diff --git a/backend/poetry.lock b/backend/poetry.lock
index 2db550422..e3aea9619 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -1233,13 +1233,13 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
[[package]]
name = "importlib-resources"
-version = "6.1.0"
+version = "6.1.1"
description = "Read resources from Python packages"
optional = false
python-versions = ">=3.8"
files = [
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[package.dependencies]
@@ -1318,12 +1318,12 @@ i18n = ["Babel (>=2.7)"]
[[package]]
name = "jsbeautifier"
-version = "1.14.9"
+version = "1.14.11"
description = "JavaScript unobfuscator and beautifier."
optional = false
python-versions = "*"
files = [
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[package.dependencies]
@@ -1503,13 +1503,13 @@ regex = ["regex"]
[[package]]
name = "linkml"
-version = "1.6.1"
+version = "1.6.2"
description = "Linked Open Data Modeling Language"
optional = false
python-versions = ">=3.8,<4.0"
files = [
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@@ -1527,7 +1527,7 @@ openpyxl = "*"
parse = "*"
prefixcommons = ">=0.1.7"
prefixmaps = ">=0.1.3"
-pydantic = "*"
+pydantic = ">=1.0.0,<3.0.0"
pyjsg = ">=0.11.6"
pyshex = ">=0.7.20"
pyshexc = ">=0.8.3"
@@ -1575,13 +1575,13 @@ pydantic = "*"
[[package]]
name = "linkml-runtime"
-version = "1.6.0"
+version = "1.6.1"
description = "Runtime environment for LinkML, the Linked open data modeling language"
optional = false
python-versions = ">=3.7.6,<4.0.0"
files = [
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[package.dependencies]
@@ -1935,13 +1935,13 @@ mkdocs = ">=1.1"
[[package]]
name = "mkdocs-material"
-version = "9.4.7"
+version = "9.4.8"
description = "Documentation that simply works"
optional = false
python-versions = ">=3.8"
files = [
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@@ -2792,13 +2792,13 @@ solrcloud = ["kazoo (>=2.5.0)"]
[[package]]
name = "pystow"
-version = "0.5.0"
+version = "0.5.2"
description = "Easily pick a place to store data for your python package."
optional = false
python-versions = ">=3.7"
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@@ -3280,121 +3280,121 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
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name = "rpds-py"
-version = "0.10.6"
+version = "0.12.0"
description = "Python bindings to Rust's persistent data structures (rpds)"
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python-versions = ">=3.8"
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files = [
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- {file = "trio-0.22.2.tar.gz", hash = "sha256:3887cf18c8bcc894433420305468388dac76932e9668afa1c49aa3806b6accb3"},
+ {file = "trio-0.23.1-py3-none-any.whl", hash = "sha256:bb4abb3f4af23f96679e7c8cdabb8b234520f2498550d2cf63ebfd95f2ce27fe"},
+ {file = "trio-0.23.1.tar.gz", hash = "sha256:16f89f7dcc8f7b9dcdec1fcd863e0c039af6d0f9a22f8dfd56f75d75ec73fd48"},
]
[package.dependencies]
@@ -4162,7 +4162,7 @@ cffi = {version = ">=1.14", markers = "os_name == \"nt\" and implementation_name
exceptiongroup = {version = ">=1.0.0rc9", markers = "python_version < \"3.11\""}
idna = "*"
outcome = "*"
-sniffio = "*"
+sniffio = ">=1.3.0"
sortedcontainers = "*"
[[package]]
diff --git a/backend/src/monarch_py/api/main.py b/backend/src/monarch_py/api/main.py
index 7bba7265a..1e0cbe98d 100644
--- a/backend/src/monarch_py/api/main.py
+++ b/backend/src/monarch_py/api/main.py
@@ -22,10 +22,10 @@ async def initialize_app():
CurieService()
-app.include_router(entity.router, prefix=f"{PREFIX}/entity")
app.include_router(association.router, prefix=f"{PREFIX}/association")
-app.include_router(search.router, prefix=PREFIX)
+app.include_router(entity.router, prefix=f"{PREFIX}/entity")
app.include_router(histopheno.router, prefix=f"{PREFIX}/histopheno")
+app.include_router(search.router, prefix=PREFIX)
app.include_router(semsim.router, prefix=f"{PREFIX}/semsim")
# Allow CORS
diff --git a/backend/src/monarch_py/api/search.py b/backend/src/monarch_py/api/search.py
index b7bf8d256..afbda3f46 100644
--- a/backend/src/monarch_py/api/search.py
+++ b/backend/src/monarch_py/api/search.py
@@ -62,3 +62,24 @@ async def autocomplete(
"""
response = solr().autocomplete(q=q)
return response
+
+
+@router.get("/mappings")
+async def mappings(
+ entity_id: Union[List[str], None] = Query(default=None),
+ subject_id: Union[List[str], None] = Query(default=None),
+ predicate_id: Union[List[str], None] = Query(default=None),
+ object_id: Union[List[str], None] = Query(default=None),
+ mapping_justification: Union[List[str], None] = Query(default=None),
+ pagination: PaginationParams = Depends(),
+):
+ response = solr().get_mappings(
+ entity_id=entity_id,
+ subject_id=subject_id,
+ predicate_id=predicate_id,
+ object_id=object_id,
+ mapping_justification=mapping_justification,
+ offset=pagination.offset,
+ limit=pagination.limit,
+ )
+ return response
diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py
index 9b1c0c41d..40ba69e15 100644
--- a/backend/src/monarch_py/cli.py
+++ b/backend/src/monarch_py/cli.py
@@ -307,5 +307,27 @@ def multi_entity_associations(
solr_cli.multi_entity_associations(**locals())
+@app.command("mappings")
+def mappings(
+ entity_id: List[str] = typer.Option(None, "--entity-id", "-e", help="entity ID to get mappings for"),
+ subject_id: List[str] = typer.Option(None, "--subject-id", "-s", help="subject ID to get mappings for"),
+ predicate_id: List[str] = typer.Option(None, "--predicate-id", "-p", help="predicate ID to get mappings for"),
+ object_id: List[str] = typer.Option(None, "--object-id", "-o", help="object ID to get mappings for"),
+ mapping_justification: List[str] = typer.Option(
+ None, "--mapping-justification", "-m", help="mapping justification to get mappings for"
+ ),
+ offset: int = typer.Option(0, "--offset", help="The offset of the first mapping to be retrieved"),
+ limit: int = typer.Option(20, "--limit", "-l", help="The number of mappings to return"),
+ fmt: str = typer.Option(
+ "json",
+ "--format",
+ "-f",
+ help="The format of the output (json, yaml, tsv, table)",
+ ),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
+):
+ solr_cli.mappings(**locals())
+
+
if __name__ == "__main__":
app()
diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index ce8d75fcc..dbe8b7e46 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -2,7 +2,7 @@
from datetime import datetime, date
from enum import Enum
from typing import List, Dict, Optional, Any, Union
-from pydantic import BaseModel as BaseModel, Field
+from pydantic import BaseModel as BaseModel, ConfigDict, Field
import sys
if sys.version_info >= (3, 8):
@@ -435,6 +435,7 @@ class Mapping(ConfiguredBaseModel):
object_id: str = Field(...)
object_label: Optional[str] = Field(None, description="""The name of the object entity""")
mapping_justification: Optional[str] = Field(None)
+ id: str = Field(...)
class Node(Entity):
@@ -456,6 +457,10 @@ class Node(Entity):
default_factory=list,
description="""A list of diseases that are known to be causally associated with a gene""",
)
+ mappings: Optional[List[ExpandedCurie]] = Field(
+ default_factory=list,
+ description="""List of ExpandedCuries with id and url for mapped entities""",
+ )
external_links: Optional[List[ExpandedCurie]] = Field(
default_factory=list, description="""ExpandedCurie with id and url for xrefs"""
)
@@ -538,6 +543,20 @@ class EntityResults(Results):
total: int = Field(..., description="""total number of items matching a query""")
+class MappingResults(Results):
+ """
+ SSSOM Mappings returned as a results collection
+ """
+
+ items: List[Mapping] = Field(
+ default_factory=list,
+ description="""A collection of items, with the type to be overriden by slot_usage""",
+ )
+ limit: int = Field(..., description="""number of items to return in a response""")
+ offset: int = Field(..., description="""offset into the total number of items""")
+ total: int = Field(..., description="""total number of items matching a query""")
+
+
class MultiEntityAssociationResults(Results):
id: str = Field(...)
@@ -684,6 +703,7 @@ class BestMatch(ConfiguredBaseModel):
AssociationTableResults.update_forward_refs()
CategoryGroupedAssociationResults.update_forward_refs()
EntityResults.update_forward_refs()
+MappingResults.update_forward_refs()
MultiEntityAssociationResults.update_forward_refs()
SearchResult.update_forward_refs()
SearchResults.update_forward_refs()
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index b28bfaebe..6458fc9b3 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -210,6 +210,15 @@ classes:
- object_id
- object_label
- mapping_justification
+ - id
+ MappingResults:
+ description: SSSOM Mappings returned as a results collection
+ is_a: Results
+ slots:
+ - items
+ slot_usage:
+ items:
+ range: Mapping
MultiEntityAssociationResults:
is_a: Results
slots:
@@ -225,6 +234,7 @@ classes:
- inheritance
- causal_gene
- causes_disease
+ - mappings
- external_links
- provided_by_link
- association_counts
@@ -517,7 +527,6 @@ slots:
qualifiers_closure_label:
multivalued: true
description: Field containing frequency_qualifier name and the names of all of it's ancestors
-
frequency_qualifier_label:
is_a: name
description: The name of the frequency_qualifier entity
@@ -578,7 +587,13 @@ slots:
stage_qualifier_closure_label:
multivalued: true
description: Field containing stage_qualifier name and the names of all of it's ancestors
-# sssom slots
+
+ # sssom slots
+ mappings:
+ description: List of ExpandedCuries with id and url for mapped entities
+ range: ExpandedCurie
+ multivalued: true
+ inlined_as_list: true
subject_id:
range: string
required: true
diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py
index 196b2ed1d..c89d923ea 100644
--- a/backend/src/monarch_py/datamodels/solr.py
+++ b/backend/src/monarch_py/datamodels/solr.py
@@ -9,6 +9,7 @@
class core(Enum):
ENTITY = "entity"
ASSOCIATION = "association"
+ SSSOM = "sssom"
class HistoPhenoKeys(Enum):
diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
index 2a78c5e49..0b2cc581d 100644
--- a/backend/src/monarch_py/implementations/solr/solr_implementation.py
+++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -11,6 +11,7 @@
CategoryGroupedAssociationResults,
Entity,
HistoPheno,
+ MappingResults,
MultiEntityAssociationResults,
Node,
NodeHierarchy,
@@ -26,6 +27,7 @@
parse_autocomplete,
parse_entity,
parse_histopheno,
+ parse_mappings,
parse_search,
)
from monarch_py.implementations.solr.solr_query_utils import (
@@ -34,6 +36,7 @@
build_association_table_query,
build_autocomplete_query,
build_histopheno_query,
+ build_mapping_query,
build_multi_entity_association_query,
build_search_query,
)
@@ -41,6 +44,7 @@
from monarch_py.interfaces.entity_interface import EntityInterface
from monarch_py.interfaces.search_interface import SearchInterface
from monarch_py.service.solr_service import SolrService
+from monarch_py.utils.entity_utils import get_expanded_curie
from monarch_py.utils.utils import get_provided_by_link, get_links_for_field
@@ -113,11 +117,25 @@ def get_entity(self, id: str, extra: bool) -> Optional[Union[Node, Entity]]:
node.association_counts = self.get_association_counts(id).items
node.external_links = get_links_for_field(node.xref) if node.xref else []
node.provided_by_link = get_provided_by_link(node.provided_by)
+ node.mappings = self._get_mapped_entities(node)
return node
### Entity helpers ###
+ def _get_mapped_entities(self, this_entity: Entity) -> list:
+ """..."""
+ mapped_entities = []
+ mappings = self.get_mappings(entity_id=this_entity.id)
+ for m in mappings.items:
+ if this_entity.id == m.subject_id:
+ mapped_entities.append(get_expanded_curie(m.object_id))
+ elif this_entity.id == m.object_id:
+ mapped_entities.append(get_expanded_curie(m.subject_id))
+ else:
+ pass
+ return mapped_entities
+
def _get_associated_entity(self, association: Association, this_entity: Entity) -> Entity:
"""Returns the id, name, and category of the other Entity in an Association given this_entity"""
if this_entity.id == association.subject:
@@ -240,7 +258,7 @@ def get_associations(
limit=limit,
)
query_result = solr.query(query)
- associations = parse_associations(query_result)
+ associations = parse_associations(query_result, offset, limit)
return associations
def get_histopheno(self, subject_closure: str = None) -> HistoPheno:
@@ -418,3 +436,29 @@ def get_association_table(
solr = SolrService(base_url=self.base_url, core=core.ASSOCIATION)
query_result = solr.query(query)
return parse_association_table(query_result, entity, offset, limit)
+
+ def get_mappings(
+ self,
+ entity_id: List[str] = None,
+ subject_id: List[str] = None,
+ predicate_id: List[str] = None,
+ object_id: List[str] = None,
+ mapping_justification: List[str] = None,
+ offset: int = 0,
+ limit: int = 20,
+ ) -> MappingResults:
+ solr = SolrService(base_url=self.base_url, core=core.SSSOM)
+ query = build_mapping_query(
+ entity_id=[entity_id] if isinstance(entity_id, str) else entity_id,
+ subject_id=[subject_id] if isinstance(subject_id, str) else subject_id,
+ predicate_id=[predicate_id] if isinstance(predicate_id, str) else predicate_id,
+ object_id=[object_id] if isinstance(object_id, str) else object_id,
+ mapping_justification=[mapping_justification]
+ if isinstance(mapping_justification, str)
+ else mapping_justification,
+ offset=offset,
+ limit=limit,
+ )
+ query_result = solr.query(query)
+ mappings = parse_mappings(query_result, offset, limit)
+ return mappings
diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
index 5c79e230d..f2dcbae2a 100644
--- a/backend/src/monarch_py/implementations/solr/solr_parsers.py
+++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -16,6 +16,8 @@
FacetValue,
HistoBin,
HistoPheno,
+ Mapping,
+ MappingResults,
SearchResult,
SearchResults,
)
@@ -168,6 +170,19 @@ def parse_autocomplete(query_result: SolrQueryResult) -> SearchResults:
return SearchResults(limit=10, offset=0, total=total, items=items)
+def parse_mappings(query_result: SolrQueryResult, offset: int = 0, limit: int = 20) -> MappingResults:
+ total = query_result.response.num_found
+ items = []
+ for doc in query_result.response.docs:
+ try:
+ result = Mapping(**doc)
+ items.append(result)
+ except ValidationError:
+ logger.error(f"Validation error for {doc}")
+ raise
+ return MappingResults(limit=limit, offset=offset, total=total, items=items)
+
+
##################
# Parser Helpers #
##################
diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
index 3556c5a75..f38a835b0 100644
--- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py
+++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -174,6 +174,29 @@ def build_autocomplete_query(q: str) -> SolrQuery:
return query
+def build_mapping_query(
+ entity_id: List[str] = None,
+ subject_id: List[str] = None,
+ predicate_id: List[str] = None,
+ object_id: List[str] = None,
+ mapping_justification: List[str] = None,
+ offset: int = 0,
+ limit: int = 20,
+) -> SolrQuery:
+ query = SolrQuery(start=offset, rows=limit)
+ if entity_id:
+ query.add_filter_query(" OR ".join([f'subject_id:"{escape(e)}" OR object_id:"{escape(e)}"' for e in entity_id]))
+ if subject_id:
+ query.add_filter_query(" OR ".join([f'subject_id:"{escape(e)}"' for e in subject_id]))
+ if predicate_id:
+ query.add_filter_query(" OR ".join([f'predicate_id:"{escape(e)}"' for e in predicate_id]))
+ if object_id:
+ query.add_filter_query(" OR ".join([f'object_id:"{escape(e)}"' for e in object_id]))
+ if mapping_justification:
+ query.add_filter_query(" OR ".join([f'mapping_justification:"{escape(e)}"' for e in mapping_justification]))
+ return query
+
+
### Search helper functions ###
diff --git a/backend/src/monarch_py/interfaces/mapping_interface.py b/backend/src/monarch_py/interfaces/mapping_interface.py
new file mode 100644
index 000000000..f5664f118
--- /dev/null
+++ b/backend/src/monarch_py/interfaces/mapping_interface.py
@@ -0,0 +1,26 @@
+from abc import ABC
+from typing import List
+
+from monarch_py.datamodels.model import MappingResults
+
+
+class MappingInterface(ABC):
+ def get_mappings(
+ self,
+ entity_id: List[str] = None,
+ subject_id: List[str] = None,
+ predicate_id: List[str] = None,
+ object_id: List[str] = None,
+ mapping_justification: List[str] = None,
+ ) -> MappingResults:
+ """
+ Get SSSOM Mappings based on the provided constraints
+
+ Args:
+ entity_id: Filter to only mappings matching the specified entity IDs. Defaults to None.
+ subject_id: Filter to only mappings matching the specified subject IDs. Defaults to None.
+ predicate_id: Filter to only mappings matching the specified predicate IDs. Defaults to None.
+ object_id: Filter to only mappings matching the specified object IDs. Defaults to None.
+ mapping_justification: Filter to only mappings matching the specified mapping justifications. Defaults to None.
+ """
+ raise NotImplementedError
diff --git a/backend/src/monarch_py/solr_cli.py b/backend/src/monarch_py/solr_cli.py
index 9d11b64af..e45807375 100644
--- a/backend/src/monarch_py/solr_cli.py
+++ b/backend/src/monarch_py/solr_cli.py
@@ -96,7 +96,7 @@ def entity(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Retrieve an entity by ID
@@ -123,11 +123,13 @@ def entity(
@solr_app.command("associations")
def associations(
- category: List[str] = typer.Option(None, "--category", "-c", help="Comma-separated list of categories"),
- subject: List[str] = typer.Option(None, "--subject", "-s", help="Comma-separated list of subjects"),
- predicate: List[str] = typer.Option(None, "--predicate", "-p", help="Comma-separated list of predicates"),
- object: List[str] = typer.Option(None, "--object", "-o", help="Comma-separated list of objects"),
- entity: List[str] = typer.Option(None, "--entity", "-e", help="Comma-separated list of entities"),
+ category: List[str] = typer.Option(None, "--category", "-c", help="Category to get associations for"),
+ subject: List[str] = typer.Option(None, "--subject", "-s", help="Subject ID to get associations for"),
+ predicate: List[str] = typer.Option(None, "--predicate", "-p", help="Predicate ID to get associations for"),
+ object: List[str] = typer.Option(None, "--object", "-o", help="Object ID to get associations for"),
+ entity: List[str] = typer.Option(
+ None, "--entity", "-e", help="Entity (subject or object) ID to get associations for"
+ ),
direct: bool = typer.Option(
False,
"--direct",
@@ -142,22 +144,22 @@ def associations(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Paginate through associations
Args:
- category: A comma-separated list of categories
- subject: A comma-separated list of subjects
- predicate: A comma-separated list of predicates
- object: A comma-separated list of objects
- entity: A comma-separated list of entities
- limit: The number of associations to return
- direct: Whether to exclude associations with subject/object as ancestors
+ category: The category of the association (multi-valued)
+ subject: The subject of the association (multi-valued)
+ predicate: The predicate of the association (multi-valued)
+ object: The object of the association (multi-valued)
+ entity: The entity (subject or object) of the association (multi-valued)
+ limit: The number of associations to return (default 20)
+ direct: Whether to exclude associations with subject/object as ancestors (default False)
offset: The offset of the first association to be retrieved
- fmt: The format of the output (json, yaml, tsv, table)
- output: The path to the output file (stdout if not specified)
+ fmt: The format of the output (json, yaml, tsv, table) (default json)
+ output: The path to the output file (stdout if not specified) (default None)
"""
args = locals()
args.pop("fmt", None)
@@ -182,7 +184,7 @@ def multi_entity_associations(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Paginate through associations for multiple entities
@@ -222,7 +224,7 @@ def search(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
# sort: str = typer.Option(None, "--sort", "-s"),
):
"""
@@ -257,7 +259,7 @@ def autocomplete(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Return entity autcomplete matches for a query string
@@ -282,7 +284,7 @@ def histopheno(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Retrieve the histopheno associations for a given subject
@@ -313,7 +315,7 @@ def association_counts(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
"""
Retrieve the association counts for a given entity
@@ -349,8 +351,36 @@ def association_table(
"-f",
help="The format of the output (json, yaml, tsv, table)",
),
- output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
):
solr = get_solr(update=False)
response = solr.get_association_table(entity=entity, category=category, q=q, limit=limit, offset=offset)
format_output(fmt, response, output)
+
+
+@solr_app.command("mappings")
+def mappings(
+ entity_id: List[str] = typer.Option(None, "--entity-id", "-e", help="entity ID to get mappings for"),
+ subject_id: List[str] = typer.Option(None, "--subject-id", "-s", help="subject ID to get mappings for"),
+ predicate_id: List[str] = typer.Option(None, "--predicate-id", "-p", help="predicate ID to get mappings for"),
+ object_id: List[str] = typer.Option(None, "--object-id", "-o", help="object ID to get mappings for"),
+ mapping_justification: List[str] = typer.Option(
+ None, "--mapping-justification", "-m", help="mapping justification to get mappings for"
+ ),
+ offset: int = typer.Option(0, "--offset", help="The offset of the first mapping to be retrieved"),
+ limit: int = typer.Option(20, "--limit", "-l", help="The number of mappings to return"),
+ fmt: str = typer.Option(
+ "json",
+ "--format",
+ "-f",
+ help="The format of the output (json, yaml, tsv, table)",
+ ),
+ output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
+):
+ args = locals()
+ args.pop("fmt", None)
+ args.pop("output", None)
+
+ solr = get_solr(update=False)
+ response = solr.get_mappings(**args)
+ format_output(fmt, response, output)
diff --git a/backend/src/monarch_py/utils/entity_utils.py b/backend/src/monarch_py/utils/entity_utils.py
index 97056219a..9cb8d032f 100644
--- a/backend/src/monarch_py/utils/entity_utils.py
+++ b/backend/src/monarch_py/utils/entity_utils.py
@@ -1,6 +1,12 @@
+from monarch_py.datamodels.model import ExpandedCurie
from monarch_py.service.curie_service import CurieService
def get_uri(id: str) -> str:
"""Returns the URI for the given CURIE."""
return CurieService().expand(id)
+
+
+def get_expanded_curie(id: str) -> ExpandedCurie:
+ """Returns the URI for the given CURIE."""
+ return ExpandedCurie(id=id, url=get_uri(id))
diff --git a/backend/tests/api/test_mapping_endpoint.py b/backend/tests/api/test_mapping_endpoint.py
new file mode 100644
index 000000000..506679c01
--- /dev/null
+++ b/backend/tests/api/test_mapping_endpoint.py
@@ -0,0 +1,17 @@
+from unittest.mock import MagicMock, patch
+
+from fastapi.testclient import TestClient
+from httpx import Response
+from monarch_py.api.search import router
+
+client = TestClient(router)
+
+
+def test_mappings(search):
+ with patch.object(
+ client, "get", MagicMock(return_value=Response(200, json=search, headers={"content-type": "application/json"}))
+ ):
+ response = client.get("/mappings?entity_id=MONDO:0000015")
+ assert response.status_code == 200
+ assert response.headers["content-type"] == "application/json"
+ assert response.json() == search
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
index b223b0016..8878112b5 100644
--- a/backend/tests/fixtures/association_counts_response.py
+++ b/backend/tests/fixtures/association_counts_response.py
@@ -5,7 +5,7 @@
def association_counts_response():
return {
"responseHeader": {
- "QTime": 1,
+ "QTime": 0,
"params": {
"facet.query": [
'(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
diff --git a/backend/tests/fixtures/mapping_query.py b/backend/tests/fixtures/mapping_query.py
new file mode 100644
index 000000000..10c157459
--- /dev/null
+++ b/backend/tests/fixtures/mapping_query.py
@@ -0,0 +1,21 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_query():
+ return {
+ "q": "*:*",
+ "rows": 20,
+ "start": 0,
+ "facet": True,
+ "facet_fields": [],
+ "facet_queries": [],
+ "filter_queries": ['subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"'],
+ "query_fields": None,
+ "def_type": "edismax",
+ "q_op": "AND",
+ "mm": "100%",
+ "boost": None,
+ "sort": None,
+ "facet_min_count": 1,
+ }
diff --git a/backend/tests/fixtures/mapping_response.py b/backend/tests/fixtures/mapping_response.py
new file mode 100644
index 000000000..7515868ce
--- /dev/null
+++ b/backend/tests/fixtures/mapping_response.py
@@ -0,0 +1,87 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_response():
+ return {
+ "responseHeader": {
+ "QTime": 0,
+ "params": {
+ "mm": "100%",
+ "q": "*:*",
+ "defType": "edismax",
+ "facet_min_count": "1",
+ "start": "0",
+ "q.op": "AND",
+ "fq": 'subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"',
+ "rows": "20",
+ "facet": "true",
+ },
+ },
+ "response": {
+ "num_found": 7,
+ "start": 0,
+ "docs": [
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "DOID:9884",
+ "object_label": "muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "ICD10CM:G71.0",
+ "object_label": "Muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "MESH:D009136",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "NCIT:C84910",
+ "object_label": "Muscular Dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "SCTID:73297009",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "UMLS:C0026850",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "Orphanet:98473",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+ },
+ ],
+ },
+ "facet_counts": {"facet_fields": {}, "facet_queries": {}},
+ }
diff --git a/backend/tests/fixtures/mappings.py b/backend/tests/fixtures/mappings.py
new file mode 100644
index 000000000..7d3e92885
--- /dev/null
+++ b/backend/tests/fixtures/mappings.py
@@ -0,0 +1,75 @@
+import pytest
+
+
+@pytest.fixture
+def mappings():
+ return {
+ "limit": 20,
+ "offset": 0,
+ "total": 7,
+ "items": [
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "DOID:9884",
+ "object_label": "muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "ICD10CM:G71.0",
+ "object_label": "Muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "MESH:D009136",
+ "object_label": None,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "NCIT:C84910",
+ "object_label": "Muscular Dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "SCTID:73297009",
+ "object_label": None,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "UMLS:C0026850",
+ "object_label": None,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "Orphanet:98473",
+ "object_label": None,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+ },
+ ],
+ }
diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py
index a25b43ff0..b37dfc336 100644
--- a/backend/tests/fixtures/node.py
+++ b/backend/tests/fixtures/node.py
@@ -19,6 +19,15 @@ def node():
"inheritance": None,
"causal_gene": [],
"causes_disease": [],
+ "mappings": [
+ {"id": "DOID:9884", "url": "http://purl.obolibrary.org/obo/DOID_9884"},
+ {"id": "ICD10CM:G71.0", "url": "https://icd.codes/icd10cm/G71.0"},
+ {"id": "MESH:D009136", "url": "http://identifiers.org/mesh/D009136"},
+ {"id": "NCIT:C84910", "url": "http://purl.obolibrary.org/obo/NCIT_C84910"},
+ {"id": "SCTID:73297009", "url": None},
+ {"id": "UMLS:C0026850", "url": "http://identifiers.org/umls/C0026850"},
+ {"id": "Orphanet:98473", "url": None},
+ ],
"external_links": [],
"provided_by_link": {
"id": "phenio",
diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
index 5fbe50b82..c2791ef80 100644
--- a/backend/tests/fixtures/search_response.py
+++ b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
def search_response():
return {
"responseHeader": {
- "QTime": 1,
+ "QTime": 0,
"params": {
"mm": "100%",
"q": "fanconi",
diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py
index 352bbffce..18aab675e 100644
--- a/backend/tests/unit/test_solr_parsers.py
+++ b/backend/tests/unit/test_solr_parsers.py
@@ -7,6 +7,7 @@
parse_autocomplete,
parse_entity,
parse_histopheno,
+ parse_mappings,
parse_search,
)
from monarch_py.utils.utils import dict_diff
@@ -65,3 +66,10 @@ def test_parse_autocomplete(autocomplete_response, autocomplete):
assert (
parsed == autocomplete
), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), autocomplete)}"
+
+
+def test_parse_mappings(mapping_response, mappings):
+ mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found")
+ solr_response = SolrQueryResult(**mapping_response)
+ parsed = parse_mappings(solr_response)
+ assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}"
diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py
index 64c58844f..0e6c75a42 100644
--- a/backend/tests/unit/test_solr_queries.py
+++ b/backend/tests/unit/test_solr_queries.py
@@ -5,6 +5,7 @@
build_association_query,
build_autocomplete_query,
build_histopheno_query,
+ build_mapping_query,
build_search_query,
)
from monarch_py.utils.utils import compare_dicts, dict_diff
@@ -111,3 +112,9 @@ def test_build_autocomplete_query(autocomplete_query):
query = build_autocomplete_query(q="fanc").dict()
expected = autocomplete_query
assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
+
+
+def test_build_mappings_query(mapping_query):
+ query = build_mapping_query(entity_id=["MONDO:0020121"]).dict()
+ expected = mapping_query
+ assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
diff --git a/frontend/fixtures/mappings.json b/frontend/fixtures/mappings.json
new file mode 100644
index 000000000..016753b75
--- /dev/null
+++ b/frontend/fixtures/mappings.json
@@ -0,0 +1,70 @@
+{
+ "limit": 20,
+ "offset": 0,
+ "total": 7,
+ "items": [
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "DOID:9884",
+ "object_label": "muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "cda26856-16a7-499c-956f-119cbaac5b96"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "ICD10CM:G71.0",
+ "object_label": "Muscular dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "25777569-b997-4c8f-a1f3-5af352a16ee1"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "MESH:D009136",
+ "object_label": null,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "NCIT:C84910",
+ "object_label": "Muscular Dystrophy",
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "SCTID:73297009",
+ "object_label": null,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "f6417283-c9d1-4289-aee6-16d30a4445b1"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "UMLS:C0026850",
+ "object_label": null,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "93968631-eedb-448b-b58a-e31e3e411dde"
+ },
+ {
+ "subject_id": "MONDO:0020121",
+ "subject_label": "muscular dystrophy",
+ "predicate_id": "skos:exactMatch",
+ "object_id": "Orphanet:98473",
+ "object_label": null,
+ "mapping_justification": "semapv:UnspecifiedMatching",
+ "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5"
+ }
+ ]
+}
diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json
index baf9051e2..d7f9825b0 100644
--- a/frontend/fixtures/node.json
+++ b/frontend/fixtures/node.json
@@ -14,6 +14,36 @@
"inheritance": null,
"causal_gene": [],
"causes_disease": [],
+ "mappings": [
+ {
+ "id": "DOID:9884",
+ "url": "http://purl.obolibrary.org/obo/DOID_9884"
+ },
+ {
+ "id": "ICD10CM:G71.0",
+ "url": "https://icd.codes/icd10cm/G71.0"
+ },
+ {
+ "id": "MESH:D009136",
+ "url": "http://identifiers.org/mesh/D009136"
+ },
+ {
+ "id": "NCIT:C84910",
+ "url": "http://purl.obolibrary.org/obo/NCIT_C84910"
+ },
+ {
+ "id": "SCTID:73297009",
+ "url": null
+ },
+ {
+ "id": "UMLS:C0026850",
+ "url": "http://identifiers.org/umls/C0026850"
+ },
+ {
+ "id": "Orphanet:98473",
+ "url": null
+ }
+ ],
"external_links": [],
"provided_by_link": {
"id": "phenio",
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 34b656aeb..522ffa0b2 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -4,6 +4,7 @@ export type ExpandedCurieId = string;
export type EntityId = string;
export type HistoPhenoId = string;
export type HistoBinId = string;
+export type MappingId = string;
export type MultiEntityAssociationResultsId = string;
export type NodeId = string;
export type SearchResultId = string;
@@ -375,6 +376,20 @@ export interface Mapping {
/** The name of the object entity */
object_label?: string,
mapping_justification?: string,
+ id: string,
+};
+/**
+ * SSSOM Mappings returned as a results collection
+ */
+export interface MappingResults extends Results {
+ /** A collection of items, with the type to be overriden by slot_usage */
+ items: Mapping[],
+ /** number of items to return in a response */
+ limit: number,
+ /** offset into the total number of items */
+ offset: number,
+ /** total number of items matching a query */
+ total: number,
};
export interface MultiEntityAssociationResults extends Results {
@@ -401,6 +416,8 @@ export interface Node extends Entity {
causal_gene?: Entity[],
/** A list of diseases that are known to be causally associated with a gene */
causes_disease?: Entity[],
+ /** List of ExpandedCuries with id and url for mapped entities */
+ mappings?: ExpandedCurie[],
/** ExpandedCurie with id and url for xrefs */
external_links?: ExpandedCurie[],
/** A link to the docs for the knowledge source that provided the node/edge. */
diff --git a/frontend/src/pages/node/SectionOverview.vue b/frontend/src/pages/node/SectionOverview.vue
index f831d3295..aae3fe9ee 100644
--- a/frontend/src/pages/node/SectionOverview.vue
+++ b/frontend/src/pages/node/SectionOverview.vue
@@ -80,13 +80,55 @@
>
+
+
+
+
+ {{ mapping.id }}
+
+
+
+
+
+
+ {{ mapping.id }}
+
+
+
+
+
+
+ {{ mapping.id }}
+
+
+
+
-
+