From 42379548c11f010602a779897732d304988d88f9 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 11:33:10 -0800 Subject: [PATCH 01/19] checkpoint --- bmt/__init__.py | 1 + bmt/toolkit_generator.py | 16 +++++++++++++++- 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/bmt/__init__.py b/bmt/__init__.py index 5ecabc1..f06959e 100644 --- a/bmt/__init__.py +++ b/bmt/__init__.py @@ -1 +1,2 @@ from bmt.toolkit import Toolkit +from bmt.toolkit import ToolkitGenerator \ No newline at end of file diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index 53f8058..055032f 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -85,7 +85,21 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ self.visit_element(slot, slot.slot_uri) - self.aliases.update({a: slot.name for a in slot.aliases}) + self.fix_aliases(slot) + self.aliases.update({a: slot.name for a in self.aliases}) + + def fix_aliases(self, aelement: Element): + if '_' in aelement.name: + new_aliases = [] + else: + new_aliases = aelement.aliases + return new_aliases + + # def fix_aliases(self, aelement: Element): + # if '_' in aelement.name: + # print(aelement.name) + + # self.aliases = {k: v for k, v in self.aliases.items() if } def visit_type(self, typ: TypeDefinition) -> None: """ From 3c8f7f18ca4e11de2053562bcd53b5e199aa5317 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 11:33:39 -0800 Subject: [PATCH 02/19] add test --- tests/unit/test_toolkit_generator.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 tests/unit/test_toolkit_generator.py diff --git a/tests/unit/test_toolkit_generator.py b/tests/unit/test_toolkit_generator.py new file mode 100644 index 0000000..6c99928 --- /dev/null +++ b/tests/unit/test_toolkit_generator.py @@ -0,0 +1,12 @@ +import pytest +from bmt import ToolkitGenerator + +REMOTE_PATH = ( + "https://raw.githubusercontent.com/biolink/biolink-model/2.2.12/biolink-model.yaml" +) + + +def test_get_generator(): + gen = ToolkitGenerator(REMOTE_PATH) + tk = gen.serialize() + print(tk) From 275c4e42c4657be3538dd1f4e7e9e000ca5dc183 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 12:04:25 -0800 Subject: [PATCH 03/19] fix tests --- bmt/toolkit_generator.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index 055032f..94c96fb 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -85,8 +85,8 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ self.visit_element(slot, slot.slot_uri) - self.fix_aliases(slot) - self.aliases.update({a: slot.name for a in self.aliases}) + new_aliases = self.fix_aliases(slot) + self.aliases.update({a: slot.name for a in new_aliases}) def fix_aliases(self, aelement: Element): if '_' in aelement.name: From 3fc48f343913626298437617341f95e275c079f5 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 12:05:34 -0800 Subject: [PATCH 04/19] remove commented out code --- bmt/toolkit_generator.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index 94c96fb..aacb4fb 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -95,11 +95,6 @@ def fix_aliases(self, aelement: Element): new_aliases = aelement.aliases return new_aliases - # def fix_aliases(self, aelement: Element): - # if '_' in aelement.name: - # print(aelement.name) - - # self.aliases = {k: v for k, v in self.aliases.items() if } def visit_type(self, typ: TypeDefinition) -> None: """ From 90c1f8ad7e242dccd6249bf4beca1795ade05d1e Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 12:21:37 -0800 Subject: [PATCH 05/19] remove commented out code --- bmt/toolkit_generator.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index aacb4fb..bb53251 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -87,6 +87,7 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: self.visit_element(slot, slot.slot_uri) new_aliases = self.fix_aliases(slot) self.aliases.update({a: slot.name for a in new_aliases}) + print(self.aliases['name']) def fix_aliases(self, aelement: Element): if '_' in aelement.name: From d967503c0071cc3b8445cce775a0fc791daaef57 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 12:26:04 -0800 Subject: [PATCH 06/19] remove commented out code --- bmt/toolkit_generator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index bb53251..ac3bf6f 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -87,7 +87,7 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: self.visit_element(slot, slot.slot_uri) new_aliases = self.fix_aliases(slot) self.aliases.update({a: slot.name for a in new_aliases}) - print(self.aliases['name']) + print(self.aliases) def fix_aliases(self, aelement: Element): if '_' in aelement.name: From 3c41dbb9dc222e35c105b3188a5ea61ad7e703f7 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 12:32:59 -0800 Subject: [PATCH 07/19] remove commented out code --- bmt/toolkit_generator.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index ac3bf6f..3ad2cd6 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -86,6 +86,7 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ self.visit_element(slot, slot.slot_uri) new_aliases = self.fix_aliases(slot) + print(new_aliases) self.aliases.update({a: slot.name for a in new_aliases}) print(self.aliases) From e6cae66cbe9c4b15117e840e4f12fa513f807f4c Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 13:26:55 -0800 Subject: [PATCH 08/19] fix locus/gene alias --- bmt/toolkit_generator.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index 3ad2cd6..3c72954 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -69,7 +69,12 @@ def visit_element(self, element: Element, element_uri: Optional[str]) -> None: self.id_prefixes[element.name].add(id_prefix) if element_uri: self.mappings[self.namespaces.uri_for(element_uri)].add(element.name) - self.aliases.update({a: element.name for a in element.aliases}) + new_aliases = self.fix_aliases(element) + if element.name == 'gene': + print(self.aliases) + self.aliases.update({a: element.name for a in new_aliases}) + if element.name == 'gene': + print(self.aliases) def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ @@ -86,9 +91,7 @@ def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ self.visit_element(slot, slot.slot_uri) new_aliases = self.fix_aliases(slot) - print(new_aliases) self.aliases.update({a: slot.name for a in new_aliases}) - print(self.aliases) def fix_aliases(self, aelement: Element): if '_' in aelement.name: @@ -97,7 +100,6 @@ def fix_aliases(self, aelement: Element): new_aliases = aelement.aliases return new_aliases - def visit_type(self, typ: TypeDefinition) -> None: """ Given a type, visit the type in the Biolink Model and pull necessary From a300c100e6fd6b58542ff0fe3aa25b0fd567c4ca Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 16:14:52 -0800 Subject: [PATCH 09/19] fix locus/gene alias --- bmt/toolkit.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 7052995..7304b5b 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -432,10 +432,14 @@ def get_element(self, name: str) -> Optional[Element]: """ parsed_name = parse_name(name) + print(parsed_name) element = self.generator.obj_for(parsed_name) if element is None and name in self.generator.aliases: + print("in aliases") + print(self.generator.aliases) element = self.get_element(self.generator.aliases[name]) if element is None and "_" in name: + print("has a _") element = self.get_element(name.replace("_", " ")) return element From 585ac28895f04f5ffaff86abc3e39f33902b1ab2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 16:28:46 -0800 Subject: [PATCH 10/19] fix locus/gene alias --- bmt/toolkit.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 7304b5b..ee493f7 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -1134,9 +1134,11 @@ def get_element_by_exact_mapping( A list of Biolink elements that correspond to the given identifier IRI/CURIE """ + print(self.generator.namespaces.uri_for(identifier)) mappings = self.generator.exact_mappings.get( self.generator.namespaces.uri_for(identifier), set() ) + print(mappings) return self._format_all_elements(mappings, formatted) @lru_cache(CACHE_SIZE) From d87d09d2e410f59bd70d1751e53ee09bbff03665 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 16:42:16 -0800 Subject: [PATCH 11/19] fix locus/gene alias --- bmt/toolkit.py | 1 - bmt/toolkit_generator.py | 18 ++++++++++++------ 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index ee493f7..7985578 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -1134,7 +1134,6 @@ def get_element_by_exact_mapping( A list of Biolink elements that correspond to the given identifier IRI/CURIE """ - print(self.generator.namespaces.uri_for(identifier)) mappings = self.generator.exact_mappings.get( self.generator.namespaces.uri_for(identifier), set() ) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index 3c72954..e1b8a71 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -54,17 +54,23 @@ def visit_element(self, element: Element, element_uri: Optional[str]) -> None: """ for curie in element.mappings: - self.mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.exact_mappings: - self.exact_mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.exact_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.close_mappings: - self.close_mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.close_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.related_mappings: - self.related_mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.related_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.narrow_mappings: - self.narrow_mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.narrow_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.broad_mappings: - self.broad_mappings[self.namespaces.uri_for(curie)].add(element.name) + if "_" not in curie: + self.broad_mappings[self.namespaces.uri_for(curie)].add(element.name) for id_prefix in element.id_prefixes: self.id_prefixes[element.name].add(id_prefix) if element_uri: From 5b73090871c0e4cbc9c8a564d304dedc421644b4 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 4 Jan 2022 16:57:15 -0800 Subject: [PATCH 12/19] model update --- bmt/toolkit.py | 2 +- bmt/toolkit_generator.py | 25 +++++++++---------------- 2 files changed, 10 insertions(+), 17 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 7985578..f019cc1 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -19,7 +19,7 @@ Path = str REMOTE_PATH = ( - "https://raw.githubusercontent.com/biolink/biolink-model/2.2.12/biolink-model.yaml" + "https://raw.githubusercontent.com/biolink/biolink-model/latest/biolink-model.yaml" ) RELATED_TO = "related to" CACHE_SIZE = 1024 diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index e1b8a71..c9b061e 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -54,33 +54,26 @@ def visit_element(self, element: Element, element_uri: Optional[str]) -> None: """ for curie in element.mappings: - if "_" not in curie: - self.mappings[self.namespaces.uri_for(curie)].add(element.name) + self.mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.exact_mappings: - if "_" not in curie: - self.exact_mappings[self.namespaces.uri_for(curie)].add(element.name) + self.exact_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.close_mappings: - if "_" not in curie: - self.close_mappings[self.namespaces.uri_for(curie)].add(element.name) + self.close_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.related_mappings: - if "_" not in curie: - self.related_mappings[self.namespaces.uri_for(curie)].add(element.name) + self.related_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.narrow_mappings: - if "_" not in curie: - self.narrow_mappings[self.namespaces.uri_for(curie)].add(element.name) + self.narrow_mappings[self.namespaces.uri_for(curie)].add(element.name) for curie in element.broad_mappings: - if "_" not in curie: - self.broad_mappings[self.namespaces.uri_for(curie)].add(element.name) + self.broad_mappings[self.namespaces.uri_for(curie)].add(element.name) for id_prefix in element.id_prefixes: self.id_prefixes[element.name].add(id_prefix) if element_uri: self.mappings[self.namespaces.uri_for(element_uri)].add(element.name) + + new_aliases = self.fix_aliases(element) - if element.name == 'gene': - print(self.aliases) self.aliases.update({a: element.name for a in new_aliases}) - if element.name == 'gene': - print(self.aliases) + def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ From ed35e9aa43fea6cc5a649eaaaeac85ec8b0b3114 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 08:42:42 -0800 Subject: [PATCH 13/19] add debugging --- bmt/toolkit.py | 4 ++++ bmt/toolkit_generator.py | 2 -- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index f019cc1..22ff461 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -1062,10 +1062,14 @@ def get_element_by_mapping( ancestors.append( [x for x in self.get_ancestors(m, mixin)[::-1] if x in mappings] ) + print(ancestors) common_ancestors = reduce( lambda s, l: s.intersection(set(l)), ancestors[1:], set(ancestors[0]) ) + print(common_ancestors) for a in ancestors[0]: + print("ancestors[0]") + print(a) if a in common_ancestors: if formatted: element = format_element(self.generator.obj_for(a)) diff --git a/bmt/toolkit_generator.py b/bmt/toolkit_generator.py index c9b061e..cd19b6b 100644 --- a/bmt/toolkit_generator.py +++ b/bmt/toolkit_generator.py @@ -70,11 +70,9 @@ def visit_element(self, element: Element, element_uri: Optional[str]) -> None: if element_uri: self.mappings[self.namespaces.uri_for(element_uri)].add(element.name) - new_aliases = self.fix_aliases(element) self.aliases.update({a: element.name for a in new_aliases}) - def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None: """ Given a slot, visit the slot in the Biolink Model and pull necessary From 59d1da43dca49d48c5613b180fa2303c24554c74 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 08:48:57 -0800 Subject: [PATCH 14/19] debugging --- bmt/toolkit.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 22ff461..e5914ac 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -1062,10 +1062,12 @@ def get_element_by_mapping( ancestors.append( [x for x in self.get_ancestors(m, mixin)[::-1] if x in mappings] ) + print("ancestors") print(ancestors) common_ancestors = reduce( lambda s, l: s.intersection(set(l)), ancestors[1:], set(ancestors[0]) ) + print("common_ancestors") print(common_ancestors) for a in ancestors[0]: print("ancestors[0]") From a44077974f77feb002857377d4902b5e071607dd Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 08:53:35 -0800 Subject: [PATCH 15/19] debugging --- bmt/toolkit.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index e5914ac..10b465e 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -1064,12 +1064,13 @@ def get_element_by_mapping( ) print("ancestors") print(ancestors) + without_empty_lists = list(filter(None, ancestors)) common_ancestors = reduce( - lambda s, l: s.intersection(set(l)), ancestors[1:], set(ancestors[0]) + lambda s, l: s.intersection(set(l)), without_empty_lists[1:], set(without_empty_lists[0]) ) print("common_ancestors") print(common_ancestors) - for a in ancestors[0]: + for a in without_empty_lists[0]: print("ancestors[0]") print(a) if a in common_ancestors: From 6fb09ef4c679c780e3a24b212c54a2e062304ef9 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 08:57:23 -0800 Subject: [PATCH 16/19] print statements to debugger statements --- bmt/toolkit.py | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 10b465e..9fc6bf0 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -432,14 +432,14 @@ def get_element(self, name: str) -> Optional[Element]: """ parsed_name = parse_name(name) - print(parsed_name) + logger.debug(parsed_name) element = self.generator.obj_for(parsed_name) if element is None and name in self.generator.aliases: - print("in aliases") - print(self.generator.aliases) + logger.debug("in aliases") + logger.debug(self.generator.aliases) element = self.get_element(self.generator.aliases[name]) if element is None and "_" in name: - print("has a _") + logger.debug("has a _") element = self.get_element(name.replace("_", " ")) return element @@ -1016,7 +1016,6 @@ def get_element_by_prefix( element = self.get_element(category) if hasattr(element, 'id_prefixes') and prefix in element.id_prefixes: categories.append(element.name) - print(categories) if len(categories) == 0: logger.warning("no biolink class found for the given curie: %s, try get_element_by_mapping?", identifier) @@ -1062,17 +1061,16 @@ def get_element_by_mapping( ancestors.append( [x for x in self.get_ancestors(m, mixin)[::-1] if x in mappings] ) - print("ancestors") - print(ancestors) + logger.debug(ancestors) without_empty_lists = list(filter(None, ancestors)) common_ancestors = reduce( lambda s, l: s.intersection(set(l)), without_empty_lists[1:], set(without_empty_lists[0]) ) - print("common_ancestors") - print(common_ancestors) + logger.debug("common_ancestors") + logger.debug(common_ancestors) for a in without_empty_lists[0]: - print("ancestors[0]") - print(a) + logger.debug("ancestors[0]") + logger.debug(a) if a in common_ancestors: if formatted: element = format_element(self.generator.obj_for(a)) @@ -1144,7 +1142,7 @@ def get_element_by_exact_mapping( mappings = self.generator.exact_mappings.get( self.generator.namespaces.uri_for(identifier), set() ) - print(mappings) + logger.debug(mappings) return self._format_all_elements(mappings, formatted) @lru_cache(CACHE_SIZE) From 88ade0a79ef64ba0724496e7d94b29c15b0a88ea Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 09:31:35 -0800 Subject: [PATCH 17/19] change schemaview to use schema instead of REMOTE_PATH --- bmt/toolkit.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index 9fc6bf0..eface40 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -42,7 +42,7 @@ def __init__( ) -> None: self.generator = ToolkitGenerator(schema) self.generator.serialize() - self.view = SchemaView(REMOTE_PATH) + self.view = SchemaView(schema) @lru_cache(CACHE_SIZE) def get_all_elements(self, formatted: bool = False) -> List[str]: From c36ea7121b400fcde48026529731e8b8f22746e1 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 09:54:24 -0800 Subject: [PATCH 18/19] revert to appropriate BM release --- bmt/toolkit.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index eface40..9bb56de 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -19,7 +19,7 @@ Path = str REMOTE_PATH = ( - "https://raw.githubusercontent.com/biolink/biolink-model/latest/biolink-model.yaml" + "https://raw.githubusercontent.com/biolink/biolink-model/2.2.13/biolink-model.yaml" ) RELATED_TO = "related to" CACHE_SIZE = 1024 From 6215bcb170bc6cd17f168c747387794374d409e5 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 5 Jan 2022 09:55:49 -0800 Subject: [PATCH 19/19] revert to appropriate BM release --- tests/unit/test_toolkit.py | 2 +- tests/unit/test_toolkit_generator.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit/test_toolkit.py b/tests/unit/test_toolkit.py index 72ee189..257404b 100644 --- a/tests/unit/test_toolkit.py +++ b/tests/unit/test_toolkit.py @@ -32,7 +32,7 @@ def toolkit(): def test_get_model_version(toolkit): version = toolkit.get_model_version() - assert version == "2.2.12" + assert version == "2.2.13" def test_get_inverse(toolkit): diff --git a/tests/unit/test_toolkit_generator.py b/tests/unit/test_toolkit_generator.py index 6c99928..950b735 100644 --- a/tests/unit/test_toolkit_generator.py +++ b/tests/unit/test_toolkit_generator.py @@ -2,7 +2,7 @@ from bmt import ToolkitGenerator REMOTE_PATH = ( - "https://raw.githubusercontent.com/biolink/biolink-model/2.2.12/biolink-model.yaml" + "https://raw.githubusercontent.com/biolink/biolink-model/2.2.13/biolink-model.yaml" )