v1.0.0-rc.178 (#88)

* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.

Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

docs/python_client/README.md

@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.177
-- Package version: 1.0.0-rc.177
+- API version: 1.0.0-rc.178
+- Package version: 1.0.0-rc.178
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 

docs/python_client/docs/DefaultApi.md

@@ -1749,7 +1749,6 @@ Can be done anytime
 
 ### Example
 
-* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -1763,15 +1762,6 @@ configuration = jfjoch_client.Configuration(
     host = "http://localhost:5232"
 )
 
-# The client must configure the authentication and authorization parameters
-# in accordance with the API server security policy.
-# Examples for each auth method are provided below, use the example that
-# satisfies your auth use case.
-
-# Configure Bearer authorization: bearerAuth
-configuration = jfjoch_client.Configuration(
-    access_token = os.environ["BEARER_TOKEN"]
-)
 
 # Enter a context with an instance of the API client
 with jfjoch_client.ApiClient(configuration) as api_client:
@@ -1799,18 +1789,17 @@ This endpoint does not need any parameter.
 
 ### Authorization
 
-[bearerAuth](../README.md#bearerAuth)
+No authorization required
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: text/plain, application/json
+ - **Accept**: application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK |  -  |
 
 [[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)
@@ -1825,7 +1814,6 @@ This can only be done when detector is `Idle`, `Error` or `Inactive` states.
 
 ### Example
 
-* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -1838,15 +1826,6 @@ configuration = jfjoch_client.Configuration(
     host = "http://localhost:5232"
 )
 
-# The client must configure the authentication and authorization parameters
-# in accordance with the API server security policy.
-# Examples for each auth method are provided below, use the example that
-# satisfies your auth use case.
-
-# Configure Bearer authorization: bearerAuth
-configuration = jfjoch_client.Configuration(
-    access_token = os.environ["BEARER_TOKEN"]
-)
 
 # Enter a context with an instance of the API client
 with jfjoch_client.ApiClient(configuration) as api_client:
@@ -1872,18 +1851,17 @@ void (empty response body)
 
 ### Authorization
 
-[bearerAuth](../README.md#bearerAuth)
+No authorization required
 
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: text/plain, application/json
+ - **Accept**: application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | All good |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
 
@@ -1902,7 +1880,6 @@ and validation of every following rugnux live collection, until it is removed wi
 
 ### Example
 
-* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -1915,15 +1892,6 @@ configuration = jfjoch_client.Configuration(
     host = "http://localhost:5232"
 )
 
-# The client must configure the authentication and authorization parameters
-# in accordance with the API server security policy.
-# Examples for each auth method are provided below, use the example that
-# satisfies your auth use case.
-
-# Configure Bearer authorization: bearerAuth
-configuration = jfjoch_client.Configuration(
-    access_token = os.environ["BEARER_TOKEN"]
-)
 
 # Enter a context with an instance of the API client
 with jfjoch_client.ApiClient(configuration) as api_client:
@@ -1953,18 +1921,17 @@ void (empty response body)
 
 ### Authorization
 
-[bearerAuth](../README.md#bearerAuth)
+No authorization required
 
 ### HTTP request headers
 
  - **Content-Type**: application/octet-stream
- - **Accept**: text/plain, application/json
+ - **Accept**: application/json
 
 ### HTTP response details
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | All good |  -  |
 **400** | Empty body, or not a model that can be read (PDB or mmCIF, optionally gzipped) |  -  |
 **413** | Model larger than 64 MiB |  -  |
@@ -1982,7 +1949,6 @@ This can only be done when detector is `Idle`, `Error` or `Inactive` states.
 
 ### Example
 
-* Bearer Authentication (bearerAuth):
 
 ```python
 import jfjoch_client
@@ -1996,15 +1962,6 @@ configuration = jfjoch_client.Configuration(
     host = "http://localhost:5232"
 )
 
-# The client must configure the authentication and authorization parameters
-# in accordance with the API server security policy.
-# Examples for each auth method are provided below, use the example that
-# satisfies your auth use case.
-
-# Configure Bearer authorization: bearerAuth
-configuration = jfjoch_client.Configuration(
-    access_token = os.environ["BEARER_TOKEN"]
-)
 
 # Enter a context with an instance of the API client
 with jfjoch_client.ApiClient(configuration) as api_client:
@@ -2034,7 +1991,7 @@ void (empty response body)
 
 ### Authorization
 
-[bearerAuth](../README.md#bearerAuth)
+No authorization required
 
 ### HTTP request headers
 
@@ -2045,7 +2002,6 @@ void (empty response body)
 
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
 **200** | Everything OK |  -  |
 **400** | Input parsing or validation error |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
@@ -3590,6 +3546,8 @@ X-ray shutter must be closed.
 This operation will reconfigure network interface of the detector. 
 During operation of the detector it is recommended to use the `POST /pedestal` operation instead.
 If storage cells are used, the execution time might be few minutes.
+It also clears the image buffer, the previous collection's plots and live rugnux status, disables live rugnux analysis and removes the rugnux model.
+It drops the previous dataset's bearer tokens and resets its settings, so nothing of that dataset stays readable.
 
 This is async function - one needs to use `POST /wait_till_done` to ensure operation is done.
 

docs/python_client/docs/RugnuxLiveStatus.md

@@ -1,6 +1,6 @@
 # RugnuxLiveStatus
 
-Live rugnux processing of the last collection; kept until the next collection starts
+Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`. Times are taken when the image puller received a message, and are in seconds since the first image (before it arrives, since now). The frame rate is `(images_received - 1) / last_image_s`. 
 
 ## Properties
 
@@ -8,16 +8,18 @@ Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **state** | **str** |  | 
 **probe** | **str** | Answer of the early lattice probe on the first 60 degrees; empty until it answers | 
-**probe_s** | **float** | When the probe answered, since the collection started | [optional] 
+**probe_s** | **float** | When the probe answered, since the first image | [optional] 
+**start_to_first_image_s** | **float** | From the START message to the first image; set once the first image arrives | [optional] 
 **message** | **str** | Why the run failed or was skipped | 
 **images_expected** | **int** |  | 
+**expected_collection_s** | **float** | How long the collection is set up to take - images_expected times the image time; absent if not known | [optional] 
 **images_received** | **int** |  | 
 **elapsed_s** | **float** |  | 
 **step_progress** | **float** | Fraction of the current pass's images | [optional] 
 **steps** | [**List[RugnuxLiveStep]**](RugnuxLiveStep.md) |  | 
-**last_image_s** | **float** | When the last image arrived (and the cutoff timer started), since the collection started | [optional] 
+**last_image_s** | **float** | When the last image arrived, since the first image; set once the collection is over | [optional] 
 **cut** | **str** | Empty, or why the analysis was cut: `deadline` (`deadline_s` after the last image) or `cancel` (`POST /cancel`). The end message then carried what was established at the cut.  | [optional] 
-**cut_s** | **float** | When the analysis was cut, since the collection started | [optional] 
+**cut_s** | **float** | When the analysis was cut, since the first image | [optional] 
 **last_image_to_written_s** | **float** | From the last image received to all results written | [optional] 
 **verdict** | **str** | OK, WARNINGS, UNUSABLE or FAILED; empty until the run is over | 
 **verdict_text** | **str** |  | 

docs/python_client/docs/RugnuxLiveStep.md

@@ -6,7 +6,7 @@
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **title** | **str** |  | 
-**started_s** | **float** | Start of the step, since the collection started | 
+**started_s** | **float** | Start of the step, since the first image (negative if before it) | 
 **duration_s** | **float** | Set once the next step starts or the run ends | [optional] 
 **notes** | **List[str]** | What the step found (e.g. lattice, space group) |