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api-spec.yaml
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components:
schemas:
ClearanceKeys:
properties:
autoproc_program:
items:
type: string
title: Autoproc Program
type: array
data_collection:
items:
type: string
title: Data Collection
type: array
data_collection_group:
items:
type: string
title: Data Collection Group
type: array
processing_job:
items:
type: string
title: Processing Job
type: array
required:
- data_collection_group
- data_collection
- processing_job
- autoproc_program
title: ClearanceKeys
type: object
ConnectionFileParameters:
properties:
destinations:
items:
type: string
title: Destinations
type: array
filename:
title: Filename
type: string
required:
- filename
- destinations
title: ConnectionFileParameters
type: object
ContextInfo:
properties:
acquisition_software:
title: Acquisition Software
type: string
experiment_type:
title: Experiment Type
type: string
required:
- experiment_type
- acquisition_software
title: ContextInfo
type: object
DCGroupParameters:
properties:
experiment_type:
title: Experiment Type
type: string
experiment_type_id:
title: Experiment Type Id
type: integer
tag:
title: Tag
type: string
required:
- experiment_type
- experiment_type_id
- tag
title: DCGroupParameters
type: object
DCParameters:
properties:
acquisition_software:
title: Acquisition Software
type: string
c2aperture:
title: C2Aperture
type: number
experiment_type:
title: Experiment Type
type: string
exposure_time:
title: Exposure Time
type: number
file_extension:
title: File Extension
type: string
image_directory:
title: Image Directory
type: string
image_size_x:
title: Image Size X
type: integer
image_size_y:
title: Image Size Y
type: integer
magnification:
title: Magnification
type: number
phase_plate:
default: false
title: Phase Plate
type: boolean
pixel_size_on_image:
title: Pixel Size On Image
type: string
slit_width:
title: Slit Width
type: number
source:
title: Source
type: string
tag:
title: Tag
type: string
total_exposed_dose:
title: Total Exposed Dose
type: number
voltage:
title: Voltage
type: number
required:
- voltage
- pixel_size_on_image
- experiment_type
- image_size_x
- image_size_y
- file_extension
- acquisition_software
- image_directory
- tag
- source
- magnification
title: DCParameters
type: object
File:
properties:
description:
title: Description
type: string
name:
title: Name
type: string
size:
title: Size
type: integer
timestamp:
title: Timestamp
type: number
required:
- name
- description
- size
- timestamp
title: File
type: object
GainReference:
properties:
gain_ref:
format: path
title: Gain Ref
type: string
required:
- gain_ref
title: GainReference
type: object
HTTPValidationError:
properties:
detail:
items:
$ref: "#/components/schemas/ValidationError"
title: Detail
type: array
title: HTTPValidationError
type: object
ProcessFile:
properties:
autoproc_program_id:
title: Autoproc Program Id
type: integer
data_collection_id:
title: Data Collection Id
type: integer
description:
title: Description
type: string
dose_per_frame:
title: Dose Per Frame
type: number
gain_ref:
title: Gain Ref
type: string
image_number:
title: Image Number
type: integer
mc_binning:
default: 1
title: Mc Binning
type: integer
mc_uuid:
title: Mc Uuid
type: integer
path:
title: Path
type: string
pixel_size:
title: Pixel Size
type: number
processing_job:
title: Processing Job
type: integer
size:
title: Size
type: integer
timestamp:
title: Timestamp
type: number
required:
- path
- description
- size
- timestamp
- processing_job
- data_collection_id
- image_number
- mc_uuid
- autoproc_program_id
- pixel_size
- dose_per_frame
title: ProcessFile
type: object
ProcessingJobParameters:
properties:
parameters:
default: {}
title: Parameters
type: object
recipe:
title: Recipe
type: string
tag:
title: Tag
type: string
required:
- tag
- recipe
title: ProcessingJobParameters
type: object
RegistrationMessage:
properties:
params:
title: Params
type: object
registration:
title: Registration
type: string
required:
- registration
title: RegistrationMessage
type: object
SPAProcessingParameters:
properties:
job_id:
title: Job Id
type: integer
required:
- job_id
title: SPAProcessingParameters
type: object
SuggestedPathParameters:
properties:
base_path:
format: path
title: Base Path
type: string
touch:
default: false
title: Touch
type: boolean
required:
- base_path
title: SuggestedPathParameters
type: object
TiltSeries:
properties:
autoproc_program_id:
title: Autoproc Program Id
type: integer
dcid:
title: Dcid
type: integer
file_tilt_list:
title: File Tilt List
type: string
manual_tilt_offset:
title: Manual Tilt Offset
type: integer
motion_corrected_path:
title: Motion Corrected Path
type: string
movie_id:
title: Movie Id
type: integer
name:
title: Name
type: string
pixel_size:
title: Pixel Size
type: number
processing_job:
title: Processing Job
type: integer
required:
- name
- file_tilt_list
- dcid
- processing_job
- autoproc_program_id
- motion_corrected_path
- movie_id
- pixel_size
- manual_tilt_offset
title: TiltSeries
type: object
ValidationError:
properties:
loc:
items:
anyOf:
- type: string
- type: integer
title: Location
type: array
msg:
title: Message
type: string
type:
title: Error Type
type: string
required:
- loc
- msg
- type
title: ValidationError
type: object
Visit:
properties:
beamline:
title: Beamline
type: string
end:
format: date-time
title: End
type: string
name:
title: Name
type: string
proposal_title:
title: Proposal Title
type: string
session_id:
title: Session Id
type: integer
start:
format: date-time
title: Start
type: string
required:
- start
- end
- session_id
- name
- beamline
- proposal_title
title: Visit
type: object
info:
title: Murfey server
version: 0.1.0
openapi: 3.0.2
paths:
/:
get:
operationId: root__get
responses:
"200":
content:
text/html:
schema:
type: string
description: Successful Response
summary: Root
/bootstrap/:
get:
description:
"Return a website containing instructions for installing the Murfey
client on a
machine with no internet access."
operationId: get_bootstrap_instructions_bootstrap__get
responses:
"200":
content:
text/html:
schema:
type: string
description: Successful Response
summary: Get Bootstrap Instructions
tags:
- bootstrap
/bootstrap/murfey.whl:
get:
description:
"Return a wheel file containing the latest release version of Murfey.
We should
not have to worry about the exact Python compatibility here, as long as
murfey.bootstrap is compatible with all relevant versions of Python.
This also ignores yanked releases, which again should be fine."
operationId: get_murfey_wheel_bootstrap_murfey_whl_get
responses:
"200":
description: Successful Response
summary: Get Murfey Wheel
tags:
- bootstrap
/bootstrap/pip.whl:
get:
description:
"Return a static version of pip. This does not need to be the newest
or best,
but has to be compatible with all supported Python versions.
This is only used during bootstrapping by the client to identify and then
download the actually newest appropriate version of pip."
operationId: get_pip_wheel_bootstrap_pip_whl_get
responses:
"200":
description: Successful Response
summary: Get Pip Wheel
tags:
- bootstrap
/connections/:
get:
operationId: connections_check_connections__get
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
summary: Connections Check
/cygwin/setup-x86_64.exe:
get:
description:
"Obtain and past though a Cygwin installer from an official source.
This is used during client bootstrapping and can download and install the
Cygwin distribution that then remains on the client machines."
operationId: get_cygwin_setup_cygwin_setup_x86_64_exe_get
responses:
"200":
description: Successful Response
summary: Get Cygwin Setup
tags:
- bootstrap
/cygwin/{request_path}:
get:
description: Forward a Cygwin setup request to an official mirror.
operationId: parse_cygwin_request_cygwin__request_path__get
parameters:
- in: path
name: request_path
required: true
schema:
title: Request Path
type: string
responses:
"200":
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Parse Cygwin Request
tags:
- bootstrap
/demo/visits_raw:
get:
operationId: get_current_visits_demo_demo_visits_raw_get
responses:
"200":
content:
application/json:
schema:
items:
$ref: "#/components/schemas/Visit"
title: Response Get Current Visits Demo Demo Visits Raw Get
type: array
description: Successful Response
summary: Get Current Visits Demo
/feedback:
post:
operationId: send_murfey_message_feedback_post
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/RegistrationMessage"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Send Murfey Message
/health/:
get:
operationId: health_check_health__get
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
summary: Health Check
/machine/:
get:
operationId: machine_info_machine__get
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
summary: Machine Info
/microscope/:
get:
operationId: get_mic_microscope__get
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
summary: Get Mic
/pypi/:
get:
description: Obtain list of all PyPI packages via the simple API (PEP 503).
operationId: get_pypi_index_pypi__get
responses:
"200":
description: Successful Response
summary: Get Pypi Index
tags:
- bootstrap
/pypi/{package}/:
get:
description:
"Obtain list of all package downloads from PyPI via the simple
API (PEP 503),
and rewrite all download URLs to point to this server,
underneath the current directory."
operationId: get_pypi_package_downloads_list_pypi__package___get
parameters:
- in: path
name: package
required: true
schema:
title: Package
type: string
responses:
"200":
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Get Pypi Package Downloads List
tags:
- bootstrap
/pypi/{package}/{filename}:
get:
description: Obtain and pass through a specific download for a PyPI package.
operationId: get_pypi_file_pypi__package___filename__get
parameters:
- in: path
name: package
required: true
schema:
title: Package
type: string
- in: path
name: filename
required: true
schema:
title: Filename
type: string
responses:
"200":
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Get Pypi File
tags:
- bootstrap
/version:
get:
operationId: get_version_version_get
parameters:
- in: query
name: client_version
required: false
schema:
default: ""
title: Client Version
type: string
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Get Version
/visits/:
get:
operationId: all_visit_info_visits__get
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
summary: All Visit Info
/visits/{visit_name}:
get:
operationId: visit_info_visits__visit_name__get
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
type: string
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Visit Info
/visits/{visit_name}/align:
post:
operationId: request_tilt_series_alignment_visits__visit_name__align_post
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/TiltSeries"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Request Tilt Series Alignment
/visits/{visit_name}/clean_state:
post:
operationId: clean_state_visits__visit_name__clean_state_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/ClearanceKeys"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Clean State
/visits/{visit_name}/context:
post:
operationId: register_context_visits__visit_name__context_post
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/ContextInfo"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Register Context
/visits/{visit_name}/files:
post:
operationId: add_file_visits__visit_name__files_post
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/File"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Add File
/visits/{visit_name}/process_gain:
post:
operationId: process_gain_visits__visit_name__process_gain_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/GainReference"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Process Gain
/visits/{visit_name}/register_data_collection_group:
post:
operationId: register_dc_group_visits__visit_name__register_data_collection_group_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/DCGroupParameters"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Register Dc Group
/visits/{visit_name}/register_processing_job:
post:
operationId: register_proc_visits__visit_name__register_processing_job_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/ProcessingJobParameters"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Register Proc
/visits/{visit_name}/spa_processing:
post:
operationId: request_spa_processing_visits__visit_name__spa_processing_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
type: string
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/SPAProcessingParameters"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Request Spa Processing
/visits/{visit_name}/start_data_collection:
post:
operationId: start_dc_visits__visit_name__start_data_collection_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/DCParameters"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Start Dc
/visits/{visit_name}/suggested_path:
post:
operationId: suggest_path_visits__visit_name__suggested_path_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/SuggestedPathParameters"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Suggest Path
/visits/{visit_name}/tomography_preprocess:
post:
operationId: request_tomography_preprocessing_visits__visit_name__tomography_preprocess_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
type: string
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/ProcessFile"
required: true
responses:
"200":
content:
application/json:
schema: {}
description: Successful Response
"422":
content:
application/json:
schema:
$ref: "#/components/schemas/HTTPValidationError"
description: Validation Error
summary: Request Tomography Preprocessing
/visits/{visit_name}/write_connections_file:
post:
operationId: write_conn_file_visits__visit_name__write_connections_file_post
parameters:
- in: path
name: visit_name
required: true
schema:
title: Visit Name
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/ConnectionFileParameters"
required: true
responses:
"200":