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# Additional Features
## Overview
This document covers additional protocols.io API features including user profiles, recently published protocols, experiment records, and notifications.
## Base URL
All endpoints use the base URL: `https://protocols.io/api/v3`
## User Profile Management
### Get User Profile
Retrieve the authenticated user's profile information.
**Endpoint:** `GET /profile`
**Response includes:**
- User ID and username
- Full name
- Email address
- Affiliation/institution
- Bio and description
- Profile image URL
- Account creation date
- Protocol count and statistics
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/profile"
```
### Update User Profile
Update profile information.
**Endpoint:** `PATCH /profile`
**Request Body:**
- `first_name`: First name
- `last_name`: Last name
- `email`: Email address
- `affiliation`: Institution or organization
- `bio`: Profile bio/description
- `location`: Geographic location
- `website`: Personal or lab website URL
- `twitter`: Twitter handle
- `orcid`: ORCID identifier
**Example Request:**
```bash
curl -X PATCH \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"affiliation": "University of Example, Department of Biology",
"bio": "Researcher specializing in CRISPR gene editing and molecular biology",
"orcid": "0000-0001-2345-6789"
}' \
"https://protocols.io/api/v3/profile"
```
### Upload Profile Image
Update profile picture.
**Endpoint:** `POST /profile/image`
**Request Format**: `multipart/form-data`
**Form Parameters:**
- `image` (required): Image file (JPEG, PNG)
**Recommended specifications:**
- Minimum size: 200x200 pixels
- Aspect ratio: Square (1:1)
- Format: JPEG or PNG
- Max file size: 5 MB
## Recently Published Protocols
### Query Published Protocols
Discover recently published public protocols.
**Endpoint:** `GET /publications`
**Query Parameters:**
- `key`: Search keywords
- `category`: Filter by category
- Example categories: `molecular-biology`, `cell-biology`, `biochemistry`, etc.
- `date_from`: Start date (ISO 8601 format: YYYY-MM-DD)
- `date_to`: End date
- `order_field`: Sort field (`published_on`, `title`, `views`)
- `order_dir`: Sort direction (`desc`, `asc`)
- `page_size`: Number of results per page (default: 10, max: 50)
- `page_id`: Page number for pagination
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/publications?category=molecular-biology&date_from=2025-01-01&order_field=published_on&order_dir=desc"
```
**Use Cases:**
- Discover trending protocols
- Monitor new publications in your field
- Find recently published protocols for specific techniques
- Track citation-worthy protocols
## Experiment Records
### Overview
Experiment records allow users to document individual runs or executions of a protocol, tracking what worked, what didn't, and any modifications made.
### Create Experiment Record
Document an execution of a protocol.
**Endpoint:** `POST /protocols/{protocol_id}/runs`
**Path Parameters:**
- `protocol_id`: The protocol's unique identifier
**Request Body:**
- `title` (required): Experiment run title
- `date`: Date of experiment execution (ISO 8601 format)
- `status`: Experiment outcome
- `success`: Experiment succeeded
- `partial`: Partially successful
- `failed`: Experiment failed
- `notes`: Detailed notes about the experiment run
- `modifications`: Protocol modifications or deviations
- `results`: Summary of results
- `attachments`: File IDs for data files or images
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"title": "CRISPR Editing - HEK293 Cells - Trial 3",
"date": "2025-10-20",
"status": "success",
"notes": "Successfully achieved 87% editing efficiency. Increased sgRNA concentration from 100nM to 150nM based on previous trials.",
"modifications": "Extended incubation time in step 3 from 30 min to 45 min",
"results": "Flow cytometry confirmed 87% GFP+ cells after 72h. Western blot showed complete knockout in positive population."
}' \
"https://protocols.io/api/v3/protocols/12345/runs"
```
### List Experiment Records
Retrieve all experiment records for a protocol.
**Endpoint:** `GET /protocols/{protocol_id}/runs`
**Query Parameters:**
- `status`: Filter by outcome (`success`, `partial`, `failed`)
- `date_from`: Start date
- `date_to`: End date
- `page_size`: Number of results per page
- `page_id`: Page number for pagination
### Update Experiment Record
**Endpoint:** `PATCH /protocols/{protocol_id}/runs/{run_id}`
**Request Body**: Same parameters as create, all optional
### Delete Experiment Record
**Endpoint:** `DELETE /protocols/{protocol_id}/runs/{run_id}`
**Use Cases:**
- Track reproducibility across multiple experiments
- Document troubleshooting and optimization
- Share successful modifications with collaborators
- Build institutional knowledge base
- Support lab notebook requirements
## Notifications
### Get User Notifications
Retrieve notifications for the authenticated user.
**Endpoint:** `GET /notifications`
**Query Parameters:**
- `type`: Filter by notification type
- `comment`: New comments on your protocols
- `mention`: You were mentioned in a comment
- `protocol_update`: Protocol you follow was updated
- `workspace`: Workspace activity
- `publication`: Protocol was published
- `read`: Filter by read status
- `true`: Only read notifications
- `false`: Only unread notifications
- Omit for all notifications
- `page_size`: Number of results per page (default: 20, max: 100)
- `page_id`: Page number for pagination
**Response includes:**
- Notification ID and type
- Message/description
- Related protocol/comment/workspace
- Timestamp
- Read status
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/notifications?read=false&type=comment"
```
### Mark Notification as Read
**Endpoint:** `PATCH /notifications/{notification_id}`
**Request Body:**
- `read`: Set to `true`
### Mark All Notifications as Read
**Endpoint:** `POST /notifications/mark-all-read`
### Delete Notification
**Endpoint:** `DELETE /notifications/{notification_id}`
## Organization Management
### Export Organization Data
Export all protocols and workspace data from an organization.
**Endpoint:** `GET /organizations/{organization_id}/export`
**Path Parameters:**
- `organization_id`: The organization's unique identifier
**Query Parameters:**
- `format`: Export format
- `json`: JSON format with full metadata
- `csv`: CSV format for spreadsheet import
- `xml`: XML format
- `include_files`: Include associated files (`true`/`false`)
- `include_comments`: Include discussions (`true`/`false`)
**Response**: Download URL for export package
**Use Cases:**
- Institutional archival
- Compliance and audit requirements
- Migration to other systems
- Backup and disaster recovery
- Data analysis and reporting
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/organizations/12345/export?format=json&include_files=true&include_comments=true"
```
## Common Integration Patterns
### 1. Protocol Discovery and Import
Build a protocol discovery workflow:
```python
# Search for relevant protocols
response = requests.get(
'https://protocols.io/api/v3/publications',
headers={'Authorization': f'Bearer {token}'},
params={'key': 'CRISPR', 'category': 'molecular-biology'}
)
# For each interesting protocol
for protocol in response.json()['items']:
# Get full details
details = requests.get(
f'https://protocols.io/api/v3/protocols/{protocol["id"]}',
headers={'Authorization': f'Bearer {token}'}
)
# Import to local system
import_protocol(details.json())
```
### 2. Experiment Tracking
Track all protocol executions:
1. Execute protocol in lab
2. Document execution: `POST /protocols/{id}/runs`
3. Upload result files to workspace
4. Link files in experiment record
5. Analyze success rates across runs
### 3. Notification System Integration
Build custom notification system:
1. Poll for new notifications: `GET /notifications?read=false`
2. Process each notification type
3. Send to internal communication system
4. Mark as read: `PATCH /notifications/{id}`
### 4. Profile Synchronization
Keep profiles synchronized across systems:
1. Retrieve profile: `GET /profile`
2. Compare with internal system
3. Update discrepancies
4. Sync profile images and metadata
## API Response Formats
### Standard Response Structure
Most API responses follow this structure:
```json
{
"status_code": 0,
"status_message": "Success",
"item": { /* single item data */ },
"items": [ /* array of items */ ],
"pagination": {
"current_page": 0,
"total_pages": 5,
"page_size": 10,
"total_items": 42
}
}
```
### Error Response Structure
```json
{
"status_code": 400,
"status_message": "Bad Request",
"error_message": "Missing required parameter: title",
"error_details": {
"field": "title",
"issue": "required"
}
}
```
## Best Practices
1. **Profile Completeness**
- Complete all profile fields
- Add ORCID for research attribution
- Keep affiliation current
2. **Experiment Documentation**
- Document all protocol executions
- Include both successes and failures
- Note all modifications
- Attach relevant data files
3. **Notification Management**
- Review notifications regularly
- Enable relevant notification types
- Disable notification types you don't need
- Respond to comments promptly
4. **Publication Discovery**
- Set up regular searches for your research area
- Follow prolific authors in your field
- Bookmark useful protocols
- Cite protocols in publications
5. **Data Export**
- Export organization data regularly
- Test restore procedures
- Store exports securely
- Document export procedures

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# Protocols.io Authentication
## Overview
The protocols.io API supports two types of access tokens for authentication, enabling access to both public and private content.
## Access Token Types
### 1. CLIENT_ACCESS_TOKEN
- **Purpose**: Enables access to public content and the private content of the client user
- **Use case**: When accessing your own protocols and public protocols
- **Scope**: Limited to the token owner's private content plus all public content
### 2. OAUTH_ACCESS_TOKEN
- **Purpose**: Grants access to specific users' private content plus all public content
- **Use case**: When building applications that need to access other users' content with their permission
- **Scope**: Full access to authorized user's private content plus all public content
## Authentication Header
All API requests must include an Authorization header:
```
Authorization: Bearer [ACCESS_TOKEN]
```
## OAuth Flow
### Step 1: Generate Authorization Link
Direct users to the authorization URL to grant access:
```
GET https://protocols.io/api/v3/oauth/authorize
```
**Parameters:**
- `client_id` (required): Your application's client ID
- `redirect_uri` (required): URL to redirect users after authorization
- `response_type` (required): Set to "code"
- `state` (optional but recommended): Random string to prevent CSRF attacks
**Example:**
```
https://protocols.io/api/v3/oauth/authorize?client_id=YOUR_CLIENT_ID&redirect_uri=YOUR_REDIRECT_URI&response_type=code&state=RANDOM_STRING
```
### Step 2: Exchange Authorization Code for Token
After user authorization, protocols.io redirects to your `redirect_uri` with an authorization code. Exchange this code for an access token:
```
POST https://protocols.io/api/v3/oauth/token
```
**Parameters:**
- `grant_type`: Set to "authorization_code"
- `code`: The authorization code received
- `client_id`: Your application's client ID
- `client_secret`: Your application's client secret
- `redirect_uri`: Must match the redirect_uri used in Step 1
**Response includes:**
- `access_token`: The OAuth access token to use for API requests
- `token_type`: "Bearer"
- `expires_in`: Token lifetime in seconds (typically 1 year)
- `refresh_token`: Token for refreshing the access token
### Step 3: Refresh Access Token
Before the access token expires (typically 1 year), use the refresh token to obtain a new access token:
```
POST https://protocols.io/api/v3/oauth/token
```
**Parameters:**
- `grant_type`: Set to "refresh_token"
- `refresh_token`: The refresh token received in Step 2
- `client_id`: Your application's client ID
- `client_secret`: Your application's client secret
## Rate Limits
Be aware of rate limiting when making API requests:
- **Standard endpoints**: 100 requests per minute per user
- **PDF endpoint** (`/view/[protocol-uri].pdf`):
- Signed-in users: 5 requests per minute
- Unsigned users: 3 requests per minute
## Best Practices
1. **Store tokens securely**: Never expose access tokens in client-side code or version control
2. **Handle token expiration**: Implement automatic token refresh before expiration
3. **Respect rate limits**: Implement exponential backoff for rate limit errors
4. **Use state parameter**: Always include a state parameter in OAuth flow for security
5. **Validate redirect_uri**: Ensure redirect URIs match exactly between authorization and token requests

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# Discussions API
## Overview
The Discussions API enables collaborative commenting on protocols. Comments can be added at both the protocol level and the individual step level, with support for threaded replies, editing, and deletion.
## Base URL
All discussion endpoints use the base URL: `https://protocols.io/api/v3`
## Protocol-Level Comments
### List Protocol Comments
Retrieve all comments for a protocol.
**Endpoint:** `GET /protocols/{protocol_id}/comments`
**Path Parameters:**
- `protocol_id`: The protocol's unique identifier
**Query Parameters:**
- `page_size`: Number of results per page (default: 10, max: 50)
- `page_id`: Page number for pagination (starts at 0)
**Response includes:**
- Comment ID and content
- Author information (name, affiliation, avatar)
- Timestamp (created and modified)
- Reply count and thread structure
### Create Protocol Comment
Add a new comment to a protocol.
**Endpoint:** `POST /protocols/{protocol_id}/comments`
**Request Body:**
- `body` (required): Comment text (supports HTML or Markdown)
- `parent_comment_id` (optional): ID of parent comment for threaded replies
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"body": "This protocol worked excellently for our CRISPR experiments. We achieved 85% editing efficiency."
}' \
"https://protocols.io/api/v3/protocols/12345/comments"
```
### Create Threaded Reply
To reply to an existing comment, include the parent comment ID:
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"body": "What cell type did you use?",
"parent_comment_id": 67890
}' \
"https://protocols.io/api/v3/protocols/12345/comments"
```
### Update Comment
Edit your own comment.
**Endpoint:** `PATCH /protocols/{protocol_id}/comments/{comment_id}`
**Request Body:**
- `body` (required): Updated comment text
**Authorization**: Only the comment author can edit their comments
### Delete Comment
Remove a comment.
**Endpoint:** `DELETE /protocols/{protocol_id}/comments/{comment_id}`
**Authorization**: Only the comment author can delete their comments
**Note**: Deleting a parent comment may affect the entire thread, depending on API implementation
## Step-Level Comments
### List Step Comments
Retrieve all comments for a specific protocol step.
**Endpoint:** `GET /protocols/{protocol_id}/steps/{step_id}/comments`
**Path Parameters:**
- `protocol_id`: The protocol's unique identifier
- `step_id`: The step's unique identifier
**Query Parameters:**
- `page_size`: Number of results per page
- `page_id`: Page number for pagination
### Create Step Comment
Add a comment to a specific step.
**Endpoint:** `POST /protocols/{protocol_id}/steps/{step_id}/comments`
**Request Body:**
- `body` (required): Comment text
- `parent_comment_id` (optional): ID of parent comment for replies
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"body": "At this step, we found that increasing the incubation time to 2 hours improved results significantly."
}' \
"https://protocols.io/api/v3/protocols/12345/steps/67890/comments"
```
### Update Step Comment
**Endpoint:** `PATCH /protocols/{protocol_id}/steps/{step_id}/comments/{comment_id}`
**Request Body:**
- `body` (required): Updated comment text
### Delete Step Comment
**Endpoint:** `DELETE /protocols/{protocol_id}/steps/{step_id}/comments/{comment_id}`
## Common Use Cases
### 1. Discussion Thread Analysis
To analyze discussions around a protocol:
1. Retrieve protocol comments: `GET /protocols/{id}/comments`
2. For each step, retrieve step-specific comments
3. Build a discussion thread tree using `parent_comment_id`
4. Analyze feedback patterns and common issues
### 2. Collaborative Protocol Improvement
To gather feedback on a protocol:
1. Publish the protocol
2. Monitor new comments: `GET /protocols/{id}/comments`
3. Respond to questions with threaded replies
4. Update protocol based on feedback
5. Publish updated version with notes acknowledging contributors
### 3. Community Engagement
To engage with protocol users:
1. Set up monitoring for new comments on your protocols
2. Respond promptly to questions and issues
3. Use step-level comments to provide detailed clarifications
4. Create threaded discussions for complex topics
### 4. Protocol Troubleshooting
To document troubleshooting experiences:
1. Identify problematic steps in a protocol
2. Add step-level comments with specific issues encountered
3. Document solutions or workarounds
4. Create a discussion thread with other users experiencing similar issues
## Comment Formatting
Comments support rich text formatting:
- **HTML**: Use standard HTML tags for formatting
- **Markdown**: Use Markdown syntax for simpler formatting
- **Links**: Include URLs to related resources or publications
- **Mentions**: Reference other users (format may vary)
**Example with Markdown:**
```json
{
"body": "## Important Note\n\nWe achieved better results with:\n\n- Increasing temperature to 37°C\n- Extending incubation to 2 hours\n- Using freshly prepared reagents\n\nSee our publication: [doi:10.xxxx/xxxxx](https://doi.org/...)"
}
```
## Best Practices
1. **Be specific**: When commenting on steps, reference specific parameters or conditions
2. **Provide context**: Include relevant experimental details (cell type, reagent batch, equipment)
3. **Use step-level comments**: Direct feedback to specific steps rather than protocol-level when appropriate
4. **Engage constructively**: Respond to questions and feedback promptly
5. **Update protocols**: Incorporate validated feedback into protocol updates
6. **Thread related discussions**: Use reply functionality to keep related comments together
7. **Document variations**: Share protocol modifications that worked in your hands
## Permissions and Privacy
- **Public protocols**: Anyone can comment on published public protocols
- **Private protocols**: Only collaborators with access can comment
- **Comment ownership**: Only comment authors can edit or delete their comments
- **Moderation**: Protocol authors may have additional moderation capabilities
## Error Handling
Common error responses:
- `400 Bad Request`: Invalid comment format or missing required fields
- `401 Unauthorized`: Missing or invalid access token
- `403 Forbidden`: Insufficient permissions (e.g., trying to edit another user's comment)
- `404 Not Found`: Protocol, step, or comment not found
- `429 Too Many Requests`: Rate limit exceeded
## Notifications
Comments may trigger notifications:
- Protocol authors receive notifications for new comments
- Comment authors receive notifications for replies
- Users can manage notification preferences in their account settings

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# File Manager API
## Overview
The File Manager API enables file operations within protocols.io workspaces, including uploading files, organizing folders, searching content, and managing file lifecycle. This is useful for attaching data files, images, documents, and other resources to protocols.
## Base URL
All file manager endpoints use the base URL: `https://protocols.io/api/v3`
## Search and Browse
### Search Workspace Files
Search for files and folders within a workspace.
**Endpoint:** `GET /workspaces/{workspace_id}/files/search`
**Path Parameters:**
- `workspace_id`: The workspace's unique identifier
**Query Parameters:**
- `query`: Search keywords (searches filenames and metadata)
- `type`: Filter by type
- `file`: Files only
- `folder`: Folders only
- `all`: Both files and folders (default)
- `folder_id`: Limit search to specific folder
- `page_size`: Number of results per page (default: 20, max: 100)
- `page_id`: Page number for pagination (starts at 0)
**Response includes:**
- File/folder ID and name
- File size and type
- Creation and modification dates
- File path in workspace
- Download URL (for files)
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/workspaces/12345/files/search?query=microscopy&type=file"
```
### List Folder Contents
Browse files and folders within a specific folder.
**Endpoint:** `GET /workspaces/{workspace_id}/folders/{folder_id}`
**Path Parameters:**
- `workspace_id`: The workspace's unique identifier
- `folder_id`: The folder's unique identifier (use `root` for workspace root)
**Query Parameters:**
- `order_by`: Sort field (`name`, `size`, `created`, `modified`)
- `order_dir`: Sort direction (`asc`, `desc`)
- `page_size`: Number of results per page
- `page_id`: Page number for pagination
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/workspaces/12345/folders/root?order_by=modified&order_dir=desc"
```
## File Upload
### Upload File
Upload a file to a workspace folder.
**Endpoint:** `POST /workspaces/{workspace_id}/files/upload`
**Request Format**: `multipart/form-data`
**Form Parameters:**
- `file` (required): The file to upload
- `folder_id`: Target folder ID (omit or use `root` for workspace root)
- `name`: Custom filename (optional, uses original filename if omitted)
- `description`: File description
- `tags`: Comma-separated tags
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-F "file=@/path/to/local/data.xlsx" \
-F "folder_id=67890" \
-F "description=Experimental results from trial #3" \
-F "tags=experiment,data,2025" \
"https://protocols.io/api/v3/workspaces/12345/files/upload"
```
### Upload Verification
After upload, verify the file was processed correctly.
**Endpoint:** `GET /workspaces/{workspace_id}/files/{file_id}/status`
**Response includes:**
- Upload status (`processing`, `complete`, `failed`)
- File metadata
- Any processing errors
## File Operations
### Download File
Download a file from the workspace.
**Endpoint:** `GET /workspaces/{workspace_id}/files/{file_id}/download`
**Path Parameters:**
- `workspace_id`: The workspace's unique identifier
- `file_id`: The file's unique identifier
**Response**: Binary file data with appropriate Content-Type header
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
-o "downloaded_file.xlsx" \
"https://protocols.io/api/v3/workspaces/12345/files/67890/download"
```
### Get File Metadata
Retrieve file information without downloading.
**Endpoint:** `GET /workspaces/{workspace_id}/files/{file_id}`
**Response includes:**
- File name, size, and type
- Upload date and author
- Description and tags
- File path and location
- Download URL
- Sharing permissions
### Update File Metadata
Update file description, tags, or other metadata.
**Endpoint:** `PATCH /workspaces/{workspace_id}/files/{file_id}`
**Request Body:**
- `name`: New filename
- `description`: Updated description
- `tags`: Updated tags (comma-separated)
- `folder_id`: Move to different folder
**Example Request:**
```bash
curl -X PATCH \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"description": "Experimental results from trial #3 - REVISED",
"tags": "experiment,data,2025,revised"
}' \
"https://protocols.io/api/v3/workspaces/12345/files/67890"
```
### Delete File
Move a file to trash (soft delete).
**Endpoint:** `DELETE /workspaces/{workspace_id}/files/{file_id}`
**Note**: Deleted files may be recoverable from trash for a limited time
### Restore File
Restore a deleted file from trash.
**Endpoint:** `POST /workspaces/{workspace_id}/files/{file_id}/restore`
## Folder Operations
### Create Folder
Create a new folder in the workspace.
**Endpoint:** `POST /workspaces/{workspace_id}/folders`
**Request Body:**
- `name` (required): Folder name
- `parent_folder_id`: Parent folder ID (omit for workspace root)
- `description`: Folder description
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"name": "2025 Experiments",
"parent_folder_id": "root",
"description": "All experimental data from 2025"
}' \
"https://protocols.io/api/v3/workspaces/12345/folders"
```
### Rename Folder
**Endpoint:** `PATCH /workspaces/{workspace_id}/folders/{folder_id}`
**Request Body:**
- `name`: New folder name
- `description`: Updated description
### Delete Folder
Delete a folder and optionally its contents.
**Endpoint:** `DELETE /workspaces/{workspace_id}/folders/{folder_id}`
**Query Parameters:**
- `recursive`: Set to `true` to delete folder and all contents (default: `false`)
**Warning**: Recursive deletion cannot be easily undone
## Common Use Cases
### 1. Protocol Data Attachment
Attach experimental data files to protocols:
1. Upload data files: `POST /workspaces/{id}/files/upload`
2. Verify upload completion
3. Reference file IDs in protocol steps
4. Include download links in protocol description
**Example Workflow:**
```bash
# Upload the data file
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-F "file=@results.csv" \
-F "description=Results from protocol execution" \
"https://protocols.io/api/v3/workspaces/12345/files/upload"
# Note the file_id from response, then reference in protocol
```
### 2. Workspace Organization
Organize files into logical folder structures:
1. Create folder hierarchy: `POST /workspaces/{id}/folders`
2. Upload files to appropriate folders
3. Use consistent naming conventions
4. Tag files for easy search
**Example Structure:**
```
Workspace Root
├── Protocols
│ ├── Published
│ └── Drafts
├── Data
│ ├── Raw
│ └── Processed
├── Images
│ ├── Microscopy
│ └── Gels
└── Documents
├── Papers
└── Presentations
```
### 3. File Search and Discovery
Find files across workspace:
1. Search by keywords: `GET /workspaces/{id}/files/search?query=keywords`
2. Filter by type and date
3. Download relevant files
4. Update metadata for better organization
### 4. Batch File Upload
Upload multiple related files:
1. Create target folder
2. For each file:
- Upload file
- Verify upload status
- Add consistent tags
3. Create index or manifest file listing all uploads
### 5. Data Backup and Export
Export workspace files for backup:
1. List all folders: `GET /workspaces/{id}/folders/root`
2. For each folder, list files
3. Download all files: `GET /workspaces/{id}/files/{file_id}/download`
4. Maintain folder structure locally
5. Store metadata separately for restoration
### 6. File Versioning
Manage file versions manually:
1. Upload new version with versioned name (e.g., `data_v2.csv`)
2. Update previous version metadata to indicate superseded
3. Maintain version history in folder structure
4. Reference specific versions in protocols
## Supported File Types
Protocols.io supports various file types:
**Data Files:**
- Spreadsheets: `.xlsx`, `.xls`, `.csv`, `.tsv`
- Statistical data: `.rds`, `.rdata`, `.sav`, `.dta`
- Plain text: `.txt`, `.log`, `.json`, `.xml`
**Images:**
- Common formats: `.jpg`, `.jpeg`, `.png`, `.gif`, `.bmp`, `.tif`, `.tiff`
- Scientific: `.czi`, `.nd2`, `.lsm` (may require special handling)
**Documents:**
- PDF: `.pdf`
- Word: `.docx`, `.doc`
- PowerPoint: `.pptx`, `.ppt`
**Code and Scripts:**
- Python: `.py`, `.ipynb`
- R: `.r`, `.rmd`
- Shell: `.sh`, `.bash`
**Multimedia:**
- Video: `.mp4`, `.avi`, `.mov`
- Audio: `.mp3`, `.wav`
**Archives:**
- Compressed: `.zip`, `.tar.gz`, `.7z`
**File Size Limits:**
- Standard files: Check workspace limits (typically 100 MB - 1 GB)
- Large files: May require chunked upload or special handling
## Best Practices
1. **File Naming**
- Use descriptive, consistent naming conventions
- Include dates in ISO format (YYYY-MM-DD)
- Avoid special characters and spaces (use underscores)
- Example: `experiment_results_2025-10-26.csv`
2. **Organization**
- Create logical folder hierarchy
- Group related files together
- Separate raw data from processed results
- Keep protocol-specific files in dedicated folders
3. **Metadata**
- Add detailed descriptions
- Tag files consistently
- Include version information
- Document processing steps
4. **Storage Management**
- Regularly review and archive old files
- Delete unnecessary duplicates
- Compress large datasets
- Monitor workspace storage limits
5. **Collaboration**
- Use clear file names for team members
- Document file purposes in descriptions
- Maintain consistent folder structures
- Communicate major organizational changes
6. **Security**
- Avoid uploading sensitive data without proper permissions
- Be aware of workspace visibility settings
- Use appropriate access controls
- Regularly audit file access
## Error Handling
Common error responses:
- `400 Bad Request`: Invalid file format or parameters
- `401 Unauthorized`: Missing or invalid access token
- `403 Forbidden`: Insufficient workspace permissions
- `404 Not Found`: File or folder not found
- `413 Payload Too Large`: File exceeds size limit
- `422 Unprocessable Entity`: File validation failed
- `429 Too Many Requests`: Rate limit exceeded
- `507 Insufficient Storage`: Workspace storage limit reached
## Performance Considerations
1. **Large Files**
- Consider chunked upload for files > 100 MB
- Use compression for large datasets
- Upload during off-peak hours if possible
2. **Batch Operations**
- Implement retry logic for failed uploads
- Use exponential backoff for rate limits
- Process uploads in parallel where possible
3. **Download Optimization**
- Cache frequently accessed files locally
- Use streaming for large file downloads
- Implement resume capability for interrupted downloads

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# Protocols API
## Overview
The Protocols API is the core functionality of protocols.io, supporting the complete protocol lifecycle from creation to publication. This includes searching, creating, updating, managing steps, handling materials, bookmarking, and generating PDFs.
## Base URL
All protocol endpoints use the base URL: `https://protocols.io/api/v3`
## Content Format Parameter
Many endpoints support a `content_format` parameter to specify how content is returned:
- `json`: Draft.js JSON format (default)
- `html`: HTML format
- `markdown`: Markdown format
Include this as a query parameter: `?content_format=html`
## List and Search Operations
### List Protocols
Retrieve protocols with filtering and pagination.
**Endpoint:** `GET /protocols`
**Query Parameters:**
- `filter`: Filter type
- `public`: Public protocols only
- `private`: Your private protocols
- `shared`: Protocols shared with you
- `user_public`: Another user's public protocols
- `key`: Search keywords in protocol title, description, and content
- `order_field`: Sort field (`activity`, `created_on`, `modified_on`, `name`, `id`)
- `order_dir`: Sort direction (`desc`, `asc`)
- `page_size`: Number of results per page (default: 10, max: 50)
- `page_id`: Page number for pagination (starts at 0)
- `fields`: Comma-separated list of fields to return
- `content_format`: Content format (`json`, `html`, `markdown`)
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/protocols?filter=public&key=CRISPR&page_size=20&content_format=html"
```
### Search by DOI
Retrieve a protocol by its DOI.
**Endpoint:** `GET /protocols/{doi}`
**Path Parameters:**
- `doi`: The protocol DOI (e.g., `dx.doi.org/10.17504/protocols.io.xxxxx`)
## Retrieve Protocol Details
### Get Protocol by ID
**Endpoint:** `GET /protocols/{protocol_id}`
**Path Parameters:**
- `protocol_id`: The protocol's unique identifier
**Query Parameters:**
- `content_format`: Content format (`json`, `html`, `markdown`)
**Response includes:**
- Protocol metadata (title, authors, description, DOI)
- All protocol steps with content
- Materials and reagents
- Guidelines and warnings
- Version information
- Publication status
## Create and Update Protocols
### Create New Protocol
**Endpoint:** `POST /protocols`
**Request Body Parameters:**
- `title` (required): Protocol title
- `description`: Protocol description
- `tags`: Array of tag strings
- `vendor_name`: Vendor/company name
- `vendor_link`: Vendor website URL
- `warning`: Warning or safety message
- `guidelines`: Usage guidelines
- `manuscript_citation`: Citation for related manuscript
- `link`: External link to related resource
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"title": "CRISPR Gene Editing Protocol",
"description": "Comprehensive protocol for CRISPR-Cas9 mediated gene editing",
"tags": ["CRISPR", "gene editing", "molecular biology"]
}' \
"https://protocols.io/api/v3/protocols"
```
### Update Protocol
**Endpoint:** `PATCH /protocols/{protocol_id}`
**Path Parameters:**
- `protocol_id`: The protocol's unique identifier
**Request Body**: Same parameters as create, all optional
## Protocol Steps Management
### Create Protocol Step
**Endpoint:** `POST /protocols/{protocol_id}/steps`
**Request Body Parameters:**
- `title` (required): Step title
- `description`: Step description (HTML, Markdown, or Draft.js JSON)
- `duration`: Step duration in seconds
- `temperature`: Temperature setting
- `components`: Array of materials/reagents used
- `software`: Software or tools required
- `commands`: Commands to execute
- `expected_result`: Expected outcome description
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"title": "Prepare sgRNA",
"description": "Design and synthesize single guide RNA (sgRNA) targeting your gene of interest",
"duration": 3600,
"temperature": 25
}' \
"https://protocols.io/api/v3/protocols/12345/steps"
```
### Update Protocol Step
**Endpoint:** `PATCH /protocols/{protocol_id}/steps/{step_id}`
**Parameters**: Same as create step, all optional
### Delete Protocol Step
**Endpoint:** `DELETE /protocols/{protocol_id}/steps/{step_id}`
### Reorder Steps
**Endpoint:** `POST /protocols/{protocol_id}/steps/reorder`
**Request Body:**
- `step_order`: Array of step IDs in desired order
## Materials and Reagents
### Get Protocol Materials
Retrieve all materials and reagents used in a protocol.
**Endpoint:** `GET /protocols/{protocol_id}/materials`
**Response includes:**
- Reagent names and descriptions
- Catalog numbers
- Vendor information
- Concentrations and amounts
- Links to product pages
## Publishing and DOI
### Publish Protocol
Issue a DOI and make the protocol publicly available.
**Endpoint:** `POST /protocols/{protocol_id}/publish`
**Request Body Parameters:**
- `version_notes`: Description of changes in this version
- `publish_type`: Publication type
- `new`: First publication
- `update`: Update to existing published protocol
**Important Notes:**
- Once published, protocols receive a permanent DOI
- Published protocols cannot be deleted, only updated with new versions
- Published protocols are publicly accessible
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"version_notes": "Initial publication",
"publish_type": "new"
}' \
"https://protocols.io/api/v3/protocols/12345/publish"
```
## Bookmarks
### Add Bookmark
Add a protocol to your bookmarks for quick access.
**Endpoint:** `POST /protocols/{protocol_id}/bookmarks`
### Remove Bookmark
**Endpoint:** `DELETE /protocols/{protocol_id}/bookmarks`
### List Bookmarked Protocols
**Endpoint:** `GET /bookmarks`
## PDF Export
### Generate Protocol PDF
Generate a formatted PDF version of a protocol.
**Endpoint:** `GET /view/{protocol_uri}.pdf`
**Query Parameters:**
- `compact`: Set to `1` for compact view without large spacing
**Rate Limits:**
- Signed-in users: 5 requests per minute
- Unsigned users: 3 requests per minute
**Example:**
```
https://protocols.io/api/v3/view/crispr-protocol-abc123.pdf?compact=1
```
## Common Use Cases
### 1. Import Existing Protocol
To import and work with an existing protocol:
1. Search for the protocol using keywords or DOI
2. Retrieve full protocol details with `/protocols/{protocol_id}`
3. Extract steps, materials, and metadata for local use
### 2. Create New Protocol from Scratch
To create a new protocol:
1. Create protocol with title and description: `POST /protocols`
2. Add steps sequentially: `POST /protocols/{id}/steps`
3. Review and test the protocol
4. Publish when ready: `POST /protocols/{id}/publish`
### 3. Update Published Protocol
To update an already-published protocol:
1. Retrieve current version: `GET /protocols/{protocol_id}`
2. Make necessary updates: `PATCH /protocols/{protocol_id}`
3. Update or add steps as needed
4. Publish new version: `POST /protocols/{protocol_id}/publish` with `publish_type: "update"`
### 4. Clone and Modify Protocol
To create a modified version of an existing protocol:
1. Retrieve original protocol details
2. Create new protocol with modified metadata
3. Copy and modify steps from original
4. Publish as new protocol
## Error Handling
Common error responses:
- `400 Bad Request`: Invalid parameters or request format
- `401 Unauthorized`: Missing or invalid access token
- `403 Forbidden`: Insufficient permissions for the operation
- `404 Not Found`: Protocol or resource not found
- `429 Too Many Requests`: Rate limit exceeded
- `500 Internal Server Error`: Server-side error
Implement retry logic with exponential backoff for `429` and `500` errors.

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# Workspaces API
## Overview
Workspaces in protocols.io enable team collaboration by organizing protocols, managing members, and controlling access permissions. The Workspaces API allows you to list workspaces, manage memberships, and access workspace-specific protocols.
## Base URL
All workspace endpoints use the base URL: `https://protocols.io/api/v3`
## Workspace Operations
### List User Workspaces
Retrieve all workspaces the authenticated user has access to.
**Endpoint:** `GET /workspaces`
**Query Parameters:**
- `page_size`: Number of results per page (default: 10, max: 50)
- `page_id`: Page number for pagination (starts at 0)
**Response includes:**
- Workspace ID and name
- Workspace type (personal, group, institutional)
- Member count
- Access level (owner, admin, member, viewer)
- Creation date
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/workspaces"
```
### Get Workspace Details
Retrieve detailed information about a specific workspace.
**Endpoint:** `GET /workspaces/{workspace_id}`
**Path Parameters:**
- `workspace_id`: The workspace's unique identifier
**Response includes:**
- Complete workspace metadata
- Member list with roles
- Workspace settings and permissions
- Protocol count and categories
## Workspace Membership
### List Workspace Members
Retrieve all members of a workspace.
**Endpoint:** `GET /workspaces/{workspace_id}/members`
**Query Parameters:**
- `page_size`: Number of results per page
- `page_id`: Page number for pagination
**Response includes:**
- Member name and email
- Role (owner, admin, member, viewer)
- Join date
- Activity status
### Request Workspace Access
Request to join a workspace.
**Endpoint:** `POST /workspaces/{workspace_id}/join-request`
**Request Body:**
- `message` (optional): Message to workspace admins explaining the request
**Example Request:**
```bash
curl -X POST \
-H "Authorization: Bearer YOUR_TOKEN" \
-H "Content-Type: application/json" \
-d '{
"message": "I am collaborating with Dr. Smith on the CRISPR project and would like to access the shared protocols."
}' \
"https://protocols.io/api/v3/workspaces/12345/join-request"
```
### Join Public Workspace
Directly join a public workspace without approval.
**Endpoint:** `POST /workspaces/{workspace_id}/join`
**Note**: Only available for workspaces configured to allow public joining
## Workspace Protocols
### List Workspace Protocols
Retrieve all protocols in a workspace.
**Endpoint:** `GET /workspaces/{workspace_id}/protocols`
**Query Parameters:**
- `filter`: Filter protocols
- `all`: All protocols in the workspace
- `own`: Only protocols you created
- `shared`: Protocols shared with you
- `key`: Search keywords
- `order_field`: Sort field (`activity`, `created_on`, `modified_on`, `name`)
- `order_dir`: Sort direction (`desc`, `asc`)
- `page_size`: Number of results per page
- `page_id`: Page number for pagination
- `content_format`: Content format (`json`, `html`, `markdown`)
**Example Request:**
```bash
curl -H "Authorization: Bearer YOUR_TOKEN" \
"https://protocols.io/api/v3/workspaces/12345/protocols?filter=all&order_field=modified_on&order_dir=desc"
```
### Create Protocol in Workspace
Create a new protocol within a specific workspace.
**Endpoint:** `POST /workspaces/{workspace_id}/protocols`
**Request Body**: Same parameters as standard protocol creation (see protocols_api.md)
**Note**: The protocol will be created within the workspace and inherit workspace permissions
## Workspace Types and Permissions
### Workspace Types
1. **Personal Workspace**
- Default workspace for individual users
- Private by default
- Can share specific protocols
2. **Group Workspace**
- Collaborative workspace for teams
- Shared access for all members
- Role-based permissions
3. **Institutional Workspace**
- Organization-wide workspace
- Often includes branding
- Centralized protocol management
### Permission Levels
1. **Owner**
- Full workspace control
- Manage members and permissions
- Delete workspace
2. **Admin**
- Manage protocols and members
- Configure workspace settings
- Cannot delete workspace
3. **Member**
- Create and edit protocols
- View all workspace protocols
- Comment and collaborate
4. **Viewer**
- View-only access
- Can comment on protocols
- Cannot create or edit
## Common Use Cases
### 1. Lab Protocol Repository
Organize lab protocols in a shared workspace:
1. Create or join lab workspace: `GET /workspaces`
2. List existing protocols: `GET /workspaces/{id}/protocols`
3. Create new protocols: `POST /workspaces/{id}/protocols`
4. Invite lab members: Share workspace invitation
5. Organize by categories or tags
### 2. Collaborative Protocol Development
Develop protocols with team members:
1. Identify target workspace: `GET /workspaces`
2. Create draft protocol in workspace
3. Share with team members automatically via workspace
4. Gather feedback through comments
5. Iterate and publish final version
### 3. Cross-Institutional Collaboration
Work with external collaborators:
1. Create or identify shared workspace
2. Request access: `POST /workspaces/{id}/join-request`
3. Once approved, access shared protocols
4. Contribute new protocols or updates
5. Maintain institutional protocol copies in personal workspace
### 4. Protocol Migration
Move protocols between workspaces:
1. List source workspace protocols: `GET /workspaces/{source_id}/protocols`
2. For each protocol, retrieve full details
3. Create protocol in target workspace: `POST /workspaces/{target_id}/protocols`
4. Copy all steps and metadata
5. Update references and links
### 5. Workspace Audit
Review workspace activity and content:
1. List all workspaces: `GET /workspaces`
2. For each workspace, get member list
3. Retrieve protocol lists with activity dates
4. Identify inactive or outdated protocols
5. Generate activity reports
## Workspace Management Best Practices
1. **Organization**
- Use consistent naming conventions
- Tag protocols by project or category
- Maintain workspace directory or index
2. **Access Control**
- Review member list regularly
- Assign appropriate permission levels
- Remove inactive members
3. **Protocol Standards**
- Establish workspace-wide protocol templates
- Define required metadata fields
- Implement quality review process
4. **Collaboration**
- Communicate workspace guidelines to members
- Encourage protocol documentation
- Facilitate knowledge sharing
5. **Backup and Archival**
- Regularly export workspace protocols
- Maintain protocol version history
- Archive completed projects
## Organizations and Workspaces
Organizations are higher-level entities that can contain multiple workspaces.
### Export Organization Data
**Endpoint:** `GET /organizations/{org_id}/export`
**Use case**: Bulk export of all protocols and workspace data for institutional archives or backups
## Notifications and Activity
Workspace activity may trigger notifications:
- New protocols added to workspace
- Protocol updates by team members
- New comments on workspace protocols
- Member joins or leaves workspace
- Permission changes
Configure notification preferences in account settings.
## Error Handling
Common error responses:
- `400 Bad Request`: Invalid workspace ID or parameters
- `401 Unauthorized`: Missing or invalid access token
- `403 Forbidden`: Insufficient workspace permissions
- `404 Not Found`: Workspace not found or no access
- `429 Too Many Requests`: Rate limit exceeded
## Integration Considerations
When integrating workspace functionality:
1. **Cache workspace list**: Avoid repeated workspace list calls
2. **Respect permissions**: Check user's role before attempting operations
3. **Handle join requests**: Implement workflow for workspace access approval
4. **Sync regularly**: Update local workspace data periodically
5. **Support offline access**: Cache protocols for offline work with sync on reconnection