adds mockup beamline configured with YAML files

Adding an example of the mockup beamline, where all HWOBJs are
configured with YAML files.

To start MXCuBE with this version of beamline, use '--repository'
command line argument. For example:

   ./mxcubeweb-server --repository demo.yaml

demo.yaml/aperture.yaml

@@ -0,0 +1,5 @@
+%YAML 1.2
+---
+class: ApertureMockup.ApertureMockup
+configuration:
+  diameter_size_list: '[10, 20, 50, 100, 150]'

demo.yaml/beam.yaml

@@ -0,0 +1,11 @@
+%YAML 1.2
+---
+class: BeamMockup.BeamMockup
+configuration:
+  beam_divergence_horizontal: 12.0
+  beam_divergence_vertical: 12.0
+  definer_type: aperture
+  username: beam
+objects:
+  aperture: aperture.yaml
+  slits: slits.yaml

demo.yaml/beamline_actions.yaml

@@ -0,0 +1,19 @@
+%YAML 1.2
+---
+class: BeamlineActionsMockup.BeamlineActionsMockup
+configuration:
+  commands: "
+  [
+    {'type': 'controller', 'name': 'Centre Beam',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.SimulatedAction'},
+    {'type': 'controller', 'name': 'Quick Realign',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.LongSimulatedAction'},
+    {'type': 'controller', 'name': 'Anneal',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.SimulatedActionError'},
+    {'type': 'annotated',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.Anneal2'},
+    {'type': 'annotated',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.QuickRealign2'},
+    {'type': 'annotated',
+     'command': 'HardwareObjects.mockup.BeamlineActionsMockup.ComboTest2'},
+  ]"

demo.yaml/beamline_config.yml

@@ -0,0 +1,157 @@
+%YAML 1.2
+---
+
+# The class to initialise, and init parameters
+class:
+  mxcubecore.HardwareObjects.Beamline.Beamline
+
+# objects
+#
+# NBNB some objects that do not currently have their own config files
+# would need those added (e.g. the centring methods)
+#
+objects:
+  # The !!omap and the lines starting with '- ' give you an *ordered* dictionary
+  # And thus a reproducible loading order
+  !!omap
+  # The values are the file paths to the configuration file for the
+  # object, relative to the configuration file path(s)
+  #
+  # NB - the order is *NOT* arbitrary, as signal connections are set
+  # on one object that require the other to be already loaded.
+  #
+  # Hardware:
+  - session: session.yaml
+  - data_publisher: data_publisher.yaml
+  - machine_info: machine_info.yaml
+  - detector: detector.yaml
+  - beam: beam.yaml
+  - transmission: transmission.yaml
+  - flux: flux.yaml
+  - cryo: cryo.yaml
+  - energy: energy.yaml
+  - resolution: resolution.yaml
+  - safety_shutter: safety_shutter.yaml
+  - fast_shutter: fast_shutter.yaml
+  - sample_changer: sample_changer.yaml
+  - sample_changer_maintenance: sample_changer_maint.yaml
+
+  # The 2 lines up have to be used for SC and the 2 line below for the plate manipulator
+  # - sample_changer: plate_manipulator.xml
+  # - sample_changer_maintenance: plate_manipulator_maint.xml
+
+  # - harvester: harvester.xml
+  # - harvester_maintenance: harvester_maintenance.xml
+
+  - diffractometer: minidiff.yaml
+  - lims: lims.yaml
+  - sample_view: sample_view.yaml
+  - queue_manager: queue_manager.yaml
+  - queue_model: queue_model.yaml
+
+  # Procedures:
+  - beamline_actions: beamline_actions.yaml
+  - workflow: ednaparams.yaml
+  - collect: mxcollect.yaml
+  - xrf_spectrum: xrf.yaml
+  - energy_scan: energy_scan.yaml
+  - gphl_connection: gphl/gphl-setup.yaml
+  - gphl_workflow: gphl/gphl-workflow.yaml
+  - xray_centring: xray_centring2.yaml
+  - xml_rpc_server: xml_rpc_server.yaml
+
+  # Analysis:
+  - offline_processing: auto_processing.yaml
+  - online_processing: parallel_processing.yaml
+  - characterisation: characterisation.yaml
+
+configuration:
+  advanced_methods:
+    - MeshScan
+    - XrayCentering
+
+  tunable_wavelength: true
+  disable_num_passes: true
+  run_processing_parallel: true
+  run_number: 1
+  click_centring_num_clicks: 3
+
+  mesh_result_format: PNG
+  use_native_mesh: true
+  enable_2d_points: true
+
+  default_acquisition_parameters:
+    default:
+      # Default values, also used for standard acquisition.
+      # Values not given in other dictionaries are taken from here
+      exp_time: 0.02  # exposure time
+      osc_start: 0.0  # Only used if no current angle can be found
+      osc_range: 0.1
+      num_passes: 1
+      first_image: 1
+      overlap: 0
+      num_images: 1
+      detector_mode: 1  # Remove as not in practice used ?
+      inverse_beam: false
+      take_dark_current: true
+      skip_existing_images: true
+      take_snapshots: true
+      sub_wedge_size: 10
+      # NB 'compression' not added as apparently never used
+
+      helical:
+        # Defaults for helical scan. Missing values are taken from default
+        number_of_images: 100
+
+    characterisation:
+      # Defaults for characterisation. Missing values are taken from default
+      exp_time: 0.05  # exposure time
+      osc_range: 1
+      overlap: -89
+      num_images: 4
+      shutterless: false
+
+    mesh:
+      # Defaults for 'advanced' acquisition. Missing values are taken from default
+      exp_time: 10  # exposure time
+      range: 10
+      num_images: 100
+      cell_counting: zig-zag
+      cell_spacing: vertical, horizontal
+      mesh_center: top-left
+
+      gphlworkflow:
+        {}
+        # Apparently this must be here, but we use all values same as default
+
+    acquisition_limit_values:
+      exposure_time:
+        - 0.02
+        - 1000
+      osc_range:
+        - -10000
+        - 10000
+      number_of_images:
+        - 1
+        - 99999
+      kappa:
+        - -5.0
+        - 240.0
+
+  available_methods:
+    datacollection: true
+    characterisation: true
+    helical: true
+    xrf_spectrum: true
+    energy_scan: true
+    mesh: true
+    ssx_chip_collection: true
+    gphlworkflow: true
+    test_collection: true
+
+    undulators:
+      - type: PPU35C_GAP
+        device_uri: //orion:10000/id/id/30
+
+      - type: PPU35D_GAP
+        device_uri: //orion:10000/id/id/30

demo.yaml/beamstop.yaml

@@ -0,0 +1,7 @@
+%YAML 1.2
+---
+class: ExporterNStateMockup.ExporterNStateMockup
+configuration:
+  use_hwstate: true
+  username: beamstop
+  values: '{"OUT": "OFF", "IN": "BEAM"}'

demo.yaml/beamstop_alignment_x.yaml

@@ -0,0 +1,9 @@
+%YAML 1.2
+---
+class: MotorMockup.MotorMockup
+configuration:
+  GUIstep: 0.1
+  exporter_address: 130.235.94.124:9001
+  motor_name: BeamstopAlignmentX
+  unit: 0.001
+  username: Beamstop Alignemnt X

demo.yaml/capillary.yaml

@@ -0,0 +1,7 @@
+%YAML 1.2
+---
+class: ExporterNStateMockup.ExporterNStateMockup
+configuration:
+  use_hwstate: true
+  username: capillary
+  values: '{"IN": "BEAM", "OUT": "OFF"}'

demo.yaml/characterisation.yaml

@@ -0,0 +1,6 @@
+%YAML 1.2
+---
+class: EDNACharacterisationMockup.EDNACharacterisationMockup
+configuration:
+  edna_command: /users/blissadm/local/bin/edna_script_bes.py
+  edna_default_file: edna_defaults.xml

demo.yaml/chip_definition.json

@@ -0,0 +1,155 @@
+{
+    "current": "SMALL_FOIL",
+    "available": {
+        "OXFORD_CHIP": {
+            "head_type": "CHIP",
+            "holder_type": "KNOWN_GEOMETRY",
+            "holder_brand": "Oxford Chip",
+            "holder_size": [
+                30.0,
+                30.0
+            ],
+            "sections": [
+                {
+                    "section_offset": [
+                        0,
+                        0
+                    ],
+                    "block_size": [
+                        30.0,
+                        30.0
+                    ],
+                    "block_spacing": [
+                        15.0,
+                        15.0
+                    ],
+                    "block_shape": "RECTANGULAR",
+                    "number_of_rows": 8,
+                    "number_of_collumns": 8,
+                    "row_labels": [
+                        "1",
+                        "2",
+                        "3",
+                        "4",
+                        "5",
+                        "6",
+                        "7",
+                        "8"
+                    ],
+                    "column_lables": [
+                        "A",
+                        "B",
+                        "C",
+                        "D",
+                        "E",
+                        "F",
+                        "G",
+                        "H"
+                    ],
+                    "targets_per_block": [
+                        20,
+                        20
+                    ]
+                }
+            ],
+            "calibration_data": {
+                "top_left": [
+                    0.0,
+                    0.0,
+                    0.0
+                ],
+                "top_right": [
+                    0.0,
+                    0.0,
+                    0.0
+                ],
+                "bottom_left": [
+                    0.0,
+                    0.0,
+                    0.0
+                ]
+            }
+        },
+        "SMALL_FOIL": {
+            "head_type": "CHIP",
+            "holder_type": "FREE_GEOMETRY",
+            "holder_brand": "FOIL",
+            "holder_size": [
+                100.0,
+                100.0
+            ],
+            "sections": [],
+            "calibration_data": {
+                "top_left": [
+                    18.0,
+                    15.8,
+                    -0.17
+                ],
+                "top_right": [
+                    22.0,
+                    15.8,
+                    -0.17
+                ],
+                "bottom_left": [
+                    18.0,
+                    24.0,
+                    -0.17
+                ]
+            }
+        },
+        "BIG_FOIL": {
+            "head_type": "CHIP",
+            "holder_type": "FREE_GEOMETRY",
+            "holder_brand": "FOIL",
+            "holder_size": [
+                100.0,
+                100.0
+            ],
+            "sections": [],
+            "calibration_data": {
+                "top_left": [
+                    7.0,
+                    3.0,
+                    0.08
+                ],
+                "top_right": [
+                    32.0,
+                    3.0,
+                    0.08
+                ],
+                "bottom_left": [
+                    7.0,
+                    28.0,
+                    0.08
+                ]
+            }
+        },
+        "CUSTOM_FOIL": {
+            "head_type": "CHIP",
+            "holder_type": "FREE_GEOMETRY",
+            "holder_brand": "FOIL",
+            "holder_size": [
+                100.0,
+                100.0
+            ],
+            "sections": [],
+            "calibration_data": {
+                "top_left": [
+                    15.0,
+                    16.0,
+                    -0.008
+                ],
+                "top_right": [
+                    23.0,
+                    16.0,
+                    -0.008
+                ],
+                "bottom_left": [
+                    15.0,
+                    24.0,
+                    -0.008
+                ]
+            }
+        }
+    }
+}

demo.yaml/cryo.yaml

@@ -0,0 +1,8 @@
+%YAML 1.2
+---
+class: ActuatorMockup.ActuatorMockup
+configuration:
+  actuator_name: Cryo
+  default_value: 200
+  read_only: true
+  username: Cryo

demo.yaml/data_publisher.yaml

@@ -0,0 +1,4 @@
+%YAML 1.2
+---
+class: DataPublisher.DataPublisher
+configuration: {}