dataimport

package
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 Go to latest Published: Nov 15, 2024 License: Apache-2.0 Imports: 32 Imported by: 0

Documentation

Overview

Implements importer triggering based on SNS queues. This decodes incoming SNS messages and extracts files ready for importer code to run

Exposes the interface of the dataset importer aka converter and selecting one automatically based on what files are in the folder being imported. The converter supports various formats as delivered by GDS or test instruments and this is inteded to be extendable further to other lab instruments and devices in future.

Example (DecodeImportTrigger_Manual)

Trigger for a manual dataset regeneration (user clicks save button on dataset edit page) 

Output:

Source Bucket: ""
Source file: ""
Dataset: "189137412"
Job: "dataimport-zmzddoytch2krd7n"
Err: "<nil>"
Example (DecodeImportTrigger_ManualBadDatasetID) 
Output:

Source Bucket: ""
Source file: ""
Dataset: ""
Job: ""
Err: "Failed to find dataset ID in reprocess trigger"
Example (DecodeImportTrigger_ManualBadLogID) 
Output:

Source Bucket: ""
Source file: ""
Dataset: ""
Job: ""
Err: "Failed to find job ID in reprocess trigger"
Example (DecodeImportTrigger_ManualBadMsg) 
Output:

Source Bucket: ""
Source file: ""
Dataset: ""
Job: ""
Err: "Unexpected or no message type embedded in triggering SNS message"
Example (DecodeImportTrigger_OCS)

Trigger from when a new zip arrives from the pipeline 

Output:

Source Bucket: "prodpipeline-rawdata202c7bd0-o40ktu17o2oj"
Source file: "189137412-07-09-2022-10-07-57.zip"
Dataset: "189137412"
Log Str Len: "43"
Err: "<nil>"
Example (DecodeImportTrigger_OCS2)

Trigger from when a new zip arrives from the pipeline 

Output:

Source Bucket: "prodpipeline-rawdata202c7bd0-o40ktu17o2oj"
Source file: "197329413-25-09-2022-14-33-39.zip"
Dataset: "197329413"
Job Str Len: "43"
Err: "<nil>"
Example (DecodeImportTrigger_OCS3)

Trigger from when a new zip arrives from the pipeline but pipeline stores it in a subdir of the bucket 

Output:

Source Bucket: "prodpipeline-rawdata202c7bd0-o40ktu17o2oj"
Source file: "data/197329413-25-09-2022-14-33-39.zip"
Dataset: "197329413"
Job Str Len: "43"
Err: "<nil>"
Example (DecodeImportTrigger_OCS_BadEventType) 
Output:

Source Bucket: ""
Source file: ""
Dataset: ""
Job: ""
Err: "Failed to decode dataset import trigger: Failed to decode sqs body to an S3 event: unexpected end of JSON input"
Example (DecodeImportTrigger_OCS_Error) 
Output:

Source Bucket: ""
Source file: ""
Dataset: ""
Job: ""
Err: "Unexpected or no message type embedded in triggering SNS message"
Example (GetUpdateType_Drive) 
Output:

housekeeping|<nil>
Example (GetUpdateType_LessContextImages) 
Output:

image|<nil>
Example (GetUpdateType_MoreContextImages) 
Output:

image|<nil>
Example (GetUpdateType_NormalSpectra) 
Output:

spectra|<nil>
Example (GetUpdateType_RTT) 
Output:

unknown|<nil>
Example (GetUpdateType_SameContextImages) 
Output:

unknown|<nil>
Example (GetUpdateType_Title) 
Output:

housekeeping|<nil>
Example (ImportForTrigger_Manual_JPL)

Import a breadboard dataset from manual uploaded zip file 

Output:

Errors: <nil>, changes: unknown, isUpdate: false
Logged "Downloading archived zip files...": true
Logged "Downloaded 0 zip files, unzipped 0 files": true
Logged "No zip files found in archive, dataset may have been manually uploaded. Trying to download...": true
Logged "Dataset test1234 downloaded 3 files from manual upload area": true
Logged "Downloading pseudo-intensity ranges...": true
Logged "Downloading user customisation files...": true
Logged "Reading 1261 files from spectrum directory...": true
Logged "Reading spectrum [1135/1260] 90%": true
Logged "PMC 1261 has 4 MSA/spectrum entries": true
Logged "WARNING: No main context image determined": true
Logged "Diffraction db saved successfully": true
Logged "Warning: No import.json found, defaults will be used": true
Logged "No auto-share destination found, so only importing user will be able to access this dataset.": false
<nil>|{"id":"test1234","title":"test1234","dataTypes":[{"dataType":"SD_XRF","count":2520}],"instrument":"JPL_BREADBOARD","instrumentConfig":"Breadboard","meta":{"DriveId":"0","RTT":"","SCLK":"0","Site":"","SiteId":"0","Sol":"","Target":"","TargetId":"0"},"contentCounts":{"BulkSpectra":2,"DwellSpectra":0,"MaxSpectra":2,"NormalSpectra":2520,"PseudoIntensities":0},"creatorUserId":"JPLImport"}
Example (ImportForTrigger_Manual_SBU)

Import a breadboard dataset from manual uploaded zip file 

Output:

Errors: <nil>, changes: unknown, isUpdate: false
Logged "Downloading archived zip files...": true
Logged "Downloaded 0 zip files, unzipped 0 files": true
Logged "No zip files found in archive, dataset may have been manually uploaded. Trying to download...": true
Logged "Dataset test1234sbu downloaded 4 files from manual upload area": true
Logged "Downloading pseudo-intensity ranges...": true
Logged "Downloading user customisation files...": true
Logged "Reading 1261 files from spectrum directory...": true
Logged "Reading spectrum [1135/1260] 90%": true
Logged "PMC 1261 has 4 MSA/spectrum entries": true
Logged "WARNING: No main context image determined": true
Logged "Diffraction db saved successfully": true
Logged "Warning: No import.json found, defaults will be used": false
Logged "No auto-share destination found, so only importing user will be able to access this dataset.": false
<nil>|{"id":"test1234sbu","title":"test1234sbu","dataTypes":[{"dataType":"SD_XRF","count":2520}],"instrument":"SBU_BREADBOARD","instrumentConfig":"StonyBrookBreadboard","meta":{"DriveId":"0","RTT":"","SCLK":"0","Site":"","SiteId":"0","Sol":"","Target":"","TargetId":"0"},"contentCounts":{"BulkSpectra":2,"DwellSpectra":0,"MaxSpectra":2,"NormalSpectra":2520,"PseudoIntensities":0},"creatorUserId":"SBUImport"}
Example (ImportForTrigger_OCS_Archive_BadData) 
func startTestWithMockMongo(name string, t *testing.T, testFunc func(mt *mtest.T)) {
	mt := mtest.New(t, mtest.NewOptions().ClientType(mtest.Mock))
	defer mt.Close()

	mt.Run(name, testFunc)
}

Import unknown dataset (simulate trigger by OCS pipeline), file goes to archive, then all files downloaded from archive, dataset create fails due to unknown data type 

Output:

Errors: Failed to determine dataset type to import., changes: , isUpdate: false
Logged "Downloading archived zip files...": true
Logged "Downloaded 2 zip files, unzipped 6 files": true
Logged "Downloading pseudo-intensity ranges...": true
Logged "Downloading user customisation files...": true
Logged "SelectDataConverter: Path contains 3 files...": true
Logged "Failed to open detector.json when determining dataset type": true
Example (ImportForTrigger_OCS_Archive_Exists)

Import FM-style (simulate trigger by OCS pipeline), file already in archive, so should do nothing 

Output:

Errors: <nil>, changes: , isUpdate: false
Logged "Archiving source file: "s3://./test-data/Archive_Exists/raw-data-bucket/70000_069-02-09-2021-06-25-13.zip"": true
Log shows exists in archive: true
Example (ImportForTrigger_OCS_Archive_OK)

Import FM-style (simulate trigger by OCS pipeline), file goes to archive, then all files downloaded from archive and dataset created 

Output:

Errors: <nil>, changes: unknown, isUpdate: false
Logged "Downloading archived zip files...": true
Logged "Downloaded 20 zip files, unzipped 364 files": true
Logged "Downloading pseudo-intensity ranges...": true
Logged "Downloading user customisation files...": true
Logged "This dataset's detector config is PIXL": true
Logged "PMC 218 has 4 MSA/spectrum entries": true
Logged "Main context image: PCW_0125_0678031992_000RCM_N00417120483005510091075J02.png": true
Logged "Diffraction db saved successfully": true
Logged "Applying custom title: Naltsos": true
Logged "Matched aligned image: PCCR0577_0718181212_000MSA_N029000020073728500030LUD01.tif, offset(0, 0), scale(1, 1). Match for aligned index: 0": true
<nil>|{"contentCounts": {"BulkSpectra": 2,"DwellSpectra": 0,"MaxSpectra": 2,"NormalSpectra": 242,"PseudoIntensities": 121},"creatorUserId": "PIXLISEImport","dataTypes": [{"count": 5,"dataType": "SD_IMAGE"},{"count": 1,"dataType": "SD_RGBU"},{"count": 242,"dataType": "SD_XRF"}],"id": "048300551","instrument": "PIXL_FM","instrumentConfig": "PIXL","meta": {"DriveId": "1712","RTT": "048300551","SCLK": "678031418","Site": "","SiteId": "4","Sol": "0125","Target": "","TargetId": "?"},"title": "Naltsos"}
Example (ImportForTrigger_OCS_DatasetEdit)

Import FM-style (simulate trigger by dataset edit screen), should create dataset with custom name+image 

Output:

Errors: <nil>, changes: unknown, isUpdate: true
Logged "Downloading archived zip files...": true
Logged "Downloaded 20 zip files, unzipped 364 files": true
Logged "Downloading pseudo-intensity ranges...": true
Logged "Downloading user customisation files...": true
Logged "This dataset's detector config is PIXL": true
Logged "PMC 218 has 4 MSA/spectrum entries": true
Logged "Main context image: PCW_0125_0678031992_000RCM_N00417120483005510091075J02.png": true
Logged "Diffraction db saved successfully": true
Logged "Applying custom title: Naltsos": true
Logged "Matched aligned image: PCCR0577_0718181212_000MSA_N029000020073728500030LUD01.tif, offset(0, 0), scale(1, 1). Match for aligned index: 0": true
<nil>|{"contentCounts": {"BulkSpectra": 2,"DwellSpectra": 0,"MaxSpectra": 2,"NormalSpectra": 242,"PseudoIntensities": 121},"creatorUserId": "PIXLISEImport","dataTypes": [{"count": 5,"dataType": "SD_IMAGE"},{"count": 1,"dataType": "SD_RGBU"},{"count": 242,"dataType": "SD_XRF"}],"id": "048300551","instrument": "PIXL_FM","instrumentConfig": "PIXL","meta": {"DriveId": "1712","RTT": "048300551","SCLK": "678031418","Site": "","SiteId": "4","Sol": "0125","Target": "","TargetId": "?"},"title": "Naltsos"}

Index

Examples

Constants

This section is empty.

Variables

View Source 
var JobIDAutoImportPrefix = "auto-import-"

Functions

func ImportDataset 

func ImportDataset(
	localFS fileaccess.FileAccess,
	remoteFS fileaccess.FileAccess,
	configBucket string,
	manualUploadBucket string,
	datasetBucket string,
	db *mongo.Database,
	datasetID string,
	log logger.ILogger,
	justArchived bool,
) (string, *protos.ScanItem, string, bool, error)

ImportFromArchive - Importing from dataset archive area. Calls ImportFromLocalFileSystem Returns: WorkingDir Saved dataset summary structure What changed (as a string), so caller can know what kind of notification to send (if any) IsUpdate flag Error (if any)

func ImportFromLocalFileSystem 

func ImportFromLocalFileSystem(
	localFS fileaccess.FileAccess,
	remoteFS fileaccess.FileAccess,
	db *mongo.Database,
	workingDir string,
	localImportPath string,
	localPseudoIntensityRangesPath string,
	datasetBucket string,
	datasetID string,
	log logger.ILogger) (string, error)

ImportFromLocalFileSystem - As the name says, imports from directory on local file system Returns: Dataset ID (in case it was modified during conversion) Error (if there was one)

func TriggerDatasetReprocessViaSNS 

func TriggerDatasetReprocessViaSNS(snsSvc awsutil.SNSInterface, jobId string, scanId string, snsTopic string) (*sns.PublishOutput, error)

Firing a trigger message. Anything calling this is triggering a dataset reimport via a lambda function

Types

type DatasetCustomMeta 

type DatasetCustomMeta struct {
	Title               string `json:"title"`
	DefaultContextImage string `json:"defaultContextImage"`
}

type ImportResult 

type ImportResult struct {
	WorkingDir   string         // so it can be cleaned up by caller if needed
	WhatChanged  string         // what changed between this import and a previous one, for notification reasons
	IsUpdate     bool           // IsUpdate flag
	DatasetTitle string         // Name of the dataset that was imported
	DatasetID    string         // ID of the dataset that was imported
	Logger       logger.ILogger // Caller must call Close() on it, otherwise we may lose the last few log events
}

Structure returned after importing NOTE: the logger must have Close() called on it, otherwise we may lose the last few log events

func ImportForTrigger 

func ImportForTrigger(
	triggerMessage []byte,
	configBucket string,
	datasetBucket string,
	manualBucket string,
	db *mongo.Database,
	log logger.ILogger,
	remoteFS fileaccess.FileAccess) (ImportResult, error)

ImportForTrigger - Parses a trigger message (from SNS) and decides what to import Returns: Result struct - NOTE: logger must have Close() called on it, otherwise we may lose the last few log events Error (or nil)

Source Files

View all Source files

Directories

Path Synopsis
Implements archiving/retrieval of dataset source zip files as delivered by GDS.
 Implements archiving/retrieval of dataset source zip files as delivered by GDS.
internal

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