Directories ¶
Path | Synopsis |
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api
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config
API configuration as read from strings/JSON and some constants defined here also
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API configuration as read from strings/JSON and some constants defined here also |
dataimport
Implements importer triggering based on SNS queues.
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Implements importer triggering based on SNS queues. |
dataimport/datasetArchive
Implements archiving/retrieval of dataset source zip files as delivered by GDS.
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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.
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Allows outputting (in PIXLISE protobuf dataset format) of in-memory representation of PIXL data that importer has read. |
filepaths
Defines all paths/file names used in S3 for storage of our data.
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Defines all paths/file names used in S3 for storage of our data. |
permission
Permission constants and helper functions for defining routes.
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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
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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.
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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.
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The guts of PIXLISE API endpoint handler/routing code. |
services
Services used by API endpoint handlers and other bits of code.
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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.
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Contains all the code needed to do an Auth0 login and retrieve a JWT. |
awsutil
AWS utility functions to wrap some functionality and provide mocking capabilities for unit testing.
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AWS utility functions to wrap some functionality and provide mocking capabilities for unit testing. |
fileaccess
Provides a higher-level file access interface which is implemented using local file storage as well as AWS S3.
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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
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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.
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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.
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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.
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Lowest-level code to connect to Mongo DB (locally in Docker and remotely) and get consistant collection names. |
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.
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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. |
utils
Exposes various utility functions for strings, generation of valid filenames and random ID strings, zipping files/directories, reading/writing images
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Exposes various utility functions for strings, generation of valid filenames and random ID strings, zipping files/directories, reading/writing images |
internal
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