Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

isinstance() instead of eval #75

Merged
merged 2 commits into from
Mar 29, 2024
Merged

isinstance() instead of eval #75

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f3abc71
`isinstance()` instead of `eval`
hrshdhgd Mar 29, 2024
22457f0
removed dbg code
hrshdhgd Mar 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions src/data/examples/examples.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Test_0:
id: CHANGE:001
type: NodeRename
old_value: '''nuclear envelope'''
new_value: '''foo bar'''
old_value: nuclear envelope
new_value: foo bar
about_node: GO:0005635
about_node_representation: curie
command_with_curie: rename GO:0005635 from 'nuclear envelope' to 'foo bar'
Expand All @@ -11,8 +11,8 @@ Test_0:
Test_1:
id: CHANGE:001
type: NodeRename
old_value: '''nucleus'''
new_value: '''bar'''
old_value: nucleus
new_value: bar
about_node: GO:0005634
about_node_representation: curie
command_with_curie: rename GO:0005634 from 'nucleus' to 'bar'
Expand Down Expand Up @@ -61,10 +61,10 @@ Test_6:
Test_7:
id: CHANGE:001
type: SynonymReplacement
old_value: '''cell nucleus'''
new_value: '''cell NUCLEUS'''
old_value: cell nucleus
new_value: cell NUCLEUS
about_node: GO:0005634
about_node_representation: curie
about_node_representation: label
command_with_curie: change synonym 'cell nucleus' for GO:0005634 to 'cell NUCLEUS'
command_with_uri: change synonym 'cell nucleus' for http://purl.obolibrary.org/obo/GO_0005634
to 'cell NUCLEUS'
Expand Down Expand Up @@ -97,7 +97,7 @@ Test_11:
about_node: GO:9999999
about_node_representation: curie
node_id: GO:9999999
name: '''foo'''
name: foo
command_with_curie: create node GO:9999999 'foo'
command_with_uri: TODO
Test_12:
Expand Down Expand Up @@ -199,15 +199,15 @@ Test_18:
Test_19:
id: CHANGE:001
type: NewTextDefinition
new_value: '''this is dummy description'''
new_value: this is dummy description
about_node: GO:0005635
about_node_representation: curie
command_with_curie: add definition 'this is dummy description' to GO:0005635
command_with_uri: add definition 'this is dummy description' to http://purl.obolibrary.org/obo/GO_0005635
Test_20:
id: CHANGE:001
type: NodeTextDefinitionChange
new_value: '''this is dummy description'''
new_value: this is dummy description
about_node: GO:0005635
about_node_representation: curie
command_with_curie: change definition of GO:0005635 to 'this is dummy description'
Expand Down
2 changes: 1 addition & 1 deletion src/docs/examples.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ type: SynonymReplacement
old_value: cell nucleus
new_value: cell NUCLEUS
about_node: GO:0005634
about_node_representation: curie
about_node_representation: label

```
## Example: Addition of a node to a subset.
Expand Down
30 changes: 21 additions & 9 deletions src/kgcl_schema/grammar/parser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -229,9 +229,12 @@ def parse_remove_synonym(tree, id):
def parse_change_synonym(tree, id):
"""Change the synonym of a class."""
entity_token = extract(tree, "entity")
old_value = extract(tree, "synonym")
new_value = extract(tree, "new_synonym")
entity, representation = get_entity_representation(entity_token)
old_token = extract(tree, "synonym")
old_value, representation = get_entity_representation(old_token)
new_token = extract(tree, "new_synonym")
new_value, representation = get_entity_representation(new_token)

return SynonymReplacement(
id=id,
about_node=entity,
Expand All @@ -254,7 +257,8 @@ def parse_create_class(tree, id):
def parse_add_definition(tree, id):
"""Add definition to class."""
entity_token = extract(tree, "entity")
new_value = extract(tree, "new_definition")
new_token = extract(tree, "new_definition")
new_value, representation = get_entity_representation(new_token)
entity, representation = get_entity_representation(entity_token)
return NewTextDefinition(
id=id,
Expand All @@ -267,8 +271,14 @@ def parse_add_definition(tree, id):
def parse_change_definition(tree, id):
"""Change the definition of a class."""
entity_token = extract(tree, "entity")
old_value = extract(tree, "old_definition")
new_value = extract(tree, "new_definition")
old_token = extract(tree, "old_definition")
if old_token:
old_value, representation = get_entity_representation(old_token)
else:
old_value = None
representation = None
new_token = extract(tree, "new_definition")
new_value, representation = get_entity_representation(new_token)
entity, representation = get_entity_representation(entity_token)
return NodeTextDefinitionChange(
id=id,
Expand Down Expand Up @@ -298,6 +308,7 @@ def parse_create(tree, id):
"""Create a node."""
term_id_token = extract(tree, "id")
label_token = extract(tree, "label")
label_value, representation = get_entity_representation(label_token)
language_token = extract(tree, "language")

entity, representation = get_entity_representation(term_id_token)
Expand All @@ -307,7 +318,7 @@ def parse_create(tree, id):
about_node=entity,
about_node_representation=representation,
node_id=entity, # was term_id_token
name=label_token,
name=label_value,
language=language_token,
)

Expand Down Expand Up @@ -588,7 +599,9 @@ def parse_obsolete(tree, id):
def parse_rename(tree, id):
"""Rename a node."""
old_token = extract(tree, "old_label")
old_value, representation = get_entity_representation(old_token)
new_token = extract(tree, "new_label")
new_value, representation = get_entity_representation(new_token)
old_language = extract(tree, "old_language")
new_language = extract(tree, "new_language")

Expand All @@ -600,13 +613,12 @@ def parse_rename(tree, id):
else:
entity = None
representation = None

return NodeRename(
id=id,
about_node=entity,
about_node_representation=representation,
old_value=old_token,
new_value=new_token,
old_value=old_value,
new_value=new_value,
old_language=old_language,
new_language=new_language,
)
Expand Down
4 changes: 2 additions & 2 deletions src/kgcl_schema/grammar/render_operations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,8 @@ def render_entity(entity, rdf_type):
entity = entity.replace("'", "")
return entity
elif rdf_type == "label":
if type(eval(entity)) == Token:
entity = eval(entity).value
if isinstance(entity, Token):
entity = entity.value
# elif "'" in entity:
# # TODO: replacing quotes with backticks
# # is only a temporary workaround
Expand Down
26 changes: 13 additions & 13 deletions tests/cases.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,8 +66,8 @@
f"rename {NUCLEAR_ENVELOPE_URI} from 'nuclear envelope' to 'foo bar'",
NodeRename(
id=UID,
old_value="'nuclear envelope'",
new_value="'foo bar'",
old_value="nuclear envelope",
new_value="foo bar",
about_node="GO:0005635",
about_node_representation="curie",
),
Expand All @@ -78,8 +78,8 @@
f"rename {NUCLEUS_URI} from 'nucleus' to 'bar'",
NodeRename(
id=UID,
old_value="'nucleus'",
new_value="'bar'",
old_value="nucleus",
new_value="bar",
about_node=NUCLEUS,
about_node_representation="curie",
),
Expand All @@ -90,8 +90,8 @@
# f"""rename {NUCLEUS} from 'nucleus' to 'bobby " tables'""",
# f"""rename {NUCLEUS_URI} from 'nucleus' to 'bobby " tables'""",
# NodeRename(id=UID,
# old_value="'nucleus'",
# new_value="'bar'",
# old_value="nucleus",
# new_value="bar",
# about_node=NUCLEUS,
# about_node_representation='curie'),
# None
Expand Down Expand Up @@ -155,9 +155,9 @@
SynonymReplacement(
id=UID,
about_node=NUCLEUS,
about_node_representation="curie",
old_value="'cell nucleus'",
new_value="'cell NUCLEUS'",
about_node_representation="label",
old_value="cell nucleus",
new_value="cell NUCLEUS",
),
None,
),
Expand Down Expand Up @@ -198,7 +198,7 @@
id=UID,
node_id=NEW_TERM, ## TODO: remove this
about_node=NEW_TERM,
name="'foo'",
name="foo",
about_node_representation="curie",
),
None,
Expand All @@ -212,7 +212,7 @@
# NodeCreation(id=UID,
# node_id=NEW_TERM, ## TODO: remove this
# about_node=NEW_TERM,
# name="'foo'",
# name="foo",
# about_node_representation='curie'),
# None
# ),
Expand Down Expand Up @@ -338,7 +338,7 @@
f"add definition 'this is dummy description' to {NUCLEAR_ENVELOPE_URI}",
NewTextDefinition(
id=UID,
new_value="'this is dummy description'",
new_value="this is dummy description",
about_node="GO:0005635",
about_node_representation="curie",
),
Expand All @@ -349,7 +349,7 @@
f"change definition of {NUCLEAR_ENVELOPE_URI} to 'this is dummy description'",
NodeTextDefinitionChange(
id=UID,
new_value="'this is dummy description'",
new_value="this is dummy description",
about_node="GO:0005635",
about_node_representation="curie",
),
Expand Down
Loading