Skip to content

iGEM sequence file url validation + strict repository_id regex #68

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

Merged
manulera merged 5 commits into from
Nov 27, 2025
Merged

iGEM sequence file url validation + strict repository_id regex #68

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
27bba94
closes https://github.com/manulera/OpenCloning_backend/issues/371
manulera Nov 27, 2025
78c2e6a
more strict repository_id validations
manulera Nov 27, 2025
99f4bdf
fix regex
manulera Nov 27, 2025
0b132ae
fix regex
manulera Nov 27, 2025
fc03e98
fix regex
manulera Nov 27, 2025
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
Binary file modified project/excel/opencloning_linkml.xlsx
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion project/jsonld/opencloning_linkml.context.jsonld
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2025-11-26T10:36:02",
"generation_date": "2025-11-27T13:31:19",
"source": "opencloning_linkml.yaml"
},
"@context": {
Expand Down
13 changes: 7 additions & 6 deletions project/jsonld/opencloning_linkml.jsonld
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2021,7 +2021,7 @@
"usage_slot_name": "repository_id",
"range": "string",
"required": true,
"pattern": "^.+\\/.+$",
"pattern": "^[^\\/]+\\/[^\\/]+$",
"@type": "SlotDefinition"
},
{
Expand All @@ -2047,7 +2047,7 @@
{
"name": "IGEMSource_repository_id",
"definition_uri": "https://opencloning.github.io/OpenCloning_LinkML/repository_id",
"description": "The unique identifier of the sequence in the iGEM collection (for now, {part_id}-{plasmid_backbone})",
"description": "The unique identifier of the sequence in the iGEM collection (for now, {part_id}-{plasmid_backbone}) pattern: ^[^-]+-[^-]+$",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"is_a": "repository_id",
"domain": "IGEMSource",
Expand Down Expand Up @@ -2080,7 +2080,7 @@
"usage_slot_name": "sequence_file_url",
"range": "string",
"required": true,
"pattern": "^https?:\\/\\/(www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b([-a-zA-Z0-9()@:%_\\+.~#?&//=]*)$",
"pattern": "^.*.gb$",
"@type": "SlotDefinition"
},
{
Expand All @@ -2100,6 +2100,7 @@
"usage_slot_name": "repository_id",
"range": "string",
"required": true,
"pattern": "^[^\\/]+\\/[^\\/]+$",
"@type": "SlotDefinition"
},
{
Expand Down Expand Up @@ -3541,9 +3542,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "opencloning_linkml.yaml",
"source_file_date": "2025-11-26T10:35:56",
"source_file_size": 26028,
"generation_date": "2025-11-26T10:36:03",
"source_file_date": "2025-11-27T13:31:15",
"source_file_size": 26128,
"generation_date": "2025-11-27T13:31:19",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/opencloning_linkml.context.jsonld",
Expand Down
7 changes: 4 additions & 3 deletions project/jsonschema/opencloning_linkml.schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1471,15 +1471,15 @@
]
},
"repository_id": {
"description": "The unique identifier of the sequence in the iGEM collection (for now, {part_id}-{plasmid_backbone})",
"description": "The unique identifier of the sequence in the iGEM collection (for now, {part_id}-{plasmid_backbone}) pattern: ^[^-]+-[^-]+$",
"type": "string"
},
"repository_name": {
"$ref": "#/$defs/RepositoryName"
},
"sequence_file_url": {
"description": "The URL of the sequence file, for now github repository",
"pattern": "^https?:\\/\\/(www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b([-a-zA-Z0-9()@:%_\\+.~#?&//=]*)$",
"pattern": "^.*.gb$",
"type": "string"
},
"type": {
Expand Down Expand Up @@ -1895,6 +1895,7 @@
},
"repository_id": {
"description": "Subpath of the sequence in the Open DNA collections repository",
"pattern": "^[^\\/]+\\/[^\\/]+$",
"type": "string"
},
"repository_name": {
Expand Down Expand Up @@ -2836,7 +2837,7 @@
},
"repository_id": {
"description": "The subpath of the plasmid in the SnapGene plasmid library. Requesting the plasmid is possible with https://www.snapgene.com/local/fetch.php?set={category_path}&plasmid={plasmid['subpath']} where category_path is the left part of the subpath before the first / and plasmid is the subpath after the /.",
"pattern": "^.+\\/.+$",
"pattern": "^[^\\/]+\\/[^\\/]+$",
"type": "string"
},
"repository_name": {
Expand Down
Loading