> For the complete documentation index, see [llms.txt](https://medomicslab.gitbook.io/medomics-docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development/backend-server/express-request-endpoints.md).

# Express Request Endpoints

#### Status and Service Lifecycle

| Method | Endpoint        | Purpose                                          | Input                                          | Success Response                                         | Notes                                    |
| ------ | --------------- | ------------------------------------------------ | ---------------------------------------------- | -------------------------------------------------------- | ---------------------------------------- |
| GET    | /status         | Get full backend runtime status                  | None                                           | success, expressPort, serverIdentity, go, mongo, jupyter | Probes live status before returning      |
| POST   | /stop-express   | Stop Express and best-effort stop child services | None                                           | success, stopped or message                              | Also attempts to stop Go, Mongo, Jupyter |
| POST   | /run-go-server  | Start or restart Go service                      | None                                           | success, running, port                                   | Kills existing Go process first          |
| POST   | /ensure-go      | Ensure Go is running (idempotent)                | preferredPort optional                         | success, running, port                                   | Preferred modern route                   |
| POST   | /ensure-mongo   | Ensure Mongo is running (idempotent)             | workspacePath optional                         | success, running, port                                   | Waits for port readiness                 |
| POST   | /ensure-jupyter | Ensure Jupyter is running (idempotent)           | workspacePath optional, preferredPort optional | success, running, port                                   | Default preferredPort is 8900            |

#### Workspace and File Tree

| Method | Endpoint               | Purpose                        | Input                        | Success Response          | Notes                                                  |
| ------ | ---------------------- | ------------------------------ | ---------------------------- | ------------------------- | ------------------------------------------------------ |
| POST   | /set-working-directory | Set active workspace on server | workspacePath required       | success, workspace        | Marks workspace as remote, reinitializes related state |
| GET    | /get-working-dir-tree  | Get directory tree for a path  | requestedPath query required | success, workingDirectory | Uses recursive directory tree output                   |

#### Mongo Data Import and Export

<table><thead><tr><th>Method</th><th width="132">Endpoint</th><th>Purpose</th><th>Input</th><th>Success Response</th><th>Notes</th></tr></thead><tbody><tr><td>POST</td><td>/insert-object-into-collection</td><td>Import file content into Mongo collection</td><td>objectPath required, medDataObject required (id, type)</td><td>success, insertedCount</td><td>Supports csv, html, png, jpg, jpeg, pkl</td></tr><tr><td>POST</td><td>/download-collection-to-file</td><td>Export collection content to file</td><td>collectionId, filePath, type required</td><td>success</td><td>Supports csv, html, json, images, pkl</td></tr></tbody></table>

#### Exploratory Services

| Method | Endpoint                      | Purpose                           | Input                                                                                                        | Success Response                                   | Notes                                        |
| ------ | ----------------------------- | --------------------------------- | ------------------------------------------------------------------------------------------------------------ | -------------------------------------------------- | -------------------------------------------- |
| POST   | /exploratory/dtale/start      | Start D-Tale and wait until ready | dataset required (id, name), requestId optional, pageId optional                                             | success, requestId, remotePort, webServerUrl, name | Starts Go automatically if needed            |
| POST   | /exploratory/dtale/progress   | Poll D-Tale startup/progress      | routeId required                                                                                             | success, progress                                  | Route-level progress                         |
| POST   | /exploratory/dtale/stop       | Stop D-Tale session               | requestId optional, remotePort optional                                                                      | success                                            | Calls D-Tale shutdown endpoint when possible |
| POST   | /exploratory/sweetviz/start   | Generate SweetViz report          | mainDataset required (id, name), compDataset optional, target optional, htmlFileID optional, pageId optional | success, htmlFileID, reportPath, expressPort       | Report served by report endpoint             |
| POST   | /exploratory/ydata/start      | Generate ydata-profiling report   | mainDataset required (id, name), compDataset optional, htmlFileID optional, pageId optional                  | success, htmlFileID, reportPath, expressPort       | Report served by report endpoint             |
| GET    | /exploratory/report/:reportId | Serve generated HTML report       | reportId path required                                                                                       | HTML response body                                 | Content-Type text/html                       |

#### Mongo Runtime and Diagnostics

| Method | Endpoint        | Purpose                        | Input                  | Success Response    | Notes                       |
| ------ | --------------- | ------------------------------ | ---------------------- | ------------------- | --------------------------- |
| POST   | /start-mongo    | Start Mongo directly           | workspacePath required | success, message    | Legacy direct route         |
| POST   | /stop-mongo     | Stop Mongo directly            | None                   | success             | Legacy direct route         |
| GET    | /get-mongo-path | Resolve mongod executable path | None                   | success, path       | 404 if not found            |
| GET    | /mongo-debug    | Get Mongo debug info           | None                   | success, mongoDebug | Useful for startup failures |

#### Jupyter Runtime

| Method | Endpoint              | Purpose                     | Input                  | Success Response   | Notes                    |
| ------ | --------------------- | --------------------------- | ---------------------- | ------------------ | ------------------------ |
| GET    | /check-jupyter-status | Check if Jupyter is running | None                   | running, error     | Lightweight status route |
| POST   | /start-jupyter-server | Start Jupyter directly      | workspacePath required | running, error     | Legacy direct route      |
| POST   | /stop-jupyter-server  | Stop Jupyter                | None                   | stop result object | Legacy direct route      |

#### Python and Requirements

| Method | Endpoint                          | Purpose                             | Input                     | Success Response         | Notes                                                                  |
| ------ | --------------------------------- | ----------------------------------- | ------------------------- | ------------------------ | ---------------------------------------------------------------------- |
| GET    | /get-bundled-python-environment   | Get bundled Python env path/details | None                      | success, pythonEnv       | Used before Go/python workflows                                        |
| GET    | /get-installed-python-packages    | Get installed Python package info   | None                      | success, packages        | Current implementation appears to return env-derived data              |
| POST   | /install-bundled-python           | Install bundled Python runtime      | None                      | success                  | Backend installer path                                                 |
| POST   | /install-required-python-packages | Install required Python packages    | pythonPath optional       | success                  | Installs required deps for backend workflows                           |
| GET    | /check-python-requirements        | Validate required Python deps       | pythonPath query optional | success, requirementsMet | Boolean result                                                         |
| GET    | /check-requirements               | Check global requirements           | None                      | success, result          | Includes Mongo/Python checks                                           |
| POST   | /install-mongo                    | Install MongoDB                     | None                      | success                  | Error response may include installerExitCode and windowsInstallerError |

### Error Behavior (Common Pattern)

* 400 for invalid or missing required inputs
* 500 for runtime/internal failures
* Typical error payload: success false, error message
* Some routes include extra diagnostics (for example mongoDebug, installerExitCode)

### Recommended Usage Pattern

1. Call /status to inspect current state.
2. Use /ensure-go, /ensure-mongo, /ensure-jupyter instead of legacy start routes.
3. For exploratory reports, start via exploratory endpoint then read via /exploratory/report/:reportId.
4. Use /mongo-debug and /check-requirements when setup fails.

<br>


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development/backend-server/express-request-endpoints.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.