From de20c1183d57cbf1ca66ed8b840bd921a8c7abf3 Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Tue, 5 May 2026 09:55:09 +0200 Subject: [PATCH 1/5] Quick fix for v5 compatibility. --- scripts/coverage/coverage.py | 6 +-- scripts/coverage/index.tpl.html | 6 +-- scripts/coverage/index_old.tpl.html | 40 +++++++++++++++++++ scripts/coverage/terminology.tpl.html | 9 ++--- scripts/coverage/terminology_old.tpl.html | 48 +++++++++++++++++++++++ 5 files changed, 96 insertions(+), 13 deletions(-) create mode 100644 scripts/coverage/index_old.tpl.html create mode 100644 scripts/coverage/terminology_old.tpl.html diff --git a/scripts/coverage/coverage.py b/scripts/coverage/coverage.py index 844393e887..71d2cecab3 100644 --- a/scripts/coverage/coverage.py +++ b/scripts/coverage/coverage.py @@ -50,8 +50,9 @@ def calculate_stats(instance_data): for key in ( "definition", "description", - "interlexIdentifier", - "knowledgeSpaceLink", + #"interlexIdentifier", + #"knowledgeSpaceLink", + "preferredCrossReference", "preferredOntologyIdentifier", "synonym", ): @@ -92,7 +93,6 @@ def main(build_dir="_coverage"): context = { "terminologies": stats } - with open(build_dir / "index.html", "w") as fp: fp.write(template_home.render(**context)) shutil.copy(this_dir / "coverage.css", build_dir) diff --git a/scripts/coverage/index.tpl.html b/scripts/coverage/index.tpl.html index 28c2745319..fec938214e 100644 --- a/scripts/coverage/index.tpl.html +++ b/scripts/coverage/index.tpl.html @@ -14,8 +14,7 @@

Terminologies

Name Definition Description - Interlex id - KS link + CrossReference id Ontology id Synonyms @@ -26,8 +25,7 @@

Terminologies

{{term_name}} {{stats.definition|int}}% {{stats.description|int}}% - {{stats.interlexIdentifier|int}}% - {{stats.knowledgeSpaceLink|int}}% + {{stats.preferredCrossReference|int}}% {{stats.preferredOntologyIdentifier|int}}% {{stats.synonym|int}}% diff --git a/scripts/coverage/index_old.tpl.html b/scripts/coverage/index_old.tpl.html new file mode 100644 index 0000000000..28c2745319 --- /dev/null +++ b/scripts/coverage/index_old.tpl.html @@ -0,0 +1,40 @@ + + + + openMINDS instance library status + + + + +

openMINDS instance library status

+

Terminologies

+ + + + + + + + + + + + + + {% for term_name, stats in terminologies.items() %} + + + + + + + + + + {% endfor %} + +
NameDefinitionDescriptionInterlex idKS linkOntology idSynonyms
{{term_name}}{{stats.definition|int}}%{{stats.description|int}}%{{stats.interlexIdentifier|int}}%{{stats.knowledgeSpaceLink|int}}%{{stats.preferredOntologyIdentifier|int}}%{{stats.synonym|int}}%
+ + + + \ No newline at end of file diff --git a/scripts/coverage/terminology.tpl.html b/scripts/coverage/terminology.tpl.html index f20802777e..fb23e231d0 100644 --- a/scripts/coverage/terminology.tpl.html +++ b/scripts/coverage/terminology.tpl.html @@ -14,8 +14,7 @@

Terminologies: {{term_name}}

Name Definition Description - Interlex id - KS link + CrossReference id Ontology id Synonyms @@ -23,8 +22,7 @@

Terminologies: {{term_name}}

{{stats.definition|int}}% {{stats.description|int}}% - {{stats.interlexIdentifier|int}}% - {{stats.knowledgeSpaceLink|int}}% + {{stats.preferredCrossReference|int}}% {{stats.preferredOntologyIdentifier|int}}% {{stats.synonym|int}}% @@ -35,8 +33,7 @@

Terminologies: {{term_name}}

{{instance.name}} - - + diff --git a/scripts/coverage/terminology_old.tpl.html b/scripts/coverage/terminology_old.tpl.html new file mode 100644 index 0000000000..f20802777e --- /dev/null +++ b/scripts/coverage/terminology_old.tpl.html @@ -0,0 +1,48 @@ + + + + openMINDS instance library status + + + + +

openMINDS instance library status

+

Terminologies: {{term_name}}

+ + + + + + + + + + + + + + + + + + + + + + + {% for instance in instances.values()|sort(attribute="name") %} + + + + + + + + + + {% endfor %} + +
NameDefinitionDescriptionInterlex idKS linkOntology idSynonyms
{{stats.definition|int}}%{{stats.description|int}}%{{stats.interlexIdentifier|int}}%{{stats.knowledgeSpaceLink|int}}%{{stats.preferredOntologyIdentifier|int}}%{{stats.synonym|int}}%
{{instance.name}}
+ + + \ No newline at end of file From 20957c4d1628de9369513d132fde4a86da11779d Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Tue, 5 May 2026 09:58:08 +0200 Subject: [PATCH 2/5] Add missing newline at end of files. --- scripts/coverage/coverage.css | 2 +- scripts/coverage/index.tpl.html | 2 +- scripts/coverage/index_old.tpl.html | 2 +- scripts/coverage/terminology.tpl.html | 2 +- scripts/coverage/terminology_old.tpl.html | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/coverage/coverage.css b/scripts/coverage/coverage.css index 4054bf95a5..435f126d90 100644 --- a/scripts/coverage/coverage.css +++ b/scripts/coverage/coverage.css @@ -21,4 +21,4 @@ th { td { min-width: 6rem; -} \ No newline at end of file +} diff --git a/scripts/coverage/index.tpl.html b/scripts/coverage/index.tpl.html index fec938214e..3afe91dc04 100644 --- a/scripts/coverage/index.tpl.html +++ b/scripts/coverage/index.tpl.html @@ -35,4 +35,4 @@

Terminologies

- \ No newline at end of file + diff --git a/scripts/coverage/index_old.tpl.html b/scripts/coverage/index_old.tpl.html index 28c2745319..6a62c68ca4 100644 --- a/scripts/coverage/index_old.tpl.html +++ b/scripts/coverage/index_old.tpl.html @@ -37,4 +37,4 @@

Terminologies

- \ No newline at end of file + diff --git a/scripts/coverage/terminology.tpl.html b/scripts/coverage/terminology.tpl.html index fb23e231d0..8cd28cb21c 100644 --- a/scripts/coverage/terminology.tpl.html +++ b/scripts/coverage/terminology.tpl.html @@ -42,4 +42,4 @@

Terminologies: {{term_name}}

- \ No newline at end of file + diff --git a/scripts/coverage/terminology_old.tpl.html b/scripts/coverage/terminology_old.tpl.html index f20802777e..9ed3d39c14 100644 --- a/scripts/coverage/terminology_old.tpl.html +++ b/scripts/coverage/terminology_old.tpl.html @@ -45,4 +45,4 @@

Terminologies: {{term_name}}

- \ No newline at end of file + From 1561c74e76a9f1391359657c9135176c35c6bc02 Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Tue, 5 May 2026 11:59:15 +0200 Subject: [PATCH 3/5] Unnecessary comment. --- scripts/coverage/coverage.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/scripts/coverage/coverage.py b/scripts/coverage/coverage.py index 71d2cecab3..1343403023 100644 --- a/scripts/coverage/coverage.py +++ b/scripts/coverage/coverage.py @@ -26,7 +26,8 @@ def get_instance_data(): """Return the data for all instances in the library.""" # At present, only covers terminologies instance_data = {} - root = Path("instances/latest") + #root = Path("instances/latest") + root = Path("/Users/raphaelgazzotti/PycharmProjects/openMINDS_instances/instances/latest") for dir in root.iterdir(): if dir.name == "terminologies": instance_data[dir.name] = {} @@ -50,8 +51,8 @@ def calculate_stats(instance_data): for key in ( "definition", "description", - #"interlexIdentifier", - #"knowledgeSpaceLink", + "interlexIdentifier", + "knowledgeSpaceLink", "preferredCrossReference", "preferredOntologyIdentifier", "synonym", From c24d39d9878b55f02cde07981e88b655256abb44 Mon Sep 17 00:00:00 2001 From: Raphael-Gazzotti <125291580+Raphael-Gazzotti@users.noreply.github.com> Date: Tue, 5 May 2026 12:00:29 +0200 Subject: [PATCH 4/5] Change instance data root path to relative Revert the root path to a relative path for instance data. --- scripts/coverage/coverage.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/coverage/coverage.py b/scripts/coverage/coverage.py index 1343403023..5d909982d5 100644 --- a/scripts/coverage/coverage.py +++ b/scripts/coverage/coverage.py @@ -26,8 +26,7 @@ def get_instance_data(): """Return the data for all instances in the library.""" # At present, only covers terminologies instance_data = {} - #root = Path("instances/latest") - root = Path("/Users/raphaelgazzotti/PycharmProjects/openMINDS_instances/instances/latest") + root = Path("instances/latest") for dir in root.iterdir(): if dir.name == "terminologies": instance_data[dir.name] = {} From 0f0c59ff43b66ddb65516ae221d4b9e61ef75aa3 Mon Sep 17 00:00:00 2001 From: Raphael-Gazzotti <125291580+Raphael-Gazzotti@users.noreply.github.com> Date: Wed, 6 May 2026 09:13:04 +0200 Subject: [PATCH 5/5] Apply suggestions from code review Co-authored-by: Lyuba Zehl --- scripts/coverage/index.tpl.html | 4 ++-- scripts/coverage/terminology.tpl.html | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/coverage/index.tpl.html b/scripts/coverage/index.tpl.html index 3afe91dc04..bde222938f 100644 --- a/scripts/coverage/index.tpl.html +++ b/scripts/coverage/index.tpl.html @@ -14,8 +14,8 @@

Terminologies

Name Definition Description - CrossReference id - Ontology id + XRef ID + Ontology ID Synonyms diff --git a/scripts/coverage/terminology.tpl.html b/scripts/coverage/terminology.tpl.html index 8cd28cb21c..e101a5337e 100644 --- a/scripts/coverage/terminology.tpl.html +++ b/scripts/coverage/terminology.tpl.html @@ -14,8 +14,8 @@

Terminologies: {{term_name}}

Name Definition Description - CrossReference id - Ontology id + XRef ID + Ontology ID Synonyms