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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,13 +7,13 @@ info: | |
| email: "[email protected]" | ||
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| servers: | ||
| - url: https://ebp.biogenoma.cat/api | ||
| - url: https://genome.crg.es/ebp/api | ||
| description: server containing all the data submitted to INSDC under the Earth Biogenome Project (PRJNA533106) umbrella | ||
| - url: https://erga.biogenoma.cat/api | ||
| - url: https://genome.crg.es/erga/api | ||
| description: server containing all the data generated under the European Reference Genome Atlas (PRJEB43510) umbrella | ||
| - url: https://dades.biogenoma.cat/api | ||
| description: server containing all the data generated under the Catalan Initiative for the Earth Biogenome Project | ||
| - url: https://lichenoteca.biogenoma.cat/api | ||
| - url: https://genome.crg.es/lichenoteca/api | ||
| description: server containing samples derived from the Lichenoteca dataset (https://doi.org/10.15468/dgecw5), accessed via GBIF.org on 2024-05-26, of the Institut Botanic de Barcelona. | ||
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| tags: | ||
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@@ -47,7 +47,7 @@ paths: | |
| type: string | ||
| format: binary | ||
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| /stats: | ||
| /lookup: | ||
| get: | ||
| tags: | ||
| - "stats" | ||
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@@ -74,11 +74,12 @@ paths: | |
| type: number | ||
| taxons: | ||
| type: number | ||
| /stats/{model}: | ||
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| /stats/{model}/{field}: | ||
| get: | ||
| tags: | ||
| - "stats" | ||
| summary: "get object properties statistics" | ||
| summary: "get model field statistics" | ||
| parameters: | ||
| - in: 'path' | ||
| name: 'model' | ||
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@@ -93,16 +94,11 @@ paths: | |
| - "experiments" | ||
| - "organisms" | ||
| - "taxons" | ||
| - in: 'query' | ||
| - in: 'path' | ||
| name: 'field' | ||
| required: true | ||
| schema: | ||
| type: string | ||
| - in: 'query' | ||
| name: 'query' | ||
| required: true | ||
| schema: | ||
| type: string | ||
| responses: | ||
| "200": | ||
| description: "successfull operations" | ||
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@@ -111,7 +107,7 @@ paths: | |
| schema: | ||
| type: object | ||
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| /tree: | ||
| /computed_tree: | ||
| get: | ||
| tags: | ||
| - "taxonomy" | ||
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@@ -124,53 +120,39 @@ paths: | |
| schema: | ||
| $ref: "#/components/schemas/TreeNode" | ||
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| /tree/{taxid}: | ||
| get: | ||
| tags: | ||
| - "taxonomy" | ||
| summary: "generate a tree using the provided taxid as root" | ||
| parameters: | ||
| - in: 'path' | ||
| name: 'taxid' | ||
| required: true | ||
| schema: | ||
| type: "string" | ||
| responses: | ||
| "200": | ||
| description: "successful operation" | ||
| content: | ||
| application/json: | ||
| schema: | ||
| $ref: "#/components/schemas/TreeNode" | ||
| "404": | ||
| description: "Taxon not found" | ||
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| /organisms: | ||
| get: | ||
| tags: | ||
| - "organisms" | ||
| summary: "Endpoint to retrieve a paginated list of organisms" | ||
| parameters: | ||
| - in: 'query' | ||
| name: 'parent_taxid' | ||
| name: 'filter' | ||
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'filter' | ||
| name: 'parent_taxon' | ||
| schema: | ||
| type: 'string' | ||
| - in: "query" | ||
| name: "country" | ||
| name: "countries" | ||
| schema: | ||
| type: "string" | ||
| description: "country code" | ||
| description: "country code, ex: US, ES" | ||
| - in: 'query' | ||
| name: 'sort_order' | ||
| schema: | ||
| type: 'string' | ||
| enum: | ||
| - "asc" | ||
| - "desc" | ||
| - in: 'query' | ||
| name: 'format' | ||
| schema: | ||
| type: 'string' | ||
| enum: | ||
| - "tsv" | ||
| - "json" | ||
| - in: 'query' | ||
| name: 'sort_column' | ||
| schema: | ||
|
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@@ -232,6 +214,26 @@ paths: | |
| "404": | ||
| description: "Organism not found" | ||
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| /organisms/{taxid}/lookup: | ||
| get: | ||
| tags: | ||
| - "organisms" | ||
| parameters: | ||
| - in: 'path' | ||
| name: 'taxid' | ||
| required: true | ||
| schema: | ||
| type: "string" | ||
| responses: | ||
| "200": | ||
| description: "successful operation" | ||
| content: | ||
| application/json: | ||
| schema: | ||
| type: object | ||
| "404": | ||
| description: "Organism not found" | ||
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| /organisms/{taxid}/lineage: | ||
| get: | ||
| tags: | ||
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@@ -395,26 +397,12 @@ paths: | |
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'assembly_level' | ||
| name: 'format' | ||
| schema: | ||
| type: "string" | ||
| type: 'string' | ||
| enum: | ||
| - "Chromosome" | ||
| - "Complete Genome" | ||
| - "Contig" | ||
| - "Scaffold" | ||
| - in: 'query' | ||
| name: 'start_date' | ||
| schema: | ||
| type: "string" | ||
| - in: 'query' | ||
| name: 'end_date' | ||
| schema: | ||
| type: "string" | ||
| - in: 'query' | ||
| name: 'submitter' | ||
| schema: | ||
| type: "string" | ||
| - "tsv" | ||
| - "json" | ||
| - in: 'query' | ||
| name: 'sort_order' | ||
| schema: | ||
|
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@@ -426,10 +414,6 @@ paths: | |
| name: 'sort_column' | ||
| schema: | ||
| type: "string" | ||
| enum: | ||
| - "contig_n50" | ||
| - "size" | ||
| - "submission_date" | ||
| - in: 'query' | ||
| name: 'blobtoolkit' | ||
| schema: | ||
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@@ -480,6 +464,26 @@ paths: | |
| "404": | ||
| description: "Assembly not found" | ||
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| /assemblies/{accession}/lookup: | ||
| get: | ||
| tags: | ||
| - "organisms" | ||
| parameters: | ||
| - in: 'path' | ||
| name: 'taxid' | ||
| required: true | ||
| schema: | ||
| type: "string" | ||
| responses: | ||
| "200": | ||
| description: "successful operation" | ||
| content: | ||
| application/json: | ||
| schema: | ||
| type: object | ||
| "404": | ||
| description: "Assembly not found" | ||
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| /assemblies/{accession}/annotations: | ||
| get: | ||
| tags: | ||
|
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@@ -502,6 +506,28 @@ paths: | |
| "404": | ||
| description: "Assembly not found" | ||
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| /assemblies/{accession}/chromosomes: | ||
| get: | ||
| tags: | ||
| - "assemblies" | ||
| parameters: | ||
| - in: 'path' | ||
| name: 'accession' | ||
| required: true | ||
| schema: | ||
| type: 'string' | ||
| responses: | ||
| "200": | ||
| description: "successful operation" | ||
| content: | ||
| application/json: | ||
| schema: | ||
| type: "array" | ||
| items: | ||
| $ref: "#/components/schemas/Chromosome" | ||
| "404": | ||
| description: "Assembly not found" | ||
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| /experiments: | ||
| get: | ||
| tags: | ||
|
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@@ -513,13 +539,12 @@ paths: | |
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'start_date' | ||
| schema: | ||
| type: "string" | ||
| - in: 'query' | ||
| name: 'end_date' | ||
| name: 'format' | ||
| schema: | ||
| type: "string" | ||
| type: 'string' | ||
| enum: | ||
| - "tsv" | ||
| - "json" | ||
| - in: 'query' | ||
| name: 'sort_order' | ||
| schema: | ||
|
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@@ -531,12 +556,6 @@ paths: | |
| name: 'sort_column' | ||
| schema: | ||
| type: "string" | ||
| enum: | ||
| - "first_created" | ||
| - in: 'query' | ||
| name: 'center' | ||
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'offset' | ||
| schema: | ||
|
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@@ -596,19 +615,16 @@ paths: | |
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'start_date' | ||
| schema: | ||
| type: "string" | ||
| - in: 'query' | ||
| name: 'end_date' | ||
| schema: | ||
| type: "string" | ||
| name: 'format' | ||
| schema: | ||
| type: 'string' | ||
| enum: | ||
| - "tsv" | ||
| - "json" | ||
| - in: "query" | ||
| name: "sort_column" | ||
| schema: | ||
| type: "string" | ||
| enum: | ||
| - "collection_date" | ||
| - in: 'query' | ||
| name: 'sort_order' | ||
| schema: | ||
|
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@@ -759,12 +775,17 @@ paths: | |
| name: 'filter' | ||
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'format' | ||
| schema: | ||
| type: 'string' | ||
| enum: | ||
| - "tsv" | ||
| - "json" | ||
| - in: "query" | ||
| name: "sort_column" | ||
| schema: | ||
| type: "string" | ||
| enum: | ||
| - "created" | ||
| - in: 'query' | ||
| name: 'sort_order' | ||
| schema: | ||
|
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@@ -857,6 +878,13 @@ paths: | |
| name: 'filter' | ||
| schema: | ||
| type: 'string' | ||
| - in: 'query' | ||
| name: 'format' | ||
| schema: | ||
| type: 'string' | ||
| enum: | ||
| - "tsv" | ||
| - "json" | ||
| - in: 'query' | ||
| name: 'offset' | ||
| schema: | ||
|
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@@ -1141,6 +1169,14 @@ components: | |
| metadata: | ||
| type: "object" | ||
| description: "INSDC biosample metadata" | ||
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| Chromosome: | ||
| type: "object" | ||
| properties: | ||
| accession_version: | ||
| type: "string" | ||
| metadata: | ||
| type: "object" | ||
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| LocalSample: | ||
| type: "object" | ||
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