broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
A rugnux live run that placed a model keeps it, with a copy of its map coefficients, beside the live status (RugnuxStructure), for as long as /rugnux/status keeps the run. Made in memory on the first request and cached, never written to disk: - GET /rugnux/model.cif: the placed model as mmCIF, labelled as WritePlacedModel labels _model.cif (PlacedModelMmcif, the labelling factored out of WritePlacedModel; the file output is unchanged). - GET /rugnux/map.ccp4?type=2fofc|fofc: the 2mFo-DFc / mFo-DFc map as a CCP4 map, FFT of the FWT/PHWT or DELFWT/PHDELWT coefficients (get_f_phi_on_grid + MapFromFPhi, sampled as ModelValidation samples), cut to the box around the model plus 5 A, with the whole cell's mean and RMS in the header. - 404 without a placed model or maps, 400 for an unknown map type; both routes protected by the dataset bearer token like /rugnux/status. rugnux_live_status gets placed_model. C++ model, python client docs, TypeScript client and redoc regenerated. Tests: a point's coefficients give a map peaking at the atom in a cropped box; the mmCIF; the structure is cleared at the next start; the auth test covers the new routes. End to end (myoglobin 2M replay with an AlphaFold model): the maps equal gemmi's FFT of the written _maps.mtz to 2.5e-6 rms. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 33124c3288ba112def3f51c0d91f5206886f3495)
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@@ -159,6 +159,8 @@ Class | Method | HTTP request | Description
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*DefaultApi* | [**preview_plot_bin_get**](docs/DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
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*DefaultApi* | [**preview_plot_get**](docs/DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
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*DefaultApi* | [**result_scan_get**](docs/DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
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*DefaultApi* | [**rugnux_map_ccp4_get**](docs/DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
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*DefaultApi* | [**rugnux_model_cif_get**](docs/DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
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*DefaultApi* | [**rugnux_status_get**](docs/DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
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*DefaultApi* | [**start_post**](docs/DefaultApi.md#start_post) | **POST** /start | Start detector
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*DefaultApi* | [**statistics_calibration_get**](docs/DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics
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@@ -62,6 +62,8 @@ Method | HTTP request | Description
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[**preview_plot_bin_get**](DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
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[**preview_plot_get**](DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
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[**result_scan_get**](DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
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[**rugnux_map_ccp4_get**](DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
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[**rugnux_model_cif_get**](DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
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[**rugnux_status_get**](DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
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[**start_post**](DefaultApi.md#start_post) | **POST** /start | Start detector
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[**statistics_calibration_get**](DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics
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@@ -4073,6 +4075,168 @@ This endpoint does not need any parameter.
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[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
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# **rugnux_map_ccp4_get**
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> bytearray rugnux_map_ccp4_get(type=type)
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Get an electron-density map of the last rugnux live run
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The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
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coefficients written to `_maps.mtz`. It covers the box around the model plus 5 A on every side, sampled
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every d_min/3; the mean and RMS in its header are those of the whole unit cell, so contour levels in
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sigma are the usual ones.
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### Example
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* Bearer Authentication (bearerAuth):
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```python
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import jfjoch_client
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from jfjoch_client.rest import ApiException
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from pprint import pprint
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# Defining the host is optional and defaults to http://localhost:5232
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# See configuration.py for a list of all supported configuration parameters.
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configuration = jfjoch_client.Configuration(
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host = "http://localhost:5232"
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)
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# The client must configure the authentication and authorization parameters
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# in accordance with the API server security policy.
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# Examples for each auth method are provided below, use the example that
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# satisfies your auth use case.
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# Configure Bearer authorization: bearerAuth
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configuration = jfjoch_client.Configuration(
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access_token = os.environ["BEARER_TOKEN"]
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)
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# Enter a context with an instance of the API client
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with jfjoch_client.ApiClient(configuration) as api_client:
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# Create an instance of the API class
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api_instance = jfjoch_client.DefaultApi(api_client)
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type = 2fofc # str | `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map (optional) (default to 2fofc)
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try:
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# Get an electron-density map of the last rugnux live run
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api_response = api_instance.rugnux_map_ccp4_get(type=type)
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print("The response of DefaultApi->rugnux_map_ccp4_get:\n")
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pprint(api_response)
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except Exception as e:
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print("Exception when calling DefaultApi->rugnux_map_ccp4_get: %s\n" % e)
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```
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### Parameters
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Name | Type | Description | Notes
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------------- | ------------- | ------------- | -------------
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**type** | **str**| `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map | [optional] [default to 2fofc]
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### Return type
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**bytearray**
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### Authorization
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[bearerAuth](../README.md#bearerAuth)
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### HTTP request headers
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- **Content-Type**: Not defined
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- **Accept**: application/octet-stream, text/plain
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### HTTP response details
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| Status code | Description | Response headers |
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|-------------|-------------|------------------|
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**200** | Map | - |
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**400** | Unknown map type | - |
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**401** | The current dataset is protected and no valid bearer token was presented. | - |
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**404** | The last rugnux live run placed no model or made no maps | - |
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[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
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# **rugnux_model_cif_get**
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> bytearray rugnux_model_cif_get()
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Get the model as placed by the last rugnux live run
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The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
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and space group of the `_model.cif` file written beside the data, with the input model's own metadata
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(entities, citation) kept. Kept as long as `/rugnux/status`.
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### Example
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* Bearer Authentication (bearerAuth):
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```python
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import jfjoch_client
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from jfjoch_client.rest import ApiException
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from pprint import pprint
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# Defining the host is optional and defaults to http://localhost:5232
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# See configuration.py for a list of all supported configuration parameters.
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configuration = jfjoch_client.Configuration(
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host = "http://localhost:5232"
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)
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# The client must configure the authentication and authorization parameters
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# in accordance with the API server security policy.
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# Examples for each auth method are provided below, use the example that
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# satisfies your auth use case.
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# Configure Bearer authorization: bearerAuth
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configuration = jfjoch_client.Configuration(
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access_token = os.environ["BEARER_TOKEN"]
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)
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# Enter a context with an instance of the API client
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with jfjoch_client.ApiClient(configuration) as api_client:
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# Create an instance of the API class
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api_instance = jfjoch_client.DefaultApi(api_client)
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try:
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# Get the model as placed by the last rugnux live run
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api_response = api_instance.rugnux_model_cif_get()
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print("The response of DefaultApi->rugnux_model_cif_get:\n")
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pprint(api_response)
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except Exception as e:
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print("Exception when calling DefaultApi->rugnux_model_cif_get: %s\n" % e)
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```
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### Parameters
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This endpoint does not need any parameter.
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### Return type
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**bytearray**
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### Authorization
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[bearerAuth](../README.md#bearerAuth)
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### HTTP request headers
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- **Content-Type**: Not defined
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- **Accept**: chemical/x-mmcif, text/plain
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### HTTP response details
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| Status code | Description | Response headers |
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|-------------|-------------|------------------|
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**200** | Placed model | - |
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**401** | The current dataset is protected and no valid bearer token was presented. | - |
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**404** | The last rugnux live run placed no model | - |
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[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
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# **rugnux_status_get**
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> RugnuxLiveStatus rugnux_status_get()
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@@ -7,6 +7,7 @@ Live rugnux processing of the last collection; kept until the next collection st
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Name | Type | Description | Notes
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------------ | ------------- | ------------- | -------------
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**state** | **str** | |
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**placed_model** | **bool** | The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from `/rugnux/map.ccp4`. |
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**probe** | **str** | Answer of the early lattice probe on the first 60 degrees; empty until it answers |
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**probe_s** | **float** | When the probe answered, since the first image | [optional]
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**start_to_first_image_s** | **float** | From the START message to the first image; set once the first image arrives | [optional]
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