Directories
¶
| Path | Synopsis |
|---|---|
|
api
|
|
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config
API configuration as read from strings/JSON and some constants defined here also
|
API configuration as read from strings/JSON and some constants defined here also |
|
dataimport
Implements importer triggering based on SNS queues.
|
Implements importer triggering based on SNS queues. |
|
dataimport/datasetArchive
Implements archiving/retrieval of dataset source zip files as delivered by GDS.
|
Implements archiving/retrieval of dataset source zip files as delivered by GDS. |
|
dataimport/internal/output
Allows outputting (in PIXLISE protobuf dataset format) of in-memory representation of PIXL data that importer has read.
|
Allows outputting (in PIXLISE protobuf dataset format) of in-memory representation of PIXL data that importer has read. |
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filepaths
Defines all paths/file names used in S3 for storage of our data.
|
Defines all paths/file names used in S3 for storage of our data. |
|
job/jobstarter
Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.
|
Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs. |
|
permission
Permission constants and helper functions for defining routes.
|
Permission constants and helper functions for defining routes. |
|
piquant
Storage/versioning and retrieval of PIQUANT configuration files and the currently selected PIQUANT pod version to be run
|
Storage/versioning and retrieval of PIQUANT configuration files and the currently selected PIQUANT pod version to be run |
|
quantification/quantRunner
Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.
|
Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs. |
|
router
The guts of PIXLISE API endpoint handler/routing code.
|
The guts of PIXLISE API endpoint handler/routing code. |
|
services
Services used by API endpoint handlers and other bits of code.
|
Services used by API endpoint handlers and other bits of code. |
|
core
|
|
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auth0login
Contains all the code needed to do an Auth0 login and retrieve a JWT.
|
Contains all the code needed to do an Auth0 login and retrieve a JWT. |
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awsutil
AWS utility functions to wrap some functionality and provide mocking capabilities for unit testing.
|
AWS utility functions to wrap some functionality and provide mocking capabilities for unit testing. |
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client/internal/cmdline
command
|
|
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client/lib
command
|
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fileaccess
Provides a higher-level file access interface which is implemented using local file storage as well as AWS S3.
|
Provides a higher-level file access interface which is implemented using local file storage as well as AWS S3. |
|
gdsfilename
File name parser and writer, allowing us to extract metadata from the strict file name conventions defined by GDS
|
File name parser and writer, allowing us to extract metadata from the strict file name conventions defined by GDS |
|
kubernetes
Utilities to connect to and command a Kubernetes cluster to start and shut down pods.
|
Utilities to connect to and command a Kubernetes cluster to start and shut down pods. |
|
logger
A common logging interface used throughout the code which has implementations using stdout and AWS cloudwatch.
|
A common logging interface used throughout the code which has implementations using stdout and AWS cloudwatch. |
|
mongoDBConnection
Lowest-level code to connect to Mongo DB (locally in Docker and remotely) and get consistant collection names.
|
Lowest-level code to connect to Mongo DB (locally in Docker and remotely) and get consistant collection names. |
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timestamper
An interface to get a unix time stamp (in seconds) with an included mock that can be pre-loaded with timestamps for predictable unit test output.
|
An interface to get a unix time stamp (in seconds) with an included mock that can be pre-loaded with timestamps for predictable unit test output. |
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utils
Exposes various utility functions for strings, generation of valid filenames and random ID strings, zipping files/directories, reading/writing images
|
Exposes various utility functions for strings, generation of valid filenames and random ID strings, zipping files/directories, reading/writing images |
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internal
|
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api
command
|
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cmd-line-tools/auth0login
command
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cmd-line-tools/dataset-converter
command
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cmd-line-tools/ij-swapper
command
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cmd-line-tools/job-runner
command
|
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cmd-line-tools/v3-importer
command
|
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lambdas/data-import
command
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