@synsci/cli-darwin-arm64 1.1.76 → 1.1.78

package/bin/skills/benchling-integration/references/api_endpoints.md

@@ -0,0 +1,883 @@
+# Benchling REST API Endpoints Reference
+
+## Base URL
+
+All API requests use the base URL format:
+```
+https://{tenant}.benchling.com/api/v2
+```
+
+Replace `{tenant}` with your Benchling tenant name.
+
+## API Versioning
+
+Current API version: `v2` (2025-10-07)
+
+The API version is specified in the URL path. Benchling maintains backward compatibility within a major version.
+
+## Authentication
+
+All requests require authentication via HTTP headers:
+
+**API Key (Basic Auth):**
+```bash
+curl -X GET \
+  https://your-tenant.benchling.com/api/v2/dna-sequences \
+  -u "your_api_key:"
+```
+
+**OAuth Bearer Token:**
+```bash
+curl -X GET \
+  https://your-tenant.benchling.com/api/v2/dna-sequences \
+  -H "Authorization: Bearer your_access_token"
+```
+
+## Common Headers
+
+```
+Authorization: Bearer {token}
+Content-Type: application/json
+Accept: application/json
+```
+
+## Response Format
+
+All responses follow a consistent JSON structure:
+
+**Single Resource:**
+```json
+{
+  "id": "seq_abc123",
+  "name": "My Sequence",
+  "bases": "ATCGATCG",
+  ...
+}
+```
+
+**List Response:**
+```json
+{
+  "results": [
+    {"id": "seq_1", "name": "Sequence 1"},
+    {"id": "seq_2", "name": "Sequence 2"}
+  ],
+  "nextToken": "token_for_next_page"
+}
+```
+
+## Pagination
+
+List endpoints support pagination:
+
+**Query Parameters:**
+- `pageSize`: Number of items per page (default: 50, max: 100)
+- `nextToken`: Token from previous response for next page
+
+**Example:**
+```bash
+curl -X GET \
+  "https://your-tenant.benchling.com/api/v2/dna-sequences?pageSize=50&nextToken=abc123"
+```
+
+## Error Responses
+
+**Format:**
+```json
+{
+  "error": {
+    "type": "NotFoundError",
+    "message": "DNA sequence not found",
+    "userMessage": "The requested sequence does not exist or you don't have access"
+  }
+}
+```
+
+**Common Status Codes:**
+- `200 OK`: Success
+- `201 Created`: Resource created
+- `400 Bad Request`: Invalid parameters
+- `401 Unauthorized`: Missing or invalid credentials
+- `403 Forbidden`: Insufficient permissions
+- `404 Not Found`: Resource doesn't exist
+- `422 Unprocessable Entity`: Validation error
+- `429 Too Many Requests`: Rate limit exceeded
+- `500 Internal Server Error`: Server error
+
+## Core Endpoints
+
+### DNA Sequences
+
+**List DNA Sequences:**
+```http
+GET /api/v2/dna-sequences
+
+Query Parameters:
+- pageSize: integer (default: 50, max: 100)
+- nextToken: string
+- folderId: string
+- schemaId: string
+- name: string (filter by name)
+- modifiedAt: string (ISO 8601 date)
+```
+
+**Get DNA Sequence:**
+```http
+GET /api/v2/dna-sequences/{sequenceId}
+```
+
+**Create DNA Sequence:**
+```http
+POST /api/v2/dna-sequences
+
+Body:
+{
+  "name": "My Plasmid",
+  "bases": "ATCGATCG",
+  "isCircular": true,
+  "folderId": "fld_abc123",
+  "schemaId": "ts_abc123",
+  "fields": {
+    "gene_name": {"value": "GFP"},
+    "resistance": {"value": "Kanamycin"}
+  },
+  "entityRegistryId": "src_abc123",  // optional for registration
+  "namingStrategy": "NEW_IDS"        // optional for registration
+}
+```
+
+**Update DNA Sequence:**
+```http
+PATCH /api/v2/dna-sequences/{sequenceId}
+
+Body:
+{
+  "name": "Updated Plasmid",
+  "fields": {
+    "gene_name": {"value": "mCherry"}
+  }
+}
+```
+
+**Archive DNA Sequence:**
+```http
+POST /api/v2/dna-sequences:archive
+
+Body:
+{
+  "dnaSequenceIds": ["seq_abc123"],
+  "reason": "Deprecated construct"
+}
+```
+
+### RNA Sequences
+
+**List RNA Sequences:**
+```http
+GET /api/v2/rna-sequences
+```
+
+**Get RNA Sequence:**
+```http
+GET /api/v2/rna-sequences/{sequenceId}
+```
+
+**Create RNA Sequence:**
+```http
+POST /api/v2/rna-sequences
+
+Body:
+{
+  "name": "gRNA-001",
+  "bases": "AUCGAUCG",
+  "folderId": "fld_abc123",
+  "fields": {
+    "target_gene": {"value": "TP53"}
+  }
+}
+```
+
+**Update RNA Sequence:**
+```http
+PATCH /api/v2/rna-sequences/{sequenceId}
+```
+
+**Archive RNA Sequence:**
+```http
+POST /api/v2/rna-sequences:archive
+```
+
+### Amino Acid (Protein) Sequences
+
+**List AA Sequences:**
+```http
+GET /api/v2/aa-sequences
+```
+
+**Get AA Sequence:**
+```http
+GET /api/v2/aa-sequences/{sequenceId}
+```
+
+**Create AA Sequence:**
+```http
+POST /api/v2/aa-sequences
+
+Body:
+{
+  "name": "GFP Protein",
+  "aminoAcids": "MSKGEELFTGVVPILVELDGDVNGHKF",
+  "folderId": "fld_abc123"
+}
+```
+
+### Custom Entities
+
+**List Custom Entities:**
+```http
+GET /api/v2/custom-entities
+
+Query Parameters:
+- schemaId: string (required to filter by type)
+- pageSize: integer
+- nextToken: string
+```
+
+**Get Custom Entity:**
+```http
+GET /api/v2/custom-entities/{entityId}
+```
+
+**Create Custom Entity:**
+```http
+POST /api/v2/custom-entities
+
+Body:
+{
+  "name": "HEK293T-Clone5",
+  "schemaId": "ts_cellline_abc",
+  "folderId": "fld_abc123",
+  "fields": {
+    "passage_number": {"value": "15"},
+    "mycoplasma_test": {"value": "Negative"}
+  }
+}
+```
+
+**Update Custom Entity:**
+```http
+PATCH /api/v2/custom-entities/{entityId}
+
+Body:
+{
+  "fields": {
+    "passage_number": {"value": "16"}
+  }
+}
+```
+
+### Mixtures
+
+**List Mixtures:**
+```http
+GET /api/v2/mixtures
+```
+
+**Create Mixture:**
+```http
+POST /api/v2/mixtures
+
+Body:
+{
+  "name": "LB-Amp Media",
+  "folderId": "fld_abc123",
+  "schemaId": "ts_mixture_abc",
+  "ingredients": [
+    {
+      "componentEntityId": "ent_lb_base",
+      "amount": {"value": "1000", "units": "mL"}
+    },
+    {
+      "componentEntityId": "ent_ampicillin",
+      "amount": {"value": "100", "units": "mg"}
+    }
+  ]
+}
+```
+
+### Containers
+
+**List Containers:**
+```http
+GET /api/v2/containers
+
+Query Parameters:
+- parentStorageId: string (filter by location/box)
+- schemaId: string
+- barcode: string
+```
+
+**Get Container:**
+```http
+GET /api/v2/containers/{containerId}
+```
+
+**Create Container:**
+```http
+POST /api/v2/containers
+
+Body:
+{
+  "name": "Sample-001",
+  "schemaId": "cont_schema_abc",
+  "barcode": "CONT001",
+  "parentStorageId": "box_abc123",
+  "fields": {
+    "concentration": {"value": "100 ng/μL"},
+    "volume": {"value": "50 μL"}
+  }
+}
+```
+
+**Update Container:**
+```http
+PATCH /api/v2/containers/{containerId}
+
+Body:
+{
+  "fields": {
+    "volume": {"value": "45 μL"}
+  }
+}
+```
+
+**Transfer Container:**
+```http
+POST /api/v2/containers:transfer
+
+Body:
+{
+  "containerIds": ["cont_abc123"],
+  "destinationStorageId": "box_xyz789"
+}
+```
+
+**Check Out Container:**
+```http
+POST /api/v2/containers:checkout
+
+Body:
+{
+  "containerIds": ["cont_abc123"],
+  "comment": "Taking to bench"
+}
+```
+
+**Check In Container:**
+```http
+POST /api/v2/containers:checkin
+
+Body:
+{
+  "containerIds": ["cont_abc123"],
+  "locationId": "bench_loc_abc"
+}
+```
+
+### Boxes
+
+**List Boxes:**
+```http
+GET /api/v2/boxes
+
+Query Parameters:
+- parentStorageId: string
+- schemaId: string
+```
+
+**Get Box:**
+```http
+GET /api/v2/boxes/{boxId}
+```
+
+**Create Box:**
+```http
+POST /api/v2/boxes
+
+Body:
+{
+  "name": "Freezer-A-Box-01",
+  "schemaId": "box_schema_abc",
+  "parentStorageId": "loc_freezer_a",
+  "barcode": "BOX001"
+}
+```
+
+### Locations
+
+**List Locations:**
+```http
+GET /api/v2/locations
+```
+
+**Get Location:**
+```http
+GET /api/v2/locations/{locationId}
+```
+
+**Create Location:**
+```http
+POST /api/v2/locations
+
+Body:
+{
+  "name": "Freezer A - Shelf 2",
+  "parentStorageId": "loc_freezer_a",
+  "barcode": "LOC-A-S2"
+}
+```
+
+### Plates
+
+**List Plates:**
+```http
+GET /api/v2/plates
+```
+
+**Get Plate:**
+```http
+GET /api/v2/plates/{plateId}
+```
+
+**Create Plate:**
+```http
+POST /api/v2/plates
+
+Body:
+{
+  "name": "PCR-Plate-001",
+  "schemaId": "plate_schema_abc",
+  "barcode": "PLATE001",
+  "wells": [
+    {"position": "A1", "entityId": "ent_abc"},
+    {"position": "A2", "entityId": "ent_xyz"}
+  ]
+}
+```
+
+### Entries (Notebook)
+
+**List Entries:**
+```http
+GET /api/v2/entries
+
+Query Parameters:
+- folderId: string
+- schemaId: string
+- modifiedAt: string
+```
+
+**Get Entry:**
+```http
+GET /api/v2/entries/{entryId}
+```
+
+**Create Entry:**
+```http
+POST /api/v2/entries
+
+Body:
+{
+  "name": "Experiment 2025-10-20",
+  "folderId": "fld_abc123",
+  "schemaId": "entry_schema_abc",
+  "fields": {
+    "objective": {"value": "Test gene expression"},
+    "date": {"value": "2025-10-20"}
+  }
+}
+```
+
+**Update Entry:**
+```http
+PATCH /api/v2/entries/{entryId}
+
+Body:
+{
+  "fields": {
+    "results": {"value": "Successful expression"}
+  }
+}
+```
+
+### Workflow Tasks
+
+**List Workflow Tasks:**
+```http
+GET /api/v2/tasks
+
+Query Parameters:
+- workflowId: string
+- statusIds: string[] (comma-separated)
+- assigneeId: string
+```
+
+**Get Task:**
+```http
+GET /api/v2/tasks/{taskId}
+```
+
+**Create Task:**
+```http
+POST /api/v2/tasks
+
+Body:
+{
+  "name": "PCR Amplification",
+  "workflowId": "wf_abc123",
+  "assigneeId": "user_abc123",
+  "schemaId": "task_schema_abc",
+  "fields": {
+    "template": {"value": "seq_abc123"},
+    "priority": {"value": "High"}
+  }
+}
+```
+
+**Update Task:**
+```http
+PATCH /api/v2/tasks/{taskId}
+
+Body:
+{
+  "statusId": "status_complete_abc",
+  "fields": {
+    "completion_date": {"value": "2025-10-20"}
+  }
+}
+```
+
+### Folders
+
+**List Folders:**
+```http
+GET /api/v2/folders
+
+Query Parameters:
+- projectId: string
+- parentFolderId: string
+```
+
+**Get Folder:**
+```http
+GET /api/v2/folders/{folderId}
+```
+
+**Create Folder:**
+```http
+POST /api/v2/folders
+
+Body:
+{
+  "name": "2025 Experiments",
+  "parentFolderId": "fld_parent_abc",
+  "projectId": "proj_abc123"
+}
+```
+
+### Projects
+
+**List Projects:**
+```http
+GET /api/v2/projects
+```
+
+**Get Project:**
+```http
+GET /api/v2/projects/{projectId}
+```
+
+### Users
+
+**Get Current User:**
+```http
+GET /api/v2/users/me
+```
+
+**List Users:**
+```http
+GET /api/v2/users
+```
+
+**Get User:**
+```http
+GET /api/v2/users/{userId}
+```
+
+### Teams
+
+**List Teams:**
+```http
+GET /api/v2/teams
+```
+
+**Get Team:**
+```http
+GET /api/v2/teams/{teamId}
+```
+
+### Schemas
+
+**List Schemas:**
+```http
+GET /api/v2/schemas
+
+Query Parameters:
+- entityType: string (e.g., "dna_sequence", "custom_entity")
+```
+
+**Get Schema:**
+```http
+GET /api/v2/schemas/{schemaId}
+```
+
+### Registries
+
+**List Registries:**
+```http
+GET /api/v2/registries
+```
+
+**Get Registry:**
+```http
+GET /api/v2/registries/{registryId}
+```
+
+## Bulk Operations
+
+### Batch Archive
+
+**Archive Multiple Entities:**
+```http
+POST /api/v2/{entity-type}:archive
+
+Body:
+{
+  "{entity}Ids": ["id1", "id2", "id3"],
+  "reason": "Cleanup"
+}
+```
+
+### Batch Transfer
+
+**Transfer Multiple Containers:**
+```http
+POST /api/v2/containers:bulk-transfer
+
+Body:
+{
+  "transfers": [
+    {"containerId": "cont_1", "destinationId": "box_a"},
+    {"containerId": "cont_2", "destinationId": "box_b"}
+  ]
+}
+```
+
+## Async Operations
+
+Some operations return task IDs for async processing:
+
+**Response:**
+```json
+{
+  "taskId": "task_abc123"
+}
+```
+
+**Check Task Status:**
+```http
+GET /api/v2/tasks/{taskId}
+
+Response:
+{
+  "id": "task_abc123",
+  "status": "RUNNING", // or "SUCCEEDED", "FAILED"
+  "message": "Processing...",
+  "response": {...}  // Available when status is SUCCEEDED
+}
+```
+
+## Field Value Format
+
+Custom schema fields use a specific format:
+
+**Simple Value:**
+```json
+{
+  "field_name": {
+    "value": "Field Value"
+  }
+}
+```
+
+**Dropdown:**
+```json
+{
+  "dropdown_field": {
+    "value": "Option1"  // Must match exact option name
+  }
+}
+```
+
+**Date:**
+```json
+{
+  "date_field": {
+    "value": "2025-10-20"  // Format: YYYY-MM-DD
+  }
+}
+```
+
+**Entity Link:**
+```json
+{
+  "entity_link_field": {
+    "value": "seq_abc123"  // Entity ID
+  }
+}
+```
+
+**Numeric:**
+```json
+{
+  "numeric_field": {
+    "value": "123.45"  // String representation
+  }
+}
+```
+
+## Rate Limiting
+
+**Limits:**
+- Default: 100 requests per 10 seconds per user/app
+- Rate limit headers included in responses:
+  - `X-RateLimit-Limit`: Total allowed requests
+  - `X-RateLimit-Remaining`: Remaining requests
+  - `X-RateLimit-Reset`: Unix timestamp when limit resets
+
+**Handling 429 Responses:**
+```json
+{
+  "error": {
+    "type": "RateLimitError",
+    "message": "Rate limit exceeded",
+    "retryAfter": 5  // Seconds to wait
+  }
+}
+```
+
+## Filtering and Searching
+
+**Common Query Parameters:**
+- `name`: Partial name match
+- `modifiedAt`: ISO 8601 datetime
+- `createdAt`: ISO 8601 datetime
+- `schemaId`: Filter by schema
+- `folderId`: Filter by folder
+- `archived`: Boolean (include archived items)
+
+**Example:**
+```bash
+curl -X GET \
+  "https://tenant.benchling.com/api/v2/dna-sequences?name=plasmid&folderId=fld_abc&archived=false"
+```
+
+## Best Practices
+
+### Request Efficiency
+
+1. **Use appropriate page sizes:**
+   - Default: 50 items
+   - Max: 100 items
+   - Adjust based on needs
+
+2. **Filter on server-side:**
+   - Use query parameters instead of client filtering
+   - Reduces data transfer and processing
+
+3. **Batch operations:**
+   - Use bulk endpoints when available
+   - Archive/transfer multiple items in one request
+
+### Error Handling
+
+```javascript
+// Example error handling
+async function fetchSequence(id) {
+  try {
+    const response = await fetch(
+      `https://tenant.benchling.com/api/v2/dna-sequences/${id}`,
+      {
+        headers: {
+          'Authorization': `Bearer ${token}`,
+          'Accept': 'application/json'
+        }
+      }
+    );
+
+    if (!response.ok) {
+      if (response.status === 429) {
+        // Rate limit - retry with backoff
+        const retryAfter = response.headers.get('Retry-After');
+        await sleep(retryAfter * 1000);
+        return fetchSequence(id);
+      } else if (response.status === 404) {
+        return null;  // Not found
+      } else {
+        throw new Error(`API error: ${response.status}`);
+      }
+    }
+
+    return await response.json();
+  } catch (error) {
+    console.error('Request failed:', error);
+    throw error;
+  }
+}
+```
+
+### Pagination Loop
+
+```javascript
+async function getAllSequences() {
+  let allSequences = [];
+  let nextToken = null;
+
+  do {
+    const url = new URL('https://tenant.benchling.com/api/v2/dna-sequences');
+    if (nextToken) {
+      url.searchParams.set('nextToken', nextToken);
+    }
+    url.searchParams.set('pageSize', '100');
+
+    const response = await fetch(url, {
+      headers: {
+        'Authorization': `Bearer ${token}`,
+        'Accept': 'application/json'
+      }
+    });
+
+    const data = await response.json();
+    allSequences = allSequences.concat(data.results);
+    nextToken = data.nextToken;
+  } while (nextToken);
+
+  return allSequences;
+}
+```
+
+## References
+
+- **API Documentation:** https://benchling.com/api/reference
+- **Interactive API Explorer:** https://your-tenant.benchling.com/api/reference (requires authentication)
+- **Changelog:** https://docs.benchling.com/changelog