggregator"
+}
\ No newline at end of file
diff --git a/src/main/resources/test-edges.jsonl b/src/main/resources/test-edges.jsonl
new file mode 100644
index 00000000..a76cc6fe
--- /dev/null
+++ b/src/main/resources/test-edges.jsonl
@@ -0,0 +1,4455 @@
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+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:has_participant","subject":"GO:0007259","object":"UniProtKB:O14543"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:temporally_related_to","subject":"GO:0038092","object":"GO:0000978"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:precedes","subject":"GO:0038092","object":"GO:0000978"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0038092","object":"GO:0000978"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0007165","object":"GO:0007165"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0007165","object":"GO:0007165"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0007224","object":"ZFIN:ZDB-GENE-070112-2232"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:caused_by","subject":"GO:0007224","object":"ZFIN:ZDB-GENE-070112-2232"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:has_part","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:has_part","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0000165","object":"GO:0003674"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0007165","object":"GO:0007165"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0007165","object":"GO:0007165"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0036498","object":"MGI:1930134"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:caused_by","subject":"GO:0036498","object":"MGI:1930134"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0007219","object":"GO:0140537"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0007219","object":"GO:0140537"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0007219","object":"GO:0007219"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0007219","object":"GO:0007219"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:overlaps","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:related_to","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:overlaps","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:related_to","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:part_of","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:part_of","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Cell","predicate":"biolink:related_to","subject":"GO:0043491","object":"CL:0000218"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Cell","predicate":"biolink:occurs_in","subject":"GO:0043491","object":"CL:0000218"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:CellularComponent","predicate":"biolink:related_to","subject":"GO:0000165","object":"GO:0032991"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:CellularComponent","predicate":"biolink:has_participant","subject":"GO:0000165","object":"GO:0032991"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:CellularComponent","predicate":"biolink:related_to","subject":"GO:0000165","object":"GO:0032991"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:CellularComponent","predicate":"biolink:has_participant","subject":"GO:0000165","object":"GO:0032991"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0032924","object":"fb:FBgn0011300"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:has_participant","subject":"GO:0032924","object":"fb:FBgn0011300"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0032924","object":"fb:FBgn0011300"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:has_participant","subject":"GO:0032924","object":"fb:FBgn0011300"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:EnvironmentalProcess","predicate":"biolink:related_to","subject":"GO:0019933","object":"GO:1904322"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:EnvironmentalProcess","predicate":"biolink:overlaps","subject":"GO:0019933","object":"GO:1904322"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Gene","predicate":"biolink:related_to","subject":"GO:0070498","object":"NCBIGene:3553"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Gene","predicate":"biolink:has_participant","subject":"GO:0070498","object":"NCBIGene:3553"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Gene","predicate":"biolink:related_to","subject":"GO:0070498","object":"NCBIGene:3553"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Gene","predicate":"biolink:has_participant","subject":"GO:0070498","object":"NCBIGene:3553"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:GrossAnatomicalStructure","predicate":"biolink:related_to","subject":"GO:0008543","object":"UBERON:0002329"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:GrossAnatomicalStructure","predicate":"biolink:occurs_in","subject":"GO:0008543","object":"UBERON:0002329"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MacromolecularComplexMixin","predicate":"biolink:related_to","subject":"GO:0038111","object":"GO:1902911"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MacromolecularComplexMixin","predicate":"biolink:has_participant","subject":"GO:0038111","object":"GO:1902911"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MacromolecularComplexMixin","predicate":"biolink:related_to","subject":"GO:0038111","object":"GO:1902911"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MacromolecularComplexMixin","predicate":"biolink:has_participant","subject":"GO:0038111","object":"GO:1902911"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:has_part","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:has_part","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0007173","object":"GO:0043539"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0038113","object":"GO:0038113"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0038113","object":"GO:0038113"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:has_participant","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:has_participant","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:overlaps","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:related_to","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:overlaps","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:related_to","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:part_of","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Behavior","predicate":"biolink:part_of","subject":"GO:0043491","object":"GO:0035176"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0070102","object":"UniProtKB:P23458"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:has_participant","subject":"GO:0070102","object":"UniProtKB:P23458"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"GO:0070102","object":"UniProtKB:P23458"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:ChemicalSubstance","predicate":"biolink:has_participant","subject":"GO:0070102","object":"UniProtKB:P23458"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"GO:0007224","object":"GO:0005262"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:MolecularActivity","predicate":"biolink:overlaps","subject":"GO:0007224","object":"GO:0005262"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:overlaps","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:part_of","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:Pathway","predicate":"biolink:part_of","subject":"GO:0097400","object":"GO:0031098"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:has_participant","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:Pathway","object_category":"biolink:PhenotypicQuality","predicate":"biolink:has_participant","subject":"GO:0097190","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0004879"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0004879"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0004879"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0004879"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:ChemicalSubstance","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:16469"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50904","object":"GO:0015129"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50904","object":"GO:0015129"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50904","object":"GO:0015129"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50904","object":"GO:0015129"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:PhenotypicQuality","predicate":"biolink:overlaps","subject":"CHEBI:50114","object":"CHEBI:50114"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50904","object":"GO:0005215"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50904","object":"GO:0005215"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:participates_in","subject":"CHEBI:50904","object":"GO:0005215"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:MolecularActivity","predicate":"biolink:related_to","subject":"CHEBI:50904","object":"GO:0005215"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:participates_in","subject":"CHEBI:50114","object":"GO:0097190"}
+{"subject_category":"biolink:PhenotypicQuality","object_category":"biolink:Pathway","predicate":"biolink:related_to","subject":"CHEBI:50114","object":"GO:0097190"}
\ No newline at end of file
diff --git a/src/main/scala/org/renci/cam/AppConfig.scala b/src/main/scala/org/renci/cam/AppConfig.scala
index ef3e1e2d..9635df72 100644
--- a/src/main/scala/org/renci/cam/AppConfig.scala
+++ b/src/main/scala/org/renci/cam/AppConfig.scala
@@ -9,6 +9,7 @@ final case class AppConfig(host: String,
location: String,
sparqlEndpoint: Uri,
trapiVersion: String,
+ biolinkVersion: String,
maturity: String,
version: String)
diff --git a/src/main/scala/org/renci/cam/LookupService.scala b/src/main/scala/org/renci/cam/LookupService.scala
index 04147063..fbc1f31f 100644
--- a/src/main/scala/org/renci/cam/LookupService.scala
+++ b/src/main/scala/org/renci/cam/LookupService.scala
@@ -11,7 +11,7 @@ import org.renci.cam.HttpClient.HttpClient
import org.renci.cam.Server.EndpointEnv
import org.renci.cam.Server.LocalTapirJsonCirce.jsonBody
import org.renci.cam.Util.IterableSPARQLOps
-import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate, IRI}
+import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate, IRI, PredicateMappings, QualifiedBiolinkPredicate}
import sttp.tapir.Endpoint
import sttp.tapir.generic.auto._
import sttp.tapir.server.http4s.ztapir.ZHttp4sServerInterpreter
@@ -95,7 +95,7 @@ object LookupService extends LazyLogging {
case class Relation(
subj: Set[LabeledIRI],
preds: Set[LabeledIRI],
- biolinkPredicates: Map[String, Set[LabeledIRI]],
+ qualifiedBiolinkPredicates: Map[String, Set[QualifiedBiolinkPredicate]],
obj: Set[LabeledIRI],
objRelations: Seq[Relation],
g: Set[String]
@@ -120,7 +120,7 @@ object LookupService extends LazyLogging {
case class Result(
queryId: String,
normalizedIds: List[LabeledIRI],
- biolinkPredicates: Map[String, Set[LabeledIRI]],
+ qualifiedBiolinkPredicates: Set[QualifiedBiolinkPredicate],
relations: Seq[Relation],
subjectTriples: Seq[ResultTriple],
objectTriples: Seq[ResultTriple]
@@ -161,7 +161,7 @@ object LookupService extends LazyLogging {
?s ${QueryService.SesameDirectType} ?subj .
?subj ${QueryService.RDFSSubClassOf} ?subjClass .
VALUES ?subjClass { ${subjectIRIs.asValues} } .
-
+
?o ${QueryService.SesameDirectType} ?obj .
?obj ${QueryService.RDFSSubClassOf} ${QueryService.BiolinkNamedThing.iri} .
@@ -175,13 +175,12 @@ object LookupService extends LazyLogging {
}"""
relationsResults <- SPARQLQueryExecutor.runSelectQuery(relationsQuery.toQuery)
preds = relationsResults.map(_.getResource("p").getURI).map(IRI(_))
- biolinkRelationMap <- QueryService.mapRelationsToLabelAndBiolink(preds.toSet)
// We want to group these by object, so we don't return a gazillion predicates for each result.
objectMap = relationsResults.groupBy(_.getResource("obj").getURI)
relations = objectMap.map { case (obj, results) =>
- val predResults = results.map { res =>
+ val predResults = results.flatMap { res =>
val predIRI = res.getResource("p").getURI
val pred = res.getLiteral("pLabel") match {
@@ -189,14 +188,10 @@ object LookupService extends LazyLogging {
case lit => LabeledIRI(predIRI, Set(lit.getString))
}
- val biolinkRes = biolinkRelationMap.get(IRI(predIRI))
- val biolink = biolinkRes match {
- case None => Set[LabeledIRI]()
- case Some((None, iri)) => Set(LabeledIRI(iri.value, Set()))
- case Some((Some(label), iri)) => Set(LabeledIRI(iri.value, Set(label)))
- }
+ val biolinkQualifiedPreds = PredicateMappings.getBiolinkQualifiedPredicates(IRI(predIRI))
- (pred, biolink)
+ // TODO: add support for qualified predicates.
+ biolinkQualifiedPreds.map(bp => (pred, bp.biolinkPredicate, bp.qualifierList))
}
val objLabeled = results
@@ -221,10 +216,13 @@ object LookupService extends LazyLogging {
)
.toSet
+ val qualifiedBiolinkPredicates =
+ predResults.map(kv => (kv._1.iri, QualifiedBiolinkPredicate(kv._2, kv._3))).groupMapReduce(_._1)(p => Set(p._2))(_ ++ _)
+
Relation(
subjLabeled,
predResults.map(_._1).toSet,
- predResults.map(kv => (kv._1.iri, kv._2)).toMap,
+ qualifiedBiolinkPredicates,
objLabeled,
Seq[Relation](), // TODO: recurse!
results.map(_.getResource("g").getURI).toSet
@@ -336,13 +334,11 @@ object LookupService extends LazyLogging {
// Get every relation from this subject.
relations <- getRelations(qualifiedIds.map(_.iri).toSet)
- biolinkPredicates: Map[String, Set[LabeledIRI]] = relations.flatMap(_.biolinkPredicates).foldLeft(Map[String, Set[LabeledIRI]]()) {
- case (map, entry) => map.updated(entry._1, map.getOrElse(entry._1, Set()) ++ entry._2)
- }
+ biolinkPredicates = relations.flatMap(_.qualifiedBiolinkPredicates.values).flatten
} yield Result(
queryId,
qualifiedIds.toList,
- biolinkPredicates,
+ biolinkPredicates.toSet,
relations.toSeq,
subjectTriples.map(fromQuerySolution),
objectTriples.map(fromQuerySolution)
diff --git a/src/main/scala/org/renci/cam/QueryService.scala b/src/main/scala/org/renci/cam/QueryService.scala
index f2a7745e..cd8becfc 100644
--- a/src/main/scala/org/renci/cam/QueryService.scala
+++ b/src/main/scala/org/renci/cam/QueryService.scala
@@ -6,13 +6,14 @@ import io.circe.syntax._
import org.apache.jena.query.QuerySolution
import org.apache.jena.rdf.model.Resource
import org.phenoscape.sparql.SPARQLInterpolation._
-import org.renci.cam.Biolink.{biolinkData, BiolinkData}
+import org.renci.cam.Biolink.{BiolinkData, biolinkData}
import org.renci.cam.HttpClient.HttpClient
import org.renci.cam.SPARQLQueryExecutor.SPARQLCache
import org.renci.cam.Util.IterableSPARQLOps
-import org.renci.cam.domain.{TRAPIAttribute, _}
-import zio.config.{getConfig, ZConfig}
-import zio.{config => _, Has, RIO, Task, UIO, ZIO}
+import org.renci.cam.domain.PredicateMappings.{getBiolinkQualifiedPredicates, mapQueryEdgePredicates}
+import org.renci.cam.domain._
+import zio.config.{ZConfig, getConfig}
+import zio.{Has, RIO, Task, UIO, ZIO, config => _}
import java.math.BigInteger
import java.nio.charset.StandardCharsets
@@ -21,6 +22,8 @@ import scala.jdk.CollectionConverters._
object QueryService extends LazyLogging {
+ val INNER_LIMIT_MULTIPLIER = 100
+
val ProvWasDerivedFrom: IRI = IRI("http://www.w3.org/ns/prov#wasDerivedFrom")
val RDFSSubClassOf: IRI = IRI("http://www.w3.org/2000/01/rdf-schema#subClassOf")
@@ -44,6 +47,7 @@ object QueryService extends LazyLogging {
val SlotMapping: IRI = IRI("http://cam.renci.org/biolink_slot")
val BiolinkNamedThing: BiolinkClass = BiolinkClass("NamedThing", IRI(s"${BiolinkTerm.namespace}NamedThing"))
+ val BiolinkRelatedTo: BiolinkPredicate = BiolinkPredicate("related_to")
/* Hints used to optimize the query (see https://github.com/blazegraph/database/wiki/QueryHints for details). */
@@ -188,8 +192,7 @@ object QueryService extends LazyLogging {
* @see
* org.renci.cam.QueryService#getTRAPIEdges
*/
- def generateTRAPIEdges(results: List[Result], relationsToLabelAndBiolinkPredicate: Map[IRI, (Option[String], IRI)])
- : RIO[ZConfig[AppConfig] with ZConfig[BiolinkData], Map[String, TRAPIEdge]] =
+ def generateTRAPIEdges(results: List[Result]): RIO[ZConfig[AppConfig] with ZConfig[BiolinkData], Map[String, TRAPIEdge]] =
for {
// Get some data we need to generate the TRAPI edges.
biolinkData <- biolinkData
@@ -207,50 +210,52 @@ object QueryService extends LazyLogging {
.orElseFail(new Exception("could not get biolink:InformationResource"))
// Generate the edges.
- edges = results.flatMap(result =>
- for {
- key <- result.edges.keys
-
- // Generate the pieces of this TRAPIEdge.
- iri = result.edges(key)
- labelAndBiolinkPredicate = relationsToLabelAndBiolinkPredicate.get(iri)
- biolinkPredicateIRI = labelAndBiolinkPredicate.map(_._2)
- biolinkPred = biolinkData.predicates.find(a => biolinkPredicateIRI.forall(_.equals(a.iri)))
- queryEdge = result.queryGraph.edges(key)
- subjectIRI = result.nodes(queryEdge.subject)
- objectIRI = result.nodes(queryEdge.`object`)
- derivedFroms = result.derivedFrom
-
- // Generate the attributes for this edge.
- aggregatorKSAttribute = TRAPIAttribute(Some("infores:cam-kp"),
- aggregatorKS.iri,
- None,
- List("infores:cam-kp"),
- Some(infoResBiolinkClass.iri),
- Some(appConfig.location),
- None,
- None)
- originalKnowledgeSources = derivedFroms.map {
- case df @ ctd if ctd.value.contains("ctdbase.org") => (df, "infores:ctd")
- case df => (df, "infores:go-cam")
- }
- originalKSAttributes = originalKnowledgeSources.map { case (derivedFrom, inforesKS) =>
- TRAPIAttribute(Some("infores:cam-kp"),
- originalKS.iri,
- None,
- List(inforesKS),
- Some(infoResBiolinkClass.iri),
- Some(derivedFrom.value),
- None,
- None)
- }
- attributes = aggregatorKSAttribute +: originalKSAttributes.toList
+ edges = results
+ .flatMap(result =>
+ for {
+ key <- result.edges.keys
+
+ // Generate the pieces of this TRAPIEdge.
+ relationIRI = result.edges(key)
+ queryEdge = result.queryGraph.edges(key)
+ subjectIRI = result.nodes(queryEdge.subject)
+ objectIRI = result.nodes(queryEdge.`object`)
+ derivedFroms = result.derivedFrom
+
+ // Generate the attributes for this edge.
+ aggregatorKSAttribute = TRAPIAttribute(Some("infores:cam-kp"),
+ aggregatorKS.iri,
+ None,
+ List("infores:cam-kp"),
+ Some(infoResBiolinkClass.iri),
+ Some(appConfig.location),
+ None,
+ None)
+ originalKnowledgeSources = derivedFroms.map {
+ case df @ ctd if ctd.value.contains("ctdbase.org") => (df, "infores:ctd")
+ case df => (df, "infores:go-cam")
+ }
+ originalKSAttributes = originalKnowledgeSources.map { case (derivedFrom, inforesKS) =>
+ TRAPIAttribute(Some("infores:cam-kp"),
+ originalKS.iri,
+ None,
+ List(inforesKS),
+ Some(infoResBiolinkClass.iri),
+ Some(derivedFrom.value),
+ None,
+ None)
+ }
+ attributes = aggregatorKSAttribute +: originalKSAttributes.toList
- // Generate the TRAPIEdge and its edge key.
- trapiEdge = TRAPIEdge(biolinkPred, subjectIRI, objectIRI, Some(attributes))
- // edgeKey = getTRAPIEdgeKey(queryEdge.subject, biolinkPred, queryEdge.`object`)
- edgeKey = result.getEdgeKey(key)
- } yield (edgeKey, trapiEdge))
+ // Generate the TRAPIEdge and its edge key.
+ biolinkPreds = getBiolinkQualifiedPredicates(relationIRI)
+ trapiEdges = biolinkPreds.zipWithIndex.map { case (qualifiedPred, index) =>
+ (result.getEdgeKey(key) + "_pred_" + index,
+ TRAPIEdge(Some(qualifiedPred.biolinkPredicate), subjectIRI, objectIRI, Some(attributes), qualifiedPred.asQualifierList))
+ }
+ // edgeKey = getTRAPIEdgeKey(queryEdge.subject, biolinkPred, queryEdge.`object`)
+ } yield trapiEdges)
+ .flatten
} yield edges.toMap
/** Generate TRAPI results from a list of Results.
@@ -263,33 +268,70 @@ object QueryService extends LazyLogging {
* @return
* An UIO that generates the list of TRAPI Results.
*/
- def generateTRAPIResults(results: List[Result]): List[TRAPIResult] =
+ def generateTRAPIResults(results: List[Result], edges: Map[String, TRAPIEdge]): List[TRAPIResult] =
for {
result <- results
nodeBindings = result.nodes
- .groupMap(_._1)(p =>
- TRAPINodeBinding(
- id = p._2,
- query_id = result.queryGraph.nodes.get(p._1) match {
- // If no nodes IDs were provided, query_id MUST be null or absent.
- case None => None
- case Some(TRAPIQueryNode(None, _, _, _)) => None
- case Some(TRAPIQueryNode(Some(List()), _, _, _)) =>
- None
- case Some(TRAPIQueryNode(Some(ids), _, _, _)) =>
- result.originalNodes.get(p._1) match {
- // According to the TRAPI 1.3 spec, we SHOULD NOT provide a query_id if it is the
- // same as the id.
- case Some(p._2) => None
- case x => x
- }
+ .groupMap(_._1) { p =>
+ val node_id = p._1
+ val node_iri = p._2
+
+ logger.info(f"Searching through nodes: ${result.queryGraph.nodes}")
+ logger.info(f"And then translating using: ${result.originalNodes}")
+
+ val nb = TRAPINodeBinding(
+ id = node_iri,
+ query_id = {
+ logger.info(
+ f"Looking for node binding for ${node_id} (${node_iri}) using query graph node ${result.queryGraph.nodes.get(node_id)}")
+
+ val query_id = result.queryGraph.nodes.get(node_id) match {
+ // If no nodes IDs were provided, query_id MUST be null or absent.
+ case None => None
+ case Some(TRAPIQueryNode(None, _, _, _)) => None
+ case Some(TRAPIQueryNode(Some(List()), _, _, _)) =>
+ None
+ case Some(TRAPIQueryNode(Some(ids), _, _, _)) =>
+ logger.info(f"Translating from ${node_iri} to ${ids} with original nodes: ${result.originalNodes.get(node_id)}")
+
+ val query_id = result.originalNodes.get(node_id) match {
+ // According to the TRAPI 1.3 spec, we SHOULD NOT provide a query_id if it is the
+ // same as the id.
+ case Some(ni) if ni == node_iri => None
+ case x => x
+ }
+
+ logger.info(f"Query ID is ${query_id}")
+
+ query_id
+ }
+ query_id
}
- ))
+ )
+
+ logger.info(f"TRAPINodeBinding generated for result ${result.index}: ${nb}")
+
+ nb
+ }
.map(p => (p._1, p._2.toList))
- edgeBindings = result.edges.keys
- .map(key => (key, List(TRAPIEdgeBinding(result.getEdgeKey(key)))))
- .toMap
+
+ edgeBindings = result.edges.keys.map { key =>
+ // This is a pretty dumb way to do this, but it should be error-proof.
+ val fullEdgeId = result.getEdgeKey(key)
+ val allPreds = edges.keySet.flatMap { p =>
+ val rMatchPreds = """^(.*)_pred_(\d+)$""".r
+ p match {
+ case rMatchPreds(edgeId, _) if edgeId == fullEdgeId => Some(p)
+ case _ => None
+ }
+ }
+
+ if (allPreds.isEmpty)
+ (key, List(TRAPIEdgeBinding(fullEdgeId)))
+ else
+ (key, allPreds.map(pred => TRAPIEdgeBinding(pred)).toList)
+ }.toMap
} yield TRAPIResult(node_bindings = nodeBindings, edge_bindings = edgeBindings)
/** Query the triplestore with a TRAPIQuery and return a TRAPIMessage with the result.
@@ -309,6 +351,13 @@ object QueryService extends LazyLogging {
_.constraints.getOrElse(List())) ++ submittedQueryGraph.edges.values.flatMap(_.attribute_constraints.getOrElse(List()))
val allQualifierConstraints = submittedQueryGraph.edges.values.flatMap(_.qualifier_constraints.getOrElse(List()))
+ // Try mapping all predicates. If any fail, we should produce appropriate errors.
+ // TODO: we shouldn't just discard these mappings! We should use them.
+ val unmappedEdges = submittedQueryGraph.edges.flatMap { case (key, edge) =>
+ val mappedPreds = mapQueryEdgePredicates(edge.predicates, edge.qualifier_constraints)
+ if (mappedPreds.isEmpty) Seq((key, edge)) else Seq()
+ }
+
if (allAttributeConstraints.nonEmpty) {
ZIO.succeed(
TRAPIResponse(
@@ -327,22 +376,28 @@ object QueryService extends LazyLogging {
)
)
)
- } else if (allQualifierConstraints.nonEmpty) {
- // Are there any qualifier constraints? If so, we can't match them, so we should return an empty list of results.
+ } else if (unmappedEdges.nonEmpty) {
+ // Generate a list of all the edges that couldn't be mapped.
+ val errorList = unmappedEdges.map { case (key, edge) =>
+ val warning = s"Edge ${key} could not be mapped to a predicate, and so cannot be matched: ${edge}"
+ logger.warn(warning)
+
+ LogEntry(
+ Some(java.time.Instant.now().toString),
+ Some("ERROR"),
+ Some("UnsupportedEdge"),
+ Some(warning)
+ )
+ }
+
+ // Are there any unmapped edges? If so, we should return them as errors.
ZIO.succeed(
TRAPIResponse(
emptyTRAPIMessage,
- Some("Success"),
+ Some("ERROR"),
None,
Some(
- List(
- LogEntry(
- Some(java.time.Instant.now().toString),
- Some("WARNING"),
- Some("UnsupportedQualifierConstraint"),
- Some(s"The following qualifier constraints are not supported: ${allQualifierConstraints}")
- )
- )
+ errorList.toList
)
)
)
@@ -354,16 +409,12 @@ object QueryService extends LazyLogging {
// Prepare the query graph for processing.
queryGraph = enforceQueryEdgeTypes(submittedQueryGraph, biolinkData.predicates)
-
- // Generate the relationsToLabelAndBiolinkPredicate.
- allPredicatesInQuery = queryGraph.edges.values.flatMap(_.predicates.getOrElse(Nil)).to(Set)
- predicatesToRelations <- mapQueryBiolinkPredicatesToRelations(allPredicatesInQuery)
- allRelationsInQuery = predicatesToRelations.values.flatten.to(Set)
- relationsToLabelAndBiolinkPredicate <- mapRelationsToLabelAndBiolink(allRelationsInQuery)
+ _ = logger.debug(s"Transformed the submitted query graph: ${submittedQueryGraph}")
+ _ = logger.debug(s"Submitted query graph transformed to: ${queryGraph}")
// Generate query solutions.
- _ = logger.debug(s"findInitialQuerySolutions($queryGraph, $predicatesToRelations, $limit)")
- initialQuerySolutions <- findInitialQuerySolutions(queryGraph, predicatesToRelations, limit)
+ _ = logger.debug(s"findInitialQuerySolutions($queryGraph, $limit)")
+ initialQuerySolutions <- findInitialQuerySolutions(queryGraph, limit)
results = initialQuerySolutions.zipWithIndex.map { case (qs, index) =>
Result.fromQuerySolution(qs, index, queryGraph)
}
@@ -372,9 +423,9 @@ object QueryService extends LazyLogging {
// From the results, generate the TRAPI nodes, edges and results.
nodes <- generateTRAPINodes(results)
_ = logger.debug(s"Nodes: $nodes")
- edges <- generateTRAPIEdges(results, relationsToLabelAndBiolinkPredicate)
+ edges <- generateTRAPIEdges(results)
_ = logger.debug(s"Edges: $edges")
- trapiResults = generateTRAPIResults(results)
+ trapiResults = generateTRAPIResults(results, edges)
_ = logger.debug(s"Results: $trapiResults")
} yield TRAPIResponse(
TRAPIMessage(Some(queryGraph), Some(TRAPIKnowledgeGraph(nodes, edges)), Some(trapiResults.distinct)),
@@ -384,6 +435,7 @@ object QueryService extends LazyLogging {
)
}
+ /*
def oldRun(limit: Int, includeExtraEdges: Boolean, submittedQueryGraph: TRAPIQueryGraph)
: RIO[ZConfig[AppConfig] with HttpClient with Has[BiolinkData] with Has[SPARQLCache], TRAPIMessage] =
for {
@@ -395,7 +447,7 @@ object QueryService extends LazyLogging {
allRelationsInQuery = predicatesToRelations.values.flatten.to(Set)
relationsToLabelAndBiolinkPredicate: Map[IRI, (Option[String], IRI)] <- mapRelationsToLabelAndBiolink(allRelationsInQuery)
_ = logger.warn(s"findInitialQuerySolutions($queryGraph, $predicatesToRelations, $limit)")
- initialQuerySolutions <- findInitialQuerySolutions(queryGraph, predicatesToRelations, limit)
+ initialQuerySolutions <- findInitialQuerySolutions(queryGraph, limit)
_ = logger.warn(s"Initial query solutions: ${initialQuerySolutions.length} (limit: $limit): $initialQuerySolutions")
_ = logger.warn(s"extractCoreTriples($initialQuerySolutions, $queryGraph)")
solutionTriples = extractCoreTriples(initialQuerySolutions, queryGraph)
@@ -441,6 +493,7 @@ object QueryService extends LazyLogging {
_ = logger.warn(s"results: $results (length: ${results.length}, limit: $limit)")
_ = logger.warn(s"results distinct: ${results.distinct} (length: ${results.distinct.length}, limit: $limit)")
} yield TRAPIMessage(Some(queryGraph), Some(TRAPIKnowledgeGraph(initialKGNodes, initialKGEdges)), Some(results.distinct))
+ */
/** Construct and execute a SPARQL query based on the provided query graph in the triplestore.
*
@@ -456,15 +509,17 @@ object QueryService extends LazyLogging {
* org.renci.cam.QueryService#Result for a more human-readable version of the query solution.
*/
def findInitialQuerySolutions(queryGraph: TRAPIQueryGraph,
- predicatesToRelations: Map[BiolinkPredicate, Set[IRI]],
limit: Int): ZIO[ZConfig[AppConfig] with HttpClient, Throwable, List[QuerySolution]] = {
+
val queryEdgeSparql = queryGraph.edges.map { case (queryEdgeID, queryEdge) =>
- val relationsForEdge = queryEdge.predicates.getOrElse(Nil).flatMap(predicatesToRelations.getOrElse(_, Set.empty)).to(Set)
- val predicatesQueryText = relationsForEdge.asSPARQLList
val edgeIDVar = Var(queryEdgeID)
val edgeSourceVar = Var(queryEdge.subject)
val edgeTargetVar = Var(queryEdge.`object`)
- val predicatesValuesClause = sparql""" FILTER( $edgeIDVar IN ( $predicatesQueryText ) )"""
+ val predicatesValuesClause = {
+ // To calculate this, we need to map every predicate using the predicate mapping information.
+ val mappedPredicates = mapQueryEdgePredicates(queryEdge.predicates, queryEdge.qualifier_constraints)
+ sparql""" FILTER( $edgeIDVar IN ( ${mappedPredicates.asSPARQLList} ) )"""
+ }
val subjectNode = queryGraph.nodes(queryEdge.subject)
val subjectNodeValuesClauses = getNodeValuesClauses(subjectNode.ids, subjectNode.categories, edgeSourceVar)
val objectNode = queryGraph.nodes(queryEdge.`object`)
@@ -483,6 +538,8 @@ object QueryService extends LazyLogging {
val nodesToDirectTypes = getNodesToDirectTypes(queryGraph.nodes)
val edgePatterns = queryEdgeSparql.fold(sparql"")(_ + _)
val limitSparql = if (limit > 0) sparql" LIMIT $limit" else sparql""
+ val innerLimit = INNER_LIMIT_MULTIPLIER * limit
+ val innerLimitSparql = if (limit > 0) sparql" LIMIT $innerLimit" else sparql""
val queryString =
sparql"""SELECT DISTINCT $typeProjections
(GROUP_CONCAT(DISTINCT ?g; SEPARATOR='|') AS ?graphs)
@@ -494,7 +551,7 @@ object QueryService extends LazyLogging {
SELECT $nodeProjections ?g
WHERE {
$edgePatterns
- }
+ } ${innerLimitSparql}
}
$BigDataQueryHintPrior $BigDataQueryHintRunFirst true .
}
@@ -574,8 +631,8 @@ object QueryService extends LazyLogging {
def enforceQueryEdgeTypes(queryGraph: TRAPIQueryGraph, biolinkPredicates: List[BiolinkPredicate]): TRAPIQueryGraph = {
val improvedEdgeMap = queryGraph.edges.map { case (edgeID, edge) =>
val newPredicates = edge.predicates match {
- case None => Some(List(BiolinkPredicate("related_to")))
- case Some(Nil) => Some(List(BiolinkPredicate("related_to")))
+ case None => Some(List(BiolinkRelatedTo))
+ case Some(Nil) => Some(List(BiolinkRelatedTo))
case predicates => predicates
}
val filteredPredicates = newPredicates.map(_.filter(pred => biolinkPredicates.contains(pred)))
@@ -819,40 +876,4 @@ object QueryService extends LazyLogging {
nodeMap
}
- // TODO:
- // - Change this to cached queries (see mapQueryBiolinkPredicatesToRelations for example)
- def mapRelationsToLabelAndBiolink(relations: Set[IRI]): RIO[ZConfig[AppConfig] with HttpClient, Map[IRI, (Option[String], IRI)]] = {
- final case class RelationInfo(relation: IRI, biolinkSlot: IRI, label: Option[String])
- val queryText = sparql"""
- SELECT DISTINCT ?relation ?biolinkSlot ?label
- WHERE {
- VALUES ?relation { ${relations.asValues} }
- ?relation $SlotMapping ?biolinkSlot .
- ?biolinkSlot a $BiolinkMLSlotDefinition .
- OPTIONAL { ?relation $RDFSLabel ?label . }
- FILTER NOT EXISTS {
- ?relation $SlotMapping ?other .
- ?other $BiolinkMLIsA+/$BiolinkMLMixins* ?biolinkSlot .
- }
- }"""
- SPARQLQueryExecutor.runSelectQueryAs[RelationInfo](queryText.toQuery).map { res =>
- res.groupMap(_.relation)(info => (info.label, info.biolinkSlot)).map { case (relationIRI, infos) => relationIRI -> infos.head }
- }
- }
-
- def mapQueryBiolinkPredicatesToRelations(
- predicates: Set[BiolinkPredicate]): RIO[ZConfig[AppConfig] with HttpClient with Has[SPARQLCache], Map[BiolinkPredicate, Set[IRI]]] = {
- final case class Predicate(biolinkPredicate: BiolinkPredicate, predicate: IRI)
- val queryText = sparql"""
- SELECT DISTINCT ?biolinkPredicate ?predicate WHERE {
- VALUES ?biolinkPredicate { ${predicates.asValues} }
- ?predicate $SlotMapping ?biolinkPredicate .
- FILTER EXISTS { ?s ?predicate ?o }
- $BigDataQueryHintQuery $BigDataQueryHintFilterExists "SubQueryLimitOne"
- }"""
- for {
- predicates <- SPARQLQueryExecutor.runSelectQueryWithCacheAs[Predicate](queryText.toQuery)
- } yield predicates.to(Set).groupMap(_.biolinkPredicate)(_.predicate)
- }
-
}
diff --git a/src/main/scala/org/renci/cam/Server.scala b/src/main/scala/org/renci/cam/Server.scala
index 3f1ff8fd..4d9a8ec9 100644
--- a/src/main/scala/org/renci/cam/Server.scala
+++ b/src/main/scala/org/renci/cam/Server.scala
@@ -155,6 +155,9 @@ object Server extends App with LazyLogging {
.toYaml
openAPIJson <- ZIO.fromEither(io.circe.yaml.parser.parse(openAPI))
info: String =
+ // TODO: note that the development URL is a reference to a file on a branch. It should be replaced with
+ // a file on a tag or something more stable.
+ // TODO: we should figure out how to separate URLs for development, production, etc.
s"""
{
"info": {
@@ -166,7 +169,12 @@ object Server extends App with LazyLogging {
},
"x-trapi": {
"version": "${appConfig.trapiVersion}",
- "operations": [ "lookup" ]
+ "operations": [ "lookup" ],
+ "test_data_location": {
+ "default": {
+ "url": "https://raw.githubusercontent.com/ExposuresProvider/cam-kp-api/generate-test-data/src/main/resources/sri-testing.json"
+ }
+ }
}
}
}
diff --git a/src/main/scala/org/renci/cam/domain/PredicateMappings.scala b/src/main/scala/org/renci/cam/domain/PredicateMappings.scala
new file mode 100644
index 00000000..965a9434
--- /dev/null
+++ b/src/main/scala/org/renci/cam/domain/PredicateMappings.scala
@@ -0,0 +1,221 @@
+package org.renci.cam.domain
+
+import io.circe.generic.auto._
+import org.phenoscape.sparql.SPARQLInterpolation.SPARQLStringContext
+import org.renci.cam.HttpClient.HttpClient
+import org.renci.cam.LookupService.LabeledIRI
+import org.renci.cam.SPARQLQueryExecutor.SPARQLCache
+import org.renci.cam.util.GenerateBiolinkPredicateMappings.logger
+import org.renci.cam.{AppConfig, QueryService, SPARQLQueryExecutor}
+import zio.blocking.{blocking, Blocking}
+import zio.config.{getConfig, ZConfig}
+import zio.stream.ZStream
+import zio.{Has, RIO, Task, ZIO}
+
+import java.io.{File, FileInputStream}
+import scala.io.Source
+
+object PredicateMappings {
+
+ case class PredicateMapping(
+ predicate: LabeledIRI,
+ biolinkPredicate: Option[BiolinkPredicate],
+ biolinkQualifiers: Option[TRAPIQualifierConstraint]
+ )
+
+ /** Retrieve the list of predicates from the triplestore, along with Biolink mappings where available.
+ *
+ * @return
+ * A sequence of PredicateMappings from the triplestore.
+ */
+ def getPredicatesFromSPARQL: RIO[ZConfig[AppConfig] with HttpClient with Has[SPARQLCache], Seq[PredicateMapping]] = {
+ val predicateQuery =
+ sparql"""SELECT DISTINCT ?pred ?pred_label ?biolink_slot WHERE {
+ OPTIONAL { ?pred ${QueryService.RDFSLabel} ?pred_label } .
+ OPTIONAL { ?pred ${QueryService.SlotMapping} ?biolink_slot }
+
+ {
+ SELECT DISTINCT ?pred WHERE { ?s ?pred ?o }
+ }
+ }""".toQuery
+
+ for {
+ result <- SPARQLQueryExecutor.runSelectQuery(predicateQuery)
+ preds <- ZStream
+ .fromIterable(result)
+ .map(
+ { qs =>
+ val predURI = qs.getResource("pred").getURI
+ val predLabel = qs.getLiteral("pred_label").getString
+ val biolinkSlot = qs.getResource("biolink_slot")
+
+ if (biolinkSlot == null) {
+ logger.warn(f"No Biolink mapping known for predicate ${predURI} (${predLabel})")
+ PredicateMapping(
+ LabeledIRI(predURI, Set(predLabel)),
+ None,
+ None
+ )
+ } else {
+ val biolinkURI = biolinkSlot.getURI
+ val shorthand = biolinkURI.replaceFirst(raw"^https://w3id.org/biolink/vocab/", "")
+
+ PredicateMapping(
+ LabeledIRI(predURI, Set(predLabel)),
+ Some(BiolinkPredicate(shorthand, IRI(biolinkURI))),
+ None
+ )
+ }
+ }
+ )
+ .runCollect
+ } yield preds
+ }
+
+ /* PREDICATE MAPPING.
+
+ For Biolink v3, the TRAPI developers created a file of predicate mappings. We use that to expand the predicates
+ currently in the
+
+ For future versions, we will either continue to rely on that file, maintain our own copy of those mappings,
+ or replace this with some other mechanism for predicate mapping.
+ */
+
+ /** A case class for predicate mappings. */
+ case class PredicateMappingRow(
+ `mapped predicate`: String,
+ `object aspect qualifier`: Option[String],
+ `object direction qualifier`: Option[String],
+ predicate: String,
+ `qualified predicate`: Option[String],
+ `exact matches`: Option[Set[String]]
+ ) {
+ def biolinkPredicate: BiolinkPredicate = BiolinkPredicate(predicate.replace(' ', '_'))
+
+ def biolinkMappedPredicate: BiolinkPredicate = BiolinkPredicate(`mapped predicate`.replace(' ', '_'))
+
+ def qualifiers: Seq[TRAPIQualifier] = (`object aspect qualifier` match {
+ case Some(aspect: String) =>
+ List(TRAPIQualifier(qualifier_type_id = "biolink:object_aspect_qualifier", qualifier_value = aspect.replace(' ', '_')))
+ case _ => List()
+ }) ++ (`object direction qualifier` match {
+ case Some(direction: String) =>
+ List(TRAPIQualifier(qualifier_type_id = "biolink:object_direction_qualifier", qualifier_value = direction.replace(' ', '_')))
+ case _ => List()
+ }) ++ (`qualified predicate` match {
+ case Some(qualified_predicate: String) =>
+ List(
+ TRAPIQualifier(qualifier_type_id = "biolink:qualified_predicate",
+ qualifier_value = BiolinkPredicate(qualified_predicate.replace(' ', '_')).withBiolinkPrefix)
+ )
+ case _ => List()
+ })
+
+ def qualifierConstraint: TRAPIQualifierConstraint = TRAPIQualifierConstraint(qualifier_set = qualifiers.toList)
+
+ def qualifierConstraintList = List(qualifierConstraint)
+ }
+
+ case class PredicateMappings(
+ `predicate mappings`: List[PredicateMappingRow]
+ )
+
+ /** To initialize this object, we need to download and parse the predicate_mapping.yaml file from the Biolink model, which needs to be
+ * downloaded to the package resources (src/main/resources) from
+ * https://github.com/biolink/biolink-model/blob/${biolinkVersion}/predicate_mapping.yaml (the raw version is available from
+ * https://raw.githubusercontent.com/biolink/biolink-model/v3.2.1/predicate_mapping.yaml)
+ */
+ val getPredicateMappingsFromGitHub: RIO[ZConfig[AppConfig] with Blocking, List[PredicateMappingRow]] =
+ for {
+ appConfig <- getConfig[AppConfig]
+ predicateMappingText <- blocking(
+ Task.effect(
+ Source
+ .fromURL(s"https://raw.githubusercontent.com/biolink/biolink-model/${appConfig.biolinkVersion}/predicate_mapping.yaml")
+ .getLines()
+ .mkString("\n")
+ )
+ )
+ predicateMappingsYaml <- ZIO.fromEither(io.circe.yaml.parser.parse(predicateMappingText))
+ predicateMappings <- ZIO.fromEither(predicateMappingsYaml.as[PredicateMappings])
+ } yield predicateMappings.`predicate mappings`
+
+ /** Compares two qualifier lists. */
+ def compareQualifierConstraints(ql1: List[TRAPIQualifier], ql2: List[TRAPIQualifier]): Boolean = {
+
+ val set1 = ql1.map(q => (q.qualifier_value, q.qualifier_type_id)).toSet
+ val set2 = ql2.map(q => (q.qualifier_value, q.qualifier_type_id)).toSet
+
+ (set1 == set2)
+ }
+
+ /** Load the predicates data so we can use it subsequently. */
+ // TODO: there's some hacky code here for handling the case where biolink/predicates.json doesn't exist. It should
+ // generally always exist, since it's included in the repository. But we should still test this so it's better.
+ // TODO: Source.fromResource() is probably better here.
+ val predicateMappingsStream =
+ if (PredicateMappings.getClass.getResourceAsStream("/biolink/predicates.json") != null)
+ PredicateMappings.getClass.getResourceAsStream("/biolink/predicates.json")
+ else
+ new FileInputStream(new File("src/main/resources/biolink/predicates.json"))
+
+ val predicatesDataAsString =
+ Source
+ .fromInputStream(predicateMappingsStream)
+ .getLines()
+ .mkString("\n")
+
+ val predicatesData =
+ if (predicateMappingsStream == null) Seq()
+ else io.circe.parser.parse(predicatesDataAsString).toTry.get.as[Seq[PredicateMapping]].toTry.get
+
+ /** Convert predicate data into a list of QualifiedBiolinkPredicates in case anyone wants a list of all the predicates we understand.
+ */
+ val qualifiedPredicatesData: Seq[QualifiedBiolinkPredicate] = predicatesData
+ .flatMap {
+ case PredicateMapping(_, Some(biolinkPredicate), None) => Some(QualifiedBiolinkPredicate(biolinkPredicate))
+ case PredicateMapping(_, Some(biolinkPredicate), Some(TRAPIQualifierConstraint(qualifierList))) =>
+ Some(QualifiedBiolinkPredicate(biolinkPredicate, qualifierList))
+ case _ => None
+ }
+
+ def mapQueryEdgePredicates(predicates: Option[List[BiolinkPredicate]],
+ qualifier_constraints: Option[List[TRAPIQualifierConstraint]]): Set[IRI] = {
+ // predicatesData consists of unique mappings between relations and (biolinkPredicate, biolinkQualifier) pairs.
+ val biolinkPredicates = predicates.toList.flatten.toSet
+ val qualifierConstraint = qualifier_constraints.toList.flatten.flatMap(_.qualifier_set)
+
+ logger.debug(s"Searching for ${predicates} with ${qualifier_constraints} in ${predicatesData}")
+
+ val relations = predicatesData.filter {
+ case pred @ PredicateMapping(_, Some(biolinkPredicate), qualifierOpt) =>
+ logger.debug(
+ f"Check if ${biolinkPredicates} contains ${biolinkPredicate} from ${pred}: ${biolinkPredicates.contains(biolinkPredicate)}")
+ if (!biolinkPredicates.contains(biolinkPredicate)) false
+ else {
+ // qualifierOpt should match qualifierConstraint, whether empty or not.
+ qualifierOpt match {
+ case None => qualifierConstraint.isEmpty
+ case Some(constraint) => compareQualifierConstraints(qualifierConstraint, constraint.qualifier_set)
+ }
+ }
+ case _ => false
+ }
+
+ relations.map(pred => IRI(pred.predicate.iri)).toSet
+ }
+
+ def getBiolinkQualifiedPredicates(relationIRI: IRI): Seq[QualifiedBiolinkPredicate] =
+ predicatesData.flatMap {
+ case PredicateMapping(relation, Some(biolinkPredicate), qualifierOpt) =>
+ if (relation.iri != relationIRI.value) None
+ else
+ qualifierOpt match {
+ case None => Some(QualifiedBiolinkPredicate(biolinkPredicate, List()))
+ case Some(constraint) if constraint.qualifier_set.isEmpty => Some(QualifiedBiolinkPredicate(biolinkPredicate, List()))
+ case Some(constraint) => Some(QualifiedBiolinkPredicate(biolinkPredicate, constraint.qualifier_set))
+ }
+ case _ => None
+ }
+
+}
diff --git a/src/main/scala/org/renci/cam/domain/package.scala b/src/main/scala/org/renci/cam/domain/package.scala
index eff4e5f9..3659a449 100644
--- a/src/main/scala/org/renci/cam/domain/package.scala
+++ b/src/main/scala/org/renci/cam/domain/package.scala
@@ -138,6 +138,26 @@ package object domain {
attribute_constraints: Option[List[TRAPIAttributeConstraint]] = None,
qualifier_constraints: Option[List[TRAPIQualifierConstraint]] = None)
+ /** A case class representing a combination of a BiolinkPredicate and the qualifiers that qualify it.
+ *
+ * At some point we might need to add attributes to this, but not at the moment.
+ *
+ * @param biolinkPredicate
+ * A Biolink predicate
+ * @param qualifierList
+ * A list of qualifiers that qualify them.
+ */
+ final case class QualifiedBiolinkPredicate(biolinkPredicate: BiolinkPredicate, qualifierList: List[TRAPIQualifier] = List.empty) {
+
+ val asQualifierList: Option[List[TRAPIQualifier]] = if (qualifierList.isEmpty) None else Some(qualifierList)
+
+ val asQualifierConstraint: Option[List[TRAPIQualifierConstraint]] =
+ if (qualifierList.isEmpty) None
+ else
+ Some(List(TRAPIQualifierConstraint(qualifierList)))
+
+ }
+
final case class TRAPIAttributeConstraint(id: IRI,
name: String,
not: Option[Boolean],
diff --git a/src/main/scala/org/renci/cam/util/GenerateBiolinkPredicateMappings.scala b/src/main/scala/org/renci/cam/util/GenerateBiolinkPredicateMappings.scala
new file mode 100644
index 00000000..92e4ce9d
--- /dev/null
+++ b/src/main/scala/org/renci/cam/util/GenerateBiolinkPredicateMappings.scala
@@ -0,0 +1,143 @@
+package org.renci.cam.util
+
+import com.typesafe.scalalogging.{LazyLogging, Logger}
+import io.circe.generic.auto._
+import io.circe.syntax._
+import org.renci.cam.LookupService.LabeledIRI
+import org.renci.cam.domain.{BiolinkPredicate, TRAPIQualifier, TRAPIQualifierConstraint}
+import org.renci.cam.domain.PredicateMappings.{getPredicateMappingsFromGitHub, getPredicatesFromSPARQL, PredicateMapping, PredicateMappingRow}
+import org.renci.cam.{AppConfig, HttpClient, SPARQLQueryExecutor}
+import zio._
+import zio.config.ZConfig
+import zio.config.typesafe.TypesafeConfig
+
+import java.nio.file.{Files, Paths}
+
+/** This class can generate Biolink predicate mappings in the src/main/resources/biolink directory, based on two input sources:
+ * 1. It queries the triplestore to download the list of all predicates in use in the triplestore, along with Biolink mappings where
+ * available.
+ *
+ * 2. It downloads the predicate mapping file from a specific Biolink model version, and uses that to map single predicates to
+ * predicate+qualifier combinations.
+ *
+ * It generates a single JSON document that can be used to handle all our predicate mapping needs:
+ * 1. Map a Biolink predicate with zero or more qualifiers to a set of triplestore predicates.
+ *
+ * 2. Map a triplestore predicate to a Biolink predicate with zero or more qualifiers.
+ *
+ * It also generates warnings for predicates not mapped.
+ */
+object GenerateBiolinkPredicateMappings extends zio.App with LazyLogging {
+ override lazy val logger: Logger = Logger(GenerateBiolinkPredicateMappings.getClass.getSimpleName);
+
+ /* Manual annotations. */
+ val manualPredicateMappings = Seq(
+ PredicateMapping(
+ predicate = LabeledIRI("http://purl.obolibrary.org/obo/RO_0002450", Set("directly positively regulates activity of")),
+ biolinkPredicate = Some(BiolinkPredicate("affects")),
+ biolinkQualifiers = Some(
+ TRAPIQualifierConstraint(
+ List(
+ TRAPIQualifier("biolink:object_aspect_qualifier", "activity_or_abundance"),
+ TRAPIQualifier("biolink:object_direction_qualifier", "increased")
+ ))
+ )
+ ),
+ PredicateMapping(
+ predicate = LabeledIRI("http://purl.obolibrary.org/obo/RO_0002449", Set("directly negatively regulates activity of")),
+ biolinkPredicate = Some(BiolinkPredicate("affects")),
+ biolinkQualifiers = Some(
+ TRAPIQualifierConstraint(
+ List(
+ TRAPIQualifier("biolink:object_aspect_qualifier", "activity_or_abundance"),
+ TRAPIQualifier("biolink:object_direction_qualifier", "decreased")
+ ))
+ )
+ ),
+ PredicateMapping(
+ predicate = LabeledIRI("http://purl.obolibrary.org/obo/RO_0002305", Set("causally upstream of, negative effect")),
+ biolinkPredicate = Some(BiolinkPredicate("regulates")),
+ biolinkQualifiers = Some(
+ TRAPIQualifierConstraint(
+ List(
+ TRAPIQualifier("biolink:object_direction_qualifier", "downregulated")
+ ))
+ )
+ )
+ )
+
+ /** Where should we save the predicates.json files? */
+ val PredicateJsonFilePath = Paths.get("src/main/resources/biolink/predicates.json")
+
+ override def run(args: List[String]): URIO[zio.ZEnv, ExitCode] = {
+ def transformPredicateWithMappedPredicateInfo(pred: PredicateMapping, mp: PredicateMappingRow): PredicateMapping = {
+ val predReplaced = PredicateMapping(
+ pred.predicate,
+ Some(mp.biolinkPredicate),
+ Some(mp.qualifierConstraint)
+ )
+
+ logger.error(f"Replacing ${pred} with ${predReplaced} with information from ${mp}")
+
+ predReplaced
+ }
+
+ val program = for {
+ preds <- getPredicatesFromSPARQL
+ mappedPredicates <- getPredicateMappingsFromGitHub
+ predsMappedByExactMatch = preds.map { pred =>
+ val foundByExactMatch = mappedPredicates.find(
+ { mp =>
+ val exactMatches = mp.`exact matches`.toList.flatten.toSet
+
+ // These are in CURIEs. Normally I would write some very complicated code to un-CURIE-fy it, but
+ // instead...
+ exactMatches
+ .map(_.replaceFirst(raw"^RO:", "http://purl.obolibrary.org/obo/RO_"))
+ .contains(pred.predicate.iri)
+ }
+ )
+
+ foundByExactMatch match {
+ case None => pred
+ case Some(mp) => transformPredicateWithMappedPredicateInfo(pred, mp)
+ }
+ }
+ qualifiedPreds: Seq[PredicateMapping] = predsMappedByExactMatch.map {
+ /* For each predicate, we need to check to see if this is a "mapped predicate". If so, we transform it
+ into a qualified predicate as per the predicate mapping.
+ */
+ case pred @ PredicateMapping(_, Some(biolinkPredicate: BiolinkPredicate), _) =>
+ // In some cases, we might be able to find the mappings by Biolink predicate.
+ val foundByBiolinkPredicate = mappedPredicates.find(mp => mp.biolinkMappedPredicate == biolinkPredicate)
+
+ foundByBiolinkPredicate match {
+ case None => pred
+ case Some(mp) => transformPredicateWithMappedPredicateInfo(pred, mp)
+ }
+
+ // If we haven't matched it, don't transform it.
+ case pred => pred
+ }
+ uniquePreds: Set[PredicateMapping] = (manualPredicateMappings ++ qualifiedPreds).toSet
+ predsOutput = uniquePreds.asJson.deepDropNullValues.spaces2SortKeys
+ } yield {
+ logger.info(f"Found ${preds.size} predicates:")
+ preds.foreach(pred => logger.info(f" - ${pred}"))
+
+ logger.info(f"Found ${mappedPredicates.size} predicate mappings:")
+ mappedPredicates.foreach(predMap => logger.info(f" - ${predMap}"))
+
+ logger.info(f"Transformed to ${qualifiedPreds.size} predicates:")
+ qualifiedPreds.foreach(pred => logger.info(f" - ${pred}"))
+
+ Files.writeString(PredicateJsonFilePath, predsOutput)
+ logger.info(f"Wrote predicate output (${predsOutput.size}) to ${PredicateJsonFilePath}")
+ }
+
+ val configLayer: Layer[Throwable, ZConfig[AppConfig]] = TypesafeConfig.fromDefaultLoader(AppConfig.config)
+ val runLayer = HttpClient.makeHttpClientLayer ++ configLayer >+> SPARQLQueryExecutor.makeCache.toLayer
+ program.provideCustomLayer(runLayer).exitCode
+ }
+
+}
diff --git a/src/main/scala/org/renci/cam/util/GenerateTestData.scala b/src/main/scala/org/renci/cam/util/GenerateTestData.scala
new file mode 100644
index 00000000..50f55be4
--- /dev/null
+++ b/src/main/scala/org/renci/cam/util/GenerateTestData.scala
@@ -0,0 +1,299 @@
+package org.renci.cam.util
+
+import com.typesafe.scalalogging.{LazyLogging, Logger}
+import io.circe.generic.auto._
+import io.circe.syntax._
+import org.phenoscape.sparql.SPARQLInterpolation._
+import org.renci.cam.Biolink.{BiolinkData, biolinkData}
+import org.renci.cam.HttpClient.HttpClient
+import org.renci.cam.QueryService.{BiolinkNamedThing, RDFSSubClassOf, SesameDirectType}
+import org.renci.cam._
+import org.renci.cam.domain.{BiolinkPredicate, IRI, PredicateMappings}
+import zio._
+import zio.blocking.Blocking
+import zio.config.ZConfig
+import zio.config.typesafe.TypesafeConfig
+import zio.stream.{ZSink, ZStream}
+
+import java.nio.file.Path
+
+/** The SRI Testing harness requires test data to be generated. This utility is
+ * designed to generate some test data. It uses the SPARQL endpoint configured in AppConfig as well as the files in src/main/resources to
+ * generate this data.
+ */
+object GenerateTestData extends zio.App with LazyLogging {
+ /* Helper classes. */
+
+ /** Model a parent-to-child relationship between two Biolink classes. For example, biolink:MolecularEntity is a child of
+ * biolink:ChemicalEntity.
+ */
+ case class ParentChildRelation(
+ parent: String,
+ child: String
+ )
+
+ /** A single test edge to be generated in the output JSONL file, as documented at
+ * https://github.com/TranslatorSRI/SRI_testing/blob/83358cb18bdebd5a45b8f4c4671cb027328df700/tests/onehop/README.md#biolink-3-revisions
+ * @param subject_category
+ * The Biolink class of the subject (e.g. `biolink:SmallMolecule`).
+ * @param object_category
+ * The Biolink class of the object (e.g. `biolink:Disease`).
+ * @param predicate
+ * The Biolink predicate of the relation (e.g. `biolink:treats`).
+ * @param subject_id
+ * The identifier of the subject (e.g. `CHEBI:3002`).
+ * @param object_id
+ * The identifier of the object (e.g. `MESH:D001249`).
+ */
+ case class TestEdge(
+ subject_category: IRI,
+ object_category: IRI,
+ predicate: IRI,
+ subject_id: IRI,
+ object_id: IRI,
+ qualifiers: List[domain.TRAPIQualifier] = List()
+ )
+
+ /** The structure of the final JSON file to generate. */
+ case class SRITestingFile(
+ source_type: String,
+ infores: String,
+ exclude_tests: List[String],
+ edges: List[TestEdge]
+ )
+
+ /* Object variables. */
+ val LinkMLClassDefinition: IRI = IRI("https://w3id.org/linkml/ClassDefinition")
+ override lazy val logger: Logger = Logger(GenerateTestData.getClass.getSimpleName);
+
+ private def generateJSONLFile(
+ jsonlPath: Path): ZIO[Blocking with ZConfig[AppConfig] with HttpClient with Has[BiolinkData], Throwable, Long] = {
+ // Get a list of all the Biolink classes (and their parents) that we know about.
+ val biolink_classes_query =
+ sparql"""
+ SELECT ?biolinkClass (GROUP_CONCAT(DISTINCT ?parentClass; SEPARATOR="|") AS ?parents) WHERE {
+ ?biolinkClass ${RDFSSubClassOf} ${BiolinkNamedThing.iri} .
+ ?biolinkClass a ${LinkMLClassDefinition} .
+
+ OPTIONAL {
+ ?biolinkClass ${RDFSSubClassOf} ?parentClass .
+ FILTER(?biolinkClass != ?parentClass) .
+ ?parentClass a ${LinkMLClassDefinition}
+ }
+ } GROUP BY ?biolinkClass"""
+
+ for {
+ biolinkData <- biolinkData
+
+ biolink_classes_solutions <- SPARQLQueryExecutor.runSelectQuery(biolink_classes_query.toQuery)
+ biolink_classes_parents = biolink_classes_solutions
+ .map { qs =>
+ (
+ qs.getResource("biolinkClass").getURI,
+ qs.getLiteral("parents").getString.split('|').toSet
+ )
+ }
+ .groupMapReduce(_._1)(_._2)(_ ++ _)
+ _ = logger.info(f"Biolink classes with parents: ${biolink_classes_parents}")
+
+ // Invert this map so we get a Map[String,
+ biolink_classes_children =
+ biolink_classes_parents
+ .flatMap { case (concept, parents) =>
+ parents.map { parent =>
+ (parent, concept)
+ }
+ }
+ .groupMap(_._1)(_._2)
+ .view
+ .mapValues(_.toSet)
+ .toMap
+
+ // Generate a list of biolink class - biolink class pairs.
+ biolink_classes_pairs = for {
+ x <- biolink_classes_parents.keySet
+ y <- biolink_classes_parents.keySet
+ } yield (x, y)
+
+ // All our relations should be part of biolink:related_to.
+ relationsSet = PredicateMappings.mapQueryEdgePredicates(Some(List(BiolinkPredicate("related_to"))), None)
+
+ // Generate test records for each Biolink pair.
+ results <- ZStream
+ .fromIterable(biolink_classes_pairs)
+ /*
+ .filter { biolinkPair =>
+ val subj = (biolinkPair._1)
+ val obj = (biolinkPair._2)
+
+ // For generating this test data, we only want the leaf nodes. So any class with
+ // children should be eliminated here.
+ val subj_is_leaf = biolink_classes_children.getOrElse(subj, Set()).isEmpty
+ val obj_is_leaf = biolink_classes_children.getOrElse(obj, Set()).isEmpty
+
+ if (subj_is_leaf && obj_is_leaf) true
+ else {
+ logger.info(s"Skipping ${subj} (Is leaf? ${subj_is_leaf}) -> ${obj} (Is leaf? ${obj_is_leaf})")
+ false
+ }
+ } */
+ .mapM { biolinkPair =>
+ val subj = IRI(biolinkPair._1)
+ val obj = IRI(biolinkPair._2)
+
+ if (relationsSet.isEmpty) {
+ throw new RuntimeException("Biolink predicate `biolink:related_to` could not be mapped to any Biolink predicates.")
+ }
+
+ // Skip any pairs where the subj or obj contain more than one hash, because this causes Jena to error.
+ if (subj.value.matches(".*#.*#.*") || obj.value.matches(".*#.*#.*")) {
+ logger.warn(s"Skipping pair $subj and $obj as one of them contains more than one '#' character.")
+ ZIO.succeed(Seq())
+ } else {
+ val subjEntitiesQuery =
+ sparql"""
+ SELECT ?a {
+ ?aClass ${subj} .
+ ?a ?aClass .
+ } LIMIT 1000
+ """
+
+ val objEntitiesQuery =
+ sparql"""
+ SELECT ?b {
+ ?bClass ${obj} .
+ ?b ?bClass .
+ } LIMIT 1000
+ """
+
+ val edges = for {
+ subjEntitiesResult <- SPARQLQueryExecutor.runSelectQuery(subjEntitiesQuery.toQuery).orElse(ZIO(Seq()))
+ subjEntities = subjEntitiesResult
+ .map(qs => qs.getResource("a").getURI)
+ // We have IRIs with multiple '#'s, which causes a Jena exception later. Let's filter those out.
+ .filterNot(_.matches(".*#.*#.*"))
+ _ = logger.info(s"Found ${subjEntities.length} subject entities for ${subj}: ${subjEntities}")
+ objEntitiesResult <- SPARQLQueryExecutor.runSelectQuery(objEntitiesQuery.toQuery).orElse(ZIO(Seq()))
+ objEntities = objEntitiesResult
+ .map(qs => qs.getResource("b").getURI)
+ // We have IRIs with multiple '#'s, which causes a Jena exception later. Let's filter those out.
+ .filterNot(_.matches(".*#.*#.*"))
+ _ = logger.info(s"Found ${objEntities.length} object entities for ${obj}: ${objEntities}")
+ relationsQuery =
+ sparql"""
+ SELECT DISTINCT ?relation WHERE {
+ VALUES ?a { ${subjEntities.map(IRI(_)).map(n => sparql" $n ").fold(sparql"")(_ + _)} } .
+ VALUES ?b { ${objEntities.map(IRI(_)).map(n => sparql" $n ").fold(sparql"")(_ + _)} } .
+ FILTER (?a != ?b) .
+ ?a ?relation ?b
+ }
+ """
+ _ = logger.info(s"Prepared relations query: ${relationsQuery.toQuery}")
+ relationsResult <- SPARQLQueryExecutor.runSelectQuery(relationsQuery.toQuery).orElse(ZIO(Seq()))
+ _ = logger.info(s"Relations result obtained: ${relationsResult}")
+ relations = relationsResult.map(qs => qs.getResource("relation").getURI)
+ _ = {
+ if (relations.isEmpty) {
+ logger.warn(f"Did not find any relations from ${subj} to ${obj}: ${relations}")
+ } else {
+ logger.info(f"Found relations: ${relations.size} from ${subj} to ${obj}: ${relations}")
+ }
+ }
+ testEdges <- ZStream
+ .fromIterable(relations)
+ .mapM { relation =>
+ val relationIRI = IRI(relation)
+ val singleTestRecordQuery =
+ sparql"""
+ SELECT ?aClass ?bClass WHERE {
+ ?aClass ${RDFSSubClassOf} ${subj} .
+ ?bClass ${RDFSSubClassOf} ${obj} .
+ ?a ${SesameDirectType} ?aClass .
+ ?b ${SesameDirectType} ?bClass .
+ ?a ${relationIRI} ?b .
+ FILTER (?a != ?b) .
+ } LIMIT 1"""
+
+ for {
+ singleTestRecordResult <- SPARQLQueryExecutor.runSelectQuery(singleTestRecordQuery.toQuery)
+ singleTestRecords = singleTestRecordResult.map(qs => (qs.getResource("aClass").getURI, qs.getResource("bClass").getURI))
+ testEdges = singleTestRecords.flatMap { singleTestRecord =>
+ val qualifiedPreds = PredicateMappings.getBiolinkQualifiedPredicates(relationIRI)
+ qualifiedPreds.map { qualifiedPred =>
+ logger.info(
+ f"- Found test edge for ${subj.value} --${relation} (${qualifiedPred.biolinkPredicate.shorthand})--> ${obj.value} (predicates: ${qualifiedPred.qualifierList})"
+ )
+
+ // So hacky as all heck.
+ TestEdge(IRI(subj.value),
+ IRI(obj.value),
+ qualifiedPred.biolinkPredicate.iri,
+ IRI(singleTestRecord._1),
+ IRI(singleTestRecord._2),
+ qualifiedPred.qualifierList)
+ }
+ }
+ } yield testEdges
+ }
+ .runCollect
+ } yield testEdges.toSet.toList
+
+ edges.map(r => r.flatten)
+ }
+ }
+ .flatMap(value =>
+ ZStream.fromIterable(value.map { v =>
+ import biolinkData.implicits._
+
+ v.asJson.deepDropNullValues.noSpacesSortKeys
+ }))
+ .intersperse("\n")
+ .run(ZSink.fromFile(jsonlPath).contramapChunks[String](_.flatMap(_.getBytes)))
+ } yield results
+ }
+
+ /** Process the command line arguments and return a ZIO program that generates the test data.
+ *
+ * @param args
+ * The command line arguments to generate.
+ * @return
+ * A ZIO program that generates an ExitCode.
+ */
+ override def run(args: List[String]): URIO[zio.ZEnv, ExitCode] = {
+ if (args.isEmpty) {
+ throw new RuntimeException("A single argument is required: the test-edges JSONL file to write.")
+ }
+ if (args.length > 1) {
+ throw new RuntimeException("Only a single argument is allowed: the test-edges JSONL file to write.")
+ }
+
+ /*
+ sriTestingFile = SRITestingFile("aggregator", "cam-kp", List(), results.toList.flatten.distinct)
+ sriTestingFileJson = sriTestingFile.asJson
+ _ = Files.writeString(sriTestingFilePath, sriTestingFileJson.deepDropNullValues.spaces2SortKeys)
+
+ */
+
+ val jsonlPath = Path.of(args.head)
+ val program = for {
+ // Generate JSONL file.
+ linesGenerated <- generateJSONLFile(jsonlPath)
+ .onError { cause =>
+ logger.error(s"Could not generate JSONL file ${jsonlPath}: $cause")
+ ZIO.succeed(ExitCode.failure)
+ }
+ } yield {
+ logger.info(s"Successfully wrote ${linesGenerated} to ${jsonlPath}")
+ ExitCode.success
+ }
+
+ // Set up layers and return program.
+ val configLayer: Layer[Throwable, ZConfig[AppConfig]] = TypesafeConfig.fromDefaultLoader(AppConfig.config)
+ val camkpapiLayer: ZLayer[Any, Throwable, HttpClient] = Blocking.live >>> HttpClient.makeHttpClientLayer
+ val layer: ZLayer[Any, Throwable, Blocking with ZConfig[AppConfig] with HttpClient with Has[BiolinkData]] =
+ configLayer ++ camkpapiLayer ++ Biolink.makeUtilitiesLayer ++ Blocking.live >+> SPARQLQueryExecutor.makeCache.toLayer
+
+ program.provideCustomLayer(layer).exitCode
+ }
+
+}
diff --git a/src/test/resources/lookup-service-test/ids.txt b/src/test/resources/lookup-service-test/ids.txt
index aef72ba4..9258daaa 100644
--- a/src/test/resources/lookup-service-test/ids.txt
+++ b/src/test/resources/lookup-service-test/ids.txt
@@ -1,7 +1,5 @@
CHEBI:17685
PUBCHEM.COMPOUND:157225
-CHEBI:22563
-CHEBI:26369
CHEBI:35660
CHEBI:35703
MONDO:0001208
@@ -31,21 +29,4 @@ HP:0025491
HP:0011105
HP:0003111
HP:0011032
-UniProtKB:O75795
-UniProtKB:P07900
-UniProtKB:P08684
-UniProtKB:P13569
-UniProtKB:P16662
-UniProtKB:P19224
-UniProtKB:P22310
-UniProtKB:P24462
-UniProtKB:P51589
-UniProtKB:P54855
-UniProtKB:P56856
-UniProtKB:P82251
-UniProtKB:Q07837
-UniProtKB:Q16651
-UniProtKB:Q9HB55
-UniProtKB:Q9HBW0
-UniProtKB:Q9NPD5
-UniProtKB:Q9NZQ3
\ No newline at end of file
+UniProtKB:P24462
\ No newline at end of file
diff --git a/src/test/scala/org/renci/cam/test/Biolink3Test.scala b/src/test/scala/org/renci/cam/test/Biolink3Test.scala
new file mode 100644
index 00000000..57b2dbbb
--- /dev/null
+++ b/src/test/scala/org/renci/cam/test/Biolink3Test.scala
@@ -0,0 +1,372 @@
+package org.renci.cam.test
+
+import com.typesafe.scalalogging.LazyLogging
+import org.renci.cam._
+import org.renci.cam.domain._
+import zio._
+import zio.config.ZConfig
+import zio.config.typesafe.TypesafeConfig
+import zio.stream.ZStream
+import zio.test.Assertion._
+import zio.test._
+
+/** This test suite tests that CAM-KP can handle Biolink 3 queries. Biolink 3 shifted from having single predicates to qualified predicates.
+ * The examples in this file are based on the example queries provided in the GitHub issues listed in the references and inline comments
+ * below.
+ *
+ * References:
+ * - https://github.com/biolink/biolink-model/blob/ac69bb2dc94d62d50f5cfab3fa07414b0ca092b1/Migration_3.0_Guide.md
+ * - https://github.com/biolink/biolink-model/blob/ac69bb2dc94d62d50f5cfab3fa07414b0ca092b1/predicate_mapping.yaml
+ * - https://github.com/NCATSTranslator/TranslatorArchitecture/issues/79
+ * - https://github.com/NCATSTranslator/TranslatorArchitecture/issues/80
+ * - https://github.com/NCATSTranslator/TranslatorArchitecture/issues/81
+ * - https://github.com/NCATSTranslator/TranslatorArchitecture/issues/82
+ */
+
+object Biolink3Test extends DefaultRunnableSpec with LazyLogging {
+
+ val biolink3conversions = {
+ case class ConversionTest(
+ biolinkPredicates: Option[List[BiolinkPredicate]],
+ trapiQualifierConstraints: Option[List[TRAPIQualifierConstraint]],
+ predicates: Set[IRI]
+ )
+
+ val biolink3conversions: Seq[ConversionTest] = Seq(
+ // related_to should include all possible predicates.
+ ConversionTest(
+ Some(List(BiolinkPredicate("related_to"))),
+ None,
+ Set(
+ IRI("http://purl.obolibrary.org/obo/RO_0002565"),
+ IRI("http://purl.obolibrary.org/obo/RO_0000057"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002224"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002087"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002500"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004007"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002131"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002436"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002160"),
+ IRI("http://purl.obolibrary.org/obo/RO_0001025"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002093"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002356"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002216"),
+ IRI("http://purl.obolibrary.org/obo/BFO_0000063"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002432"),
+ IRI("http://purl.obolibrary.org/obo/BFO_0000051"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002349"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002488"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004034"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002497"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004033"),
+ IRI("http://purl.obolibrary.org/obo/RO_0001015"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002434"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002263"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002496"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002331"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002608"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002333"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002298"),
+ IRI("http://purl.obolibrary.org/obo/RO_0000056"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002229"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004032"),
+// IRI("http://translator.renci.org/ubergraph-axioms.ofn#acts_upstream_of_o_enabled_by"), -- this maps to a qualified term, weirdly enough.
+ IRI("http://purl.obolibrary.org/obo/RO_0000052"),
+ IRI("http://purl.obolibrary.org/obo/BFO_0000066"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002348"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002588"),
+ IRI("http://purl.obolibrary.org/obo/BFO_0000062"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002211"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002205"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002604"),
+ IRI("http://purl.obolibrary.org/obo/RO_0003001"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002448"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002344"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002232"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002338"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002592"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002315"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002234"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002327"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002492"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002090"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002412"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002296"),
+ IRI("http://purl.obolibrary.org/obo/GOREL_0001006"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002230"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002299"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002264"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002092"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002084"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002297"),
+ IRI("http://purl.obolibrary.org/obo/RO_0003000"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004009"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002223"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002219"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002339"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002221"),
+ // IRI("http://purl.obolibrary.org/obo/RO_0002313"), -- maps to a qualified predicate
+ IRI("http://purl.obolibrary.org/obo/RO_0004008"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002326"),
+ IRI("http://purl.obolibrary.org/obo/BFO_0000050"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002220"),
+ IRI("http://purl.obolibrary.org/obo/RO_0001019"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002215"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002231"),
+ IRI("http://purl.obolibrary.org/obo/RO_0012003"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002411"),
+ IRI("http://purl.obolibrary.org/obo/RO_0004035"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002590"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002328"),
+ IRI("http://purl.obolibrary.org/obo/RO_0002233")
+ )
+ ),
+
+ // biomarker_for isn't present in our triplestore, so it should return an empty set.
+ ConversionTest(Some(List(BiolinkPredicate("biomarker_for"))), None, Set()),
+
+ // "increases expression of" should be mapped to http://purl.obolibrary.org/obo/RO_0003003, since this is what
+ // predicate_mapping.yaml tells us.
+ ConversionTest(
+ Some(List(BiolinkPredicate("affects"))),
+ Some(
+ List(
+ TRAPIQualifierConstraint(
+ qualifier_set = List(
+ TRAPIQualifier("biolink:object_aspect_qualifier", "activity_or_abundance"),
+ TRAPIQualifier("biolink:object_direction_qualifier", "decreased")
+ )
+ )
+ )
+ ),
+ Set(IRI("http://purl.obolibrary.org/obo/RO_0002449"))
+ )
+ )
+
+ suite("biolink3conversions")(
+ suiteM("Test whether we can map predicates to relations") {
+ ZStream
+ .fromIterable(biolink3conversions)
+ .map { ct: ConversionTest =>
+ test(s"Testing ${ct.biolinkPredicates} with ${ct.trapiQualifierConstraints} to ${ct.predicates}") {
+ assert(PredicateMappings.mapQueryEdgePredicates(ct.biolinkPredicates, ct.trapiQualifierConstraints))(
+ Assertion.hasSubset(ct.predicates))
+ }
+ }
+ .runCollect
+ },
+ suiteM("Make sure we can map relations to predicates") {
+
+ ZStream
+ .fromIterable(biolink3conversions)
+ .flatMap { ct: ConversionTest =>
+ val biolinkPreds = ct.biolinkPredicates.toList.flatten.toSet
+
+ ZStream
+ .fromIterable(ct.predicates)
+ .map(
+ { pred =>
+ test(s"Testing ${pred} to ${ct.biolinkPredicates} with ${ct.trapiQualifierConstraints}") {
+ val preds = PredicateMappings.getBiolinkQualifiedPredicates(pred)
+
+ val qualifiersActual = preds.filter(p => biolinkPreds.contains(p.biolinkPredicate)).flatMap(_.qualifierList).toSet
+ val qualifiersExpected = ct.trapiQualifierConstraints.getOrElse(List()).flatMap(_.qualifier_set).toSet
+
+ assert(preds.map(_.biolinkPredicate).toSet)(Assertion.hasSubset(ct.biolinkPredicates.getOrElse(List()).toSet)) &&
+ assert(qualifiersActual)(Assertion.equalTo(qualifiersExpected))
+ }
+ }
+ )
+ }
+ .runCollect
+ }
+ )
+ }
+
+ def generateQualifiedEdge(obj: String,
+ subj: String,
+ preds: Option[List[BiolinkPredicate]],
+ knowledge_type: Option[String],
+ qualifier_aspect: Option[String],
+ qualified_direction: Option[String]) = {
+ val qualifier_constraints: List[TRAPIQualifier] = (qualifier_aspect match {
+ case Some(aspect: String) => List(TRAPIQualifier(qualifier_type_id = "biolink:object_aspect_qualifier", qualifier_value = aspect))
+ case _ => List()
+ }) ++ (qualified_direction match {
+ case Some(direction: String) =>
+ List(TRAPIQualifier(qualifier_type_id = "biolink:object_direction_qualifier", qualifier_value = direction))
+ case _ => List()
+ })
+
+ TRAPIQueryEdge(
+ `object` = obj,
+ subject = subj,
+ predicates = preds,
+ knowledge_type = knowledge_type,
+ qualifier_constraints = (qualifier_constraints match {
+ case Seq() => None
+ case list: List[TRAPIQualifier] => Some(List(TRAPIQualifierConstraint(qualifier_set = list)))
+ })
+ )
+ }
+
+ val queries = Map(
+ /* Example Biolink 3 query from https://github.com/NCATSTranslator/TranslatorArchitecture/issues/79
+ * using http://identifiers.org/ncbigene/2859 ("G protein-coupled receptor 35"), which produces the
+ * protein http://identifiers.org/uniprot/Q9HC97.
+ *
+ * We know via /lookup that we know that this protein participates in http://purl.obolibrary.org/obo/GO_0007204
+ * ("positive regulation of cytosolic calcium ion concentration"), so we would expect calcium ions to appear here.
+ *
+ * We don't have NCBIGene:2859, but we do have NCBIGene:340061 ("stimulator of interferon response cGAMP interactor 1")
+ */
+ "STING1-increases-chemical" -> TRAPIQueryGraph(
+ nodes = Map(
+ "gene" -> TRAPIQueryNode(
+ ids = Some(List(IRI("http://identifiers.org/ncbigene/340061"))),
+ categories = Some(List(BiolinkClass("Gene"))),
+ None,
+ None
+ ),
+ "chemical" -> TRAPIQueryNode(None, Some(List(BiolinkClass("ChemicalEntity"))), None, None)
+ ),
+ edges = Map(
+ "t_edge" -> generateQualifiedEdge(
+ "gene",
+ "chemical",
+ Some(List(BiolinkPredicate("affects"))),
+ knowledge_type = Some("inferred"),
+ qualifier_aspect = Some("activity_or_abundance"),
+ qualified_direction = Some("increased")
+ )
+ )
+ ),
+
+ /*
+ * Example Biolink 3 query from https://github.com/NCATSTranslator/TranslatorArchitecture/issues/80
+ * using http://identifiers.org/ncbigene/2859 ("G protein-coupled receptor 35"), which produces the
+ * protein http://identifiers.org/uniprot/Q9HC97.
+ *
+ * We know via /lookup that we know that this protein participates in http://purl.obolibrary.org/obo/GO_0007204
+ * ("positive regulation of cytosolic calcium ion concentration"), so we would expect calcium ions to appear here.
+ *
+ * We don't have NCBIGene:2859, but we do have NCBIGene:598 ("BCL2 like 1")
+ */
+ "BCL2L1-decreases-chemical" -> TRAPIQueryGraph(
+ nodes = Map(
+ "gene" -> TRAPIQueryNode(
+ ids = Some(List(IRI("http://identifiers.org/ncbigene/598"))),
+ categories = Some(List(BiolinkClass("Gene"))),
+ None,
+ None
+ ),
+ "chemical" -> TRAPIQueryNode(None, Some(List(BiolinkClass("ChemicalEntity"))), None, None)
+ ),
+ edges = Map(
+ "t_edge" -> generateQualifiedEdge(
+ "gene",
+ "chemical",
+ Some(List(BiolinkPredicate("affects"))),
+ knowledge_type = Some("inferred"),
+ qualifier_aspect = Some("activity_or_abundance"),
+ qualified_direction = Some("decreased")
+ )
+ )
+ ),
+
+ /*
+ * Example Biolink 3 query from https://github.com/NCATSTranslator/TranslatorArchitecture/issues/81
+ * using valproic acid (PUBCHEM.COMPOUND:88111 = CHEBI:39867).
+ *
+ * Okay, we don't seem to have this information, but we do have it for CHEBI:51143 ("nitrogen molecular entity"),
+ * so let's include that instead.
+ *
+ */
+ "pyruvate-increases-chemical" -> TRAPIQueryGraph(
+ nodes = Map(
+ "gene" -> TRAPIQueryNode(None, Some(List(BiolinkClass("Gene"))), None, None),
+ "chemical" -> TRAPIQueryNode(ids = Some(List(IRI("http://purl.obolibrary.org/obo/CHEBI_51143"))),
+ categories = Some(List(BiolinkClass("ChemicalEntity"))),
+ None,
+ None)
+ ),
+ edges = Map(
+ "t_edge" -> generateQualifiedEdge(
+ "gene",
+ "chemical",
+ Some(List(BiolinkPredicate("affects"))),
+ knowledge_type = Some("inferred"),
+ qualifier_aspect = Some("activity_or_abundance"),
+ qualified_direction = Some("increased")
+ )
+ )
+ ),
+
+ /*
+ * Example Biolink 3 query from https://github.com/NCATSTranslator/TranslatorArchitecture/issues/82
+ * using valproic acid (PUBCHEM.COMPOUND:88111 = CHEBI:39867).
+ *
+ * (Another one we could use is pyruvate (http://purl.obolibrary.org/obo/CHEBI_15361).
+ *
+ * Okay, we don't seem to have this information, but we do have it for CHEBI:51143 ("nitrogen molecular entity"),
+ * so let's include that instead.
+ */
+ "valproic-acid-decreases-chemical" -> TRAPIQueryGraph(
+ nodes = Map(
+ "gene" -> TRAPIQueryNode(None, Some(List(BiolinkClass("Gene"))), None, None),
+ "chemical" -> TRAPIQueryNode(ids = Some(List(IRI("http://purl.obolibrary.org/obo/CHEBI_51143"))),
+ categories = Some(List(BiolinkClass("ChemicalEntity"))),
+ None,
+ None)
+ ),
+ edges = Map(
+ "t_edge" -> generateQualifiedEdge(
+ "gene",
+ "chemical",
+ Some(List(BiolinkPredicate("affects"))),
+ knowledge_type = Some("inferred"),
+ qualifier_aspect = Some("activity_or_abundance"),
+ qualified_direction = Some("decreased")
+ )
+ )
+ )
+ )
+
+ /** The new Biolink3 code has an error in it -- the knowledge graph edge names don't match with the result edge names. To test for that,
+ * we'll make sure that all the queries we make here have no knowledge graph edge results that are not also present in the results.
+ */
+ def checkKnowledgeGraphIDs(message: TRAPIMessage): TestResult = {
+ val kgEdgeIds: Set[String] = message.knowledge_graph.map(_.edges.keySet).toSet.flatten
+ val resultEdgeIds: Set[String] = message.results.map(_.flatMap(_.edge_bindings.values.flatMap(_.map(_.id)))).toList.flatten.toSet
+
+ assert(kgEdgeIds)(Assertion.equalTo(resultEdgeIds))
+ }
+
+ val biolink3exampleQueries = suiteM("biolink3exampleQueries") {
+ ZStream
+ .fromIterable(queries)
+ .map { case (testName, queryGraph) =>
+ testM(f"Test example Biolink 3 query ${testName}") {
+ for {
+ response <- QueryService
+ .run(100, queryGraph)
+ _ = logger.info(s"Response: ${response}")
+ } yield (
+ assert(response.status)(Assertion.isSome(Assertion.equalTo("Success"))) &&
+ assert(response.message.results)(Assertion.isSome(Assertion.isNonEmpty)) &&
+ checkKnowledgeGraphIDs(response.message)
+ )
+ }
+ }
+ .runCollect
+ }
+
+ val configLayer: Layer[Throwable, ZConfig[AppConfig]] = TypesafeConfig.fromDefaultLoader(AppConfig.config)
+ val testLayer = HttpClient.makeHttpClientLayer ++ Biolink.makeUtilitiesLayer ++ configLayer >+> SPARQLQueryExecutor.makeCache.toLayer
+
+ def spec = suite("Biolink 3 example queries")(
+ biolink3conversions,
+ biolink3exampleQueries
+ ).provideCustomLayer(testLayer.mapError(TestFailure.die))
+
+}
diff --git a/src/test/scala/org/renci/cam/test/LimitTest.scala b/src/test/scala/org/renci/cam/test/LimitTest.scala
index a24ed763..15843280 100644
--- a/src/test/scala/org/renci/cam/test/LimitTest.scala
+++ b/src/test/scala/org/renci/cam/test/LimitTest.scala
@@ -18,10 +18,10 @@ object LimitTest extends DefaultRunnableSpec with LazyLogging {
* from 1..50 return the correct number of expected results.
*/
val testQueryWithExpectedResults = {
- // Expected results as of 2022-may-18 for the test query
- val queryGraphExpectedResults = 30
+ // Expected results as of 2023-mar-17 for the test query
+ val queryGraphExpectedResults = 1583
// The limits to test -- this should be set up to go neatly within
- val limitsToTest = Seq(1, 2, 3, 4, 5, 10, 20, 30, 40, 50)
+ val limitsToTest = Seq(1, 2, 3, 4, 5, 10, 20, 30, 60, 90, 150, 300, 500, 700, 1000, 1200, 1500, 1583)
// The test query: pyruvate related_to $[NamedThing]
val testQueryGraph = TRAPIQueryGraph(
Map(
diff --git a/src/test/scala/org/renci/cam/test/LookupServiceTest.scala b/src/test/scala/org/renci/cam/test/LookupServiceTest.scala
index b2a1e774..61071da7 100644
--- a/src/test/scala/org/renci/cam/test/LookupServiceTest.scala
+++ b/src/test/scala/org/renci/cam/test/LookupServiceTest.scala
@@ -13,8 +13,10 @@ import zio.blocking.effectBlockingIO
import zio.cache.Cache
import zio.config.ZConfig
import zio.config.typesafe.TypesafeConfig
+import zio.duration.durationInt
import zio.interop.catz.concurrentInstance
import zio.stream.ZStream
+import zio.test.environment.Live
import zio.test.{assert, _}
import zio.{Layer, Task, ZIO, ZLayer, ZManaged}
@@ -24,6 +26,9 @@ import java.io.{File, FileWriter, PrintWriter}
*/
object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
+ /** The time limit for an individual lookup query (in testIdentifier()). */
+ val LOOKUP_TIME_LIMIT = 60.second
+
/** Node normalization endpoint. Defaults to the production NodeNorm, but can be overriden by setting the NODE_NORM_URL environmental
* variable.
*/
@@ -49,7 +54,7 @@ object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
assert(result.subjectTriples)(Assertion.isNonEmpty) &&
assert(result.objectTriples)(Assertion.isNonEmpty) &&
assert(result.relations)(Assertion.isNonEmpty) &&
- assert(result.biolinkPredicates)(Assertion.isNonEmpty)
+ assert(result.qualifiedBiolinkPredicates)(Assertion.isNonEmpty)
}
}
@@ -64,7 +69,7 @@ object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
* @return
* A ZSpec that will test the single identifier being queried.
*/
- def testIdentifier(id: String): ZSpec[EndpointEnv, Throwable] =
+ def testIdentifier(id: String): ZSpec[Live with EndpointEnv, Throwable] =
testM(s"Test whether we can retrieve results for identifier ${id}") {
val idFilenameSafe = id.replaceAll("\\W", "_")
val outputFile = new File(s"./src/test/resources/lookup-service-test/${idFilenameSafe}.json")
@@ -79,8 +84,9 @@ object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
response <- server(Request(GET, uri))
content <- EntityDecoder.decodeText(response)
resultOrErrorJson <- ZIO.fromEither(io.circe.parser.parse(content))
+ _ = logger.debug(s"Raw JSON results for identifier ${id}: ${resultOrErrorJson.deepDropNullValues.spaces2SortKeys}")
result <- ZIO.fromEither(resultOrErrorJson.as[LookupService.Result])
- _ = logger.debug(s"Results for identifier ${id}: ${result.asJson.deepDropNullValues.spaces2SortKeys}")
+ // _ = logger.debug(s"Results for identifier ${id}: ${result.asJson.deepDropNullValues.spaces2SortKeys}")
fileWritten <- effectBlockingIO(new PrintWriter(new FileWriter(outputFile)))
.bracketAuto { pw =>
pw.println(result.asJson.deepDropNullValues.spaces2SortKeys)
@@ -95,7 +101,7 @@ object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
// assert(result.relations)(Assertion.isNonEmpty) &&
// assert(result.biolinkPredicates)(Assertion.isNonEmpty) &&
assert(fileWritten)(Assertion.isTrue)
- }
+ } @@ TestAspect.timeout(LOOKUP_TIME_LIMIT)
/* Generate tests for all the identifiers in the lookupServiceIdFile. */
@@ -103,7 +109,7 @@ object LookupServiceTest extends DefaultRunnableSpec with LazyLogging {
val lookupServiceIdFile = new File("./src/test/resources/lookup-service-test/ids.txt")
/** A spec made up of tests for every identifier in the lookupServiceIdFile. */
- val testIdentifiersInFile: Spec[EndpointEnv, TestFailure[Throwable], TestSuccess] =
+ val testIdentifiersInFile: Spec[Live with EndpointEnv, TestFailure[Throwable], TestSuccess] =
suiteM(s"Test identifiers in ${lookupServiceIdFile}") {
ZStream
.fromIteratorManaged(
diff --git a/src/test/scala/org/renci/cam/test/QueryServiceTest.scala b/src/test/scala/org/renci/cam/test/QueryServiceTest.scala
index d870040d..67838871 100644
--- a/src/test/scala/org/renci/cam/test/QueryServiceTest.scala
+++ b/src/test/scala/org/renci/cam/test/QueryServiceTest.scala
@@ -71,9 +71,7 @@ object QueryServiceTest extends DefaultRunnableSpec with LazyLogging {
} yield assert(nodeBindings.keys)(
contains("n0") && contains("n1")
) && assertTrue(
- nodeBindings
- .get("n0")
- .get
+ nodeBindings("n0")
.map(a => a.id)
.contains(IRI("http://purl.obolibrary.org/obo/go/extensions/reacto.owl#REACTO_R-HSA-166103")))
}
@@ -459,7 +457,10 @@ object QueryServiceTest extends DefaultRunnableSpec with LazyLogging {
e0: TRAPIQueryEdge = TRAPIQueryEdge(
subject = "n0",
`object` = "n1",
- predicates = Some(List(BiolinkPredicate("positively_regulates")))
+ predicates = Some(List(BiolinkPredicate("regulates"))),
+ qualifier_constraints = Some(
+ List(TRAPIQualifierConstraint(
+ List(TRAPIQualifier("biolink:object_direction_qualifier", "downregulated")))))
)) =
TRAPIQueryGraph(Map("n0" -> n0, "n1" -> n1), Map("e0" -> e0))
@@ -467,21 +468,23 @@ object QueryServiceTest extends DefaultRunnableSpec with LazyLogging {
testM("Ensure that query_id is absent for nodes without ids") {
for {
response <- QueryService
- .run(1000, createTestTRAPIQueryGraph(TRAPIQueryNode(None, Some(List(BiolinkClass("BiologicalProcessOrActivity"))), None)))
+ .run(100, createTestTRAPIQueryGraph(TRAPIQueryNode(None, Some(List(BiolinkClass("BiologicalProcessOrActivity"))), None)))
// _ = logger.warn(s"Response: ${response}")
nodeBindings = response.message.results.get.flatMap(_.node_bindings.getOrElse("n0", List()))
queryIds = nodeBindings.map(_.query_id)
- } yield assert(response.message.results)(Assertion.isSome(Assertion.hasSize(Assertion.equalTo(1000)))) &&
+ } yield assert(response.message.results)(Assertion.isSome(Assertion.hasSize(Assertion.equalTo(100)))) &&
assert(queryIds)(Assertion.forall(Assertion.isNone))
},
testM(
"Ensure that query_id is present only when the identifier is ambiguous for a process (GO:0033549, MAP kinase phosphatase activity)") {
val iriToQuery = IRI("http://purl.obolibrary.org/obo/GO_0033549")
+ val query = createTestTRAPIQueryGraph(TRAPIQueryNode(Some(List(iriToQuery)), None))
for {
response <- QueryService
- .run(1000, createTestTRAPIQueryGraph(TRAPIQueryNode(Some(List(iriToQuery)), None)))
- // _ = logger.warn(s"Response: ${response}")
+ .run(100, query)
+ _ = logger.warn(s"Response query_id is present only when the identifier is ambiguous query: ${query}")
+ _ = logger.warn(s"Response query_id is present only when the identifier is ambiguous response: ${response}")
nodeBindings = response.message.results.get.flatMap(_.node_bindings.getOrElse("n0", List()))
queryIds = nodeBindings.map(_.query_id)
queryIdsUnambiguous = nodeBindings.filter(_.id == iriToQuery).map(_.query_id)
@@ -500,7 +503,7 @@ object QueryServiceTest extends DefaultRunnableSpec with LazyLogging {
for {
response <- QueryService
.run(
- 1000,
+ 100,
createTestTRAPIQueryGraph(
TRAPIQueryNode(Some(List(cytoplasm)), None),
TRAPIQueryNode(None, categories = Some(List(BiolinkClass("BiologicalProcessOrActivity"))), None),
@@ -529,26 +532,30 @@ object QueryServiceTest extends DefaultRunnableSpec with LazyLogging {
val glucose = IRI("http://purl.obolibrary.org/obo/CHEBI_17234")
val rna = IRI("http://purl.obolibrary.org/obo/CHEBI_33697")
+ val query = createTestTRAPIQueryGraph(
+ TRAPIQueryNode(Some(List(glucose, rna)), None),
+ TRAPIQueryNode(None, categories = Some(List(BiolinkClass("BiologicalProcessOrActivity"))), None),
+ TRAPIQueryEdge(
+ subject = "n1",
+ `object` = "n0",
+ predicates = Some(List(BiolinkPredicate("has_participant")))
+ )
+ )
+
+ logger.info(f"Glucose query: ${query}")
+
for {
response <- QueryService
.run(
- 1000,
- createTestTRAPIQueryGraph(
- TRAPIQueryNode(Some(List(glucose, rna)), None),
- TRAPIQueryNode(None, categories = Some(List(BiolinkClass("BiologicalProcessOrActivity"))), None),
- TRAPIQueryEdge(
- subject = "n1",
- `object` = "n0",
- predicates = Some(List(BiolinkPredicate("has_participant")))
- )
- )
+ 10,
+ query
)
// _ = logger.warn(s"Response: ${response}")
node0Bindings = response.message.results.get.flatMap(_.node_bindings.getOrElse("n0", List()))
queryIdsUnambiguous = node0Bindings.filter(b => b.id == glucose || b.id == rna).map(_.query_id)
idsAmbiguousGlucose = node0Bindings.filter(_.query_id.contains(glucose)).map(_.id)
idsAmbiguousRNA = node0Bindings.filter(_.query_id.contains(rna)).map(_.id)
- } yield assert(response.message.results)(Assertion.isSome(Assertion.hasSize(Assertion.isGreaterThanEqualTo(50)))) &&
+ } yield assert(response.message.results)(Assertion.isSome(Assertion.hasSize(Assertion.isGreaterThanEqualTo(10)))) &&
// All unambiguous IDs -- glucose and RNA -- should have empty query_ids.
assert(queryIdsUnambiguous)(Assertion.isNonEmpty) &&
assert(queryIdsUnambiguous)(Assertion.forall(Assertion.isNone)) &&
diff --git a/src/test/scala/org/renci/cam/test/TRAPITest.scala b/src/test/scala/org/renci/cam/test/TRAPITest.scala
index 2217daa8..6a195b11 100644
--- a/src/test/scala/org/renci/cam/test/TRAPITest.scala
+++ b/src/test/scala/org/renci/cam/test/TRAPITest.scala
@@ -11,7 +11,7 @@ import org.renci.cam.Biolink.biolinkData
import org.renci.cam.HttpClient.HttpClient
import org.renci.cam.Server.EndpointEnv
import org.renci.cam._
-import org.renci.cam.domain.{BiolinkClass, BiolinkPredicate, IRI, LogEntry, TRAPIAttribute, TRAPIResponse}
+import org.renci.cam.domain.{LogEntry, TRAPIAttribute, TRAPIResponse}
import zio.cache.Cache
import zio.config.ZConfig
import zio.config.typesafe.TypesafeConfig
@@ -121,7 +121,7 @@ object TRAPITest extends DefaultRunnableSpec with LazyLogging {
"qualifier_value": "abundance"
}, {
"qualifier_type_id": "biolink:subject_direction_qualifier",
- "qualifier_value": "decreased"
+ "qualifier_value": "exactly-the-same"
}]
}]
}
@@ -157,13 +157,19 @@ object TRAPITest extends DefaultRunnableSpec with LazyLogging {
logs = trapiResponse.logs
logWarningOfQualifierConstraints = logs.getOrElse(List()).filter {
// We've made this up ourselves.
- case LogEntry(_, Some("WARNING"), Some("UnsupportedQualifierConstraint"), _) => true
- case _ => false
+ case LogEntry(
+ _,
+ Some("ERROR"),
+ Some("UnsupportedEdge"),
+ Some(
+ "Edge e0 could not be mapped to a predicate, and so cannot be matched: TRAPIQueryEdge(Some(List(BiolinkPredicate(part_of,IRI(https://w3id.org/biolink/vocab/part_of)))),n0,n1,None,None,Some(List(TRAPIQualifierConstraint(List(TRAPIQualifier(biolink:subject_aspect_qualifier,abundance), TRAPIQualifier(biolink:subject_direction_qualifier,exactly-the-same))))))")) =>
+ true
+ case _ => false
}
} yield assert(response.status)(Assertion.hasField("isSuccess", _.isSuccess, Assertion.isTrue)) &&
assert(content)(Assertion.isNonEmptyString) &&
- // Should return an overall status of Success
- assert(trapiResponse.status)(Assertion.isSome(Assertion.equalTo("Success"))) &&
+ // Should return an overall status of Error (because an edge couldn't be interpreted)
+ assert(trapiResponse.status)(Assertion.isSome(Assertion.equalTo("ERROR"))) &&
// ... and in the logs
assert(logs)(Assertion.isSome(Assertion.isNonEmpty)) &&
assert(logWarningOfQualifierConstraints)(Assertion.isNonEmpty) &&