{"id":20215526,"url":"https://github.com/kitwaremedical/alleninstitutemocklims","last_synced_at":"2025-06-19T18:43:25.613Z","repository":{"id":117425174,"uuid":"276751100","full_name":"KitwareMedical/AllenInstituteMockLIMS","owner":"KitwareMedical","description":"Allen Institute Mock LIMS implementation","archived":false,"fork":false,"pushed_at":"2022-06-02T14:24:20.000Z","size":15,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-24T07:06:50.846Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KitwareMedical.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-07-02T21:45:37.000Z","updated_at":"2022-06-02T14:24:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"a5833365-d186-41a8-a4e8-faa2c74cc23c","html_url":"https://github.com/KitwareMedical/AllenInstituteMockLIMS","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FAllenInstituteMockLIMS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FAllenInstituteMockLIMS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FAllenInstituteMockLIMS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FAllenInstituteMockLIMS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KitwareMedical","download_url":"https://codeload.github.com/KitwareMedical/AllenInstituteMockLIMS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241652964,"owners_count":19997578,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-14T06:22:52.334Z","updated_at":"2025-03-03T11:19:42.012Z","avatar_url":"https://github.com/KitwareMedical.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Allen Institute Mock LIMS implementation\n\nTested on Python 3.8 with Flask 1.1.2\n\n# Getting Started\n\n1. Download source\n\n    ```bash\n    git clone https://github.com/KitwareMedical/AllenInstituteMockLIMS\n    cd AllenInstituteMockLIMS\n    ```\n\n2. Create virtual environment\n\n    ```bash\n    python3 -m venv venv\n    . venv/bin/activate\n    ```\n\n3. Install requirements\n\n    ```bash\n    pip install -r requirements.txt\n    ```\n\n4. Start the flask application\n\n    ```bash\n    python -m flask run\n    ```\n\n# Endpoints:\n\n## Fetch Specimen Metadata\n\n`GET` `/specimen_metadata/view`\n\nReturns json metadata of a specimen based on the kind of metadata.\n\n### Query Parameters\n\n|Parameter|Type|Description|\n|---|---|---|\n|`specimen_id`|`integer`|Unique id property of the Specimen entry in the LIMS that the metadata is associated with|\n|`kind`|`string`|The kind of metadata that is to be retrieved (eg. \"IVSCC cell locations\")|\n|`version_number` (opt.)|`integer`|The version of the metadata, which may be defined by the kind of metadata|\n\n### Response\n\n#### Success `200`\n\n```json\n{\n  \"version_number\": 2,\n  \"data\": {\"foo\": \"bar\"}\n}\n```\n\n#### Error\n\n|Status Code|Body|\n|---|---|\n|`500`|`{ \"status\": 500, \"message\": \"Something went wrong\" }`|\n|`404`|`{ \"status\": 404, \"message\": \"Record not found\" }`|\n|`400`|`{ \"status\": 400, \"message\": \"Param foo is missing\" }`|\n\n### Sample Call\n\nRequest:\n\n`GET` `/specimen_metadata/view?specimen_id=1234\u0026kind=IVSCC%20cell%20locations`\n\nResponse:\n\n```json\n{\n  \"version_number\": 2,\n  \"data\": {\"foo\": \"bar\"}\n}\n```\n\n### Notes\n\nIf version_number is not specified, then the current version will be returned\n\n## Store Specimen Metadata\n\n`POST` `/specimen_metadata/store`\n\nStores json metadata of a specimen based on the kind of metadata.\n\n### URL Params\n\nNone. If URL params are provided, the request will be rejected with code 400\n\n### POST body\n\n#### Required:\n\n|Value|Type|Description|\n|---|---|---|\n|`specimen_id`|`integer`|Unique id property of the Specimen entry in the LIMS that the metadata is associated with|\n|`kind`|`string`|The kind of metadata that is to be retrieved (eg. \"IVSCC cell locations\")|\n|`data`|`object`|The metadata to be stored. 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