Merge pull request #345 from pixlise/feature/em-import

Feature/em import
pixlise · Nov 7, 2024 · 30633aa · 30633aa
2 parents a227328 + c075e98
commit 30633aa
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Showing 4 changed files with 19 additions and 9 deletions.
diff --git a/api/dataimport/for-trigger_test.go b/api/dataimport/for-trigger_test.go
@@ -521,7 +521,9 @@ func Test_ImportForTrigger_Manual_SBU_NoAutoShare_FailForPipeline(t *testing.T)
 	}
 }
 */
-// Import a breadboard dataset from manual uploaded zip file
+
+// DISABLED 5/Nov/2024, rewrite importer for EM to work differently so these tests are no longer relevant. Will have to write new tests for new functionality
+/*
 func Example_importForTrigger_Manual_EM() {
 	remoteFS, log, configBucket, datasetBucket, manualBucket, db := initTest("Manual_EM", "ManualEM_OK", specialUserIds.PIXLISESystemUserId, "PIXLFMGroupId")
 
@@ -587,7 +589,7 @@ func Example_importForTrigger_Manual_EM_WithBeamV2() {
 	// Logged "No auto-share destination found, so only importing user will be able to access this dataset.": false
 	// Logged "Saving as beam geometry tool version: 2": true
 	// <nil>|{"id":"048300551","title":"048300551","dataTypes":[{"dataType":"SD_IMAGE","count":4},{"dataType":"SD_XRF","count":242}],"instrument":"PIXL_EM","instrumentConfig":"PIXL-EM-E2E","meta":{"DriveId":"1712","RTT":"048300551","SCLK":"678031418","Site":"","SiteId":"4","Sol":"0125","Target":"","TargetId":"?"},"contentCounts":{"BulkSpectra":2,"DwellSpectra":0,"MaxSpectra":2,"NormalSpectra":242,"PseudoIntensities":121},"creatorUserId":"PIXLISEImport"}
-}
+}*/
 
 /* NOT TESTED YET, because it's not done yet!
 

diff --git a/api/dataimport/sdfToRSI/scanSDF_test.go b/api/dataimport/sdfToRSI/scanSDF_test.go
@@ -3,6 +3,8 @@ package sdfToRSI
 import "fmt"
 
 func Example_scanSDF() {
+	ensureSDFRawExists()
+
 	refs, err := scanSDF("./test-data/BadPath.txt")
 	fmt.Printf("%v|%v\n", len(refs), err)
 

diff --git a/api/dataimport/sdfToRSI/sdfToRSI_test.go b/api/dataimport/sdfToRSI/sdfToRSI_test.go
@@ -9,6 +9,18 @@ import (
 )
 
 func Example_ConvertSDFtoRSI() {
+	ensureSDFRawExists()
+
+	fmt.Printf("Mkdir output: %v\n", os.MkdirAll("./output", 0644))
+	files, rtts, err := ConvertSDFtoRSIs("./test-data/sdf_raw.txt", "./output/")
+	fmt.Printf("%v, %v: %v\n", files, rtts, err)
+
+	// Output:
+	// Mkdir output: <nil>
+	// [RSI-208536069.csv RSI-208601602.csv], [208536069 208601602]: <nil>
+}
+
+func ensureSDFRawExists() {
 	// If it's not here, unzip it
 	_, err := os.Stat("./test-data/sdf_raw.txt")
 	if err != nil {
@@ -39,10 +51,4 @@ func Example_ConvertSDFtoRSI() {
 			}
 		}
 	}
-
-	files, rtts, err := ConvertSDFtoRSIs("./test-data/sdf_raw.txt", "./output/")
-	fmt.Printf("%v, %v: %v\n", files, rtts, err)
-
-	// Output:
-	// [RSI-208536069.csv RSI-208601602.csv], [208536069 208601602]: <nil>
 }
diff --git a/core/mongoDBConnection/remote.go b/core/mongoDBConnection/remote.go
@@ -120,7 +120,7 @@ func makeMongoCommandMonitor(log logger.ILogger) *event.CommandMonitor {
 			log.Debugf("Mongo success:\n%v", evt.CommandFinishedEvent)
 		},
 		Failed: func(_ context.Context, evt *event.CommandFailedEvent) {
-			log.Errorf("Mongo FAIL:\n%v", evt.Failure)
+			log.Errorf("Mongo err:\n%v", evt.Failure)
 		},
 	}
 }