Add sample_project field to imaging metadata (#275)

Author: ethanjli

.github/workflows/build.yml

@@ -4,9 +4,9 @@ on:
   push: 
     branches: 
       - main
-      - gh-readonly-queue/dev/**
   pull_request:
     branches: [ main ]
+  merge_group:
   workflow_dispatch:
 
 jobs:

.github/workflows/codeql-analysis.yml

@@ -8,6 +8,7 @@ on:
   pull_request:
     # The branches below must be a subset of the branches above
     branches: [ main ]
+  merge_group:
   schedule:
     - cron: '11 0 * * 5'
 

Makefile

@@ -84,7 +84,7 @@ release: install buildweb
 	goreleaser --clean
 
 .PHONY: run-live
-run: ## go run
+run-live: ## go run
 	@go run -race ./cmd/pslive
 
 .PHONY: run-local

internal/app/pslive/routes/instruments/planktoscope.go

@@ -393,7 +393,7 @@ func replaceImagerStream(
 }
 
 func handleImagerSettings(
-	sampleID, imagingRaw, direction, stepVolumeRaw, stepDelayRaw, stepsRaw string,
+	sampleProjectID, sampleID, imagingRaw, direction, stepVolumeRaw, stepDelayRaw, stepsRaw string,
 	pc *planktoscope.Client,
 ) (err error) {
 	imaging := strings.ToLower(imagingRaw) == "start"
@@ -425,7 +425,7 @@ func handleImagerSettings(
 		if err != nil {
 			return echo.NewHTTPError(http.StatusBadRequest, errors.Wrap(err, "couldn't parse steps"))
 		}
-		if token, err = pc.SetMetadata(sampleID, time.Now()); err != nil {
+		if token, err = pc.SetMetadata(sampleProjectID, sampleID, time.Now()); err != nil {
 			return err
 		}
 		// TODO: instead of waiting forever, have a timeout before redirecting and displaying a
@@ -542,7 +542,7 @@ func (h *Handlers) HandleImagerPost() auth.HTTPHandlerFunc {
 			)
 		}
 		if err = handleImagerSettings(
-			instrument.Name, c.FormValue("imaging"), c.FormValue("direction"),
+			instrument.Name, "gui", c.FormValue("imaging"), c.FormValue("direction"),
 			c.FormValue("step-volume"), c.FormValue("step-delay"), c.FormValue("steps"), pc,
 		); err != nil {
 			return err

internal/clients/planktoscope/actions.go

@@ -50,15 +50,16 @@ func (c *Client) RunStopPumpAction(ctx context.Context) error {
 // Imager Actions
 
 type PlanktoscopeImagingParams struct {
-	SampleID   string  `hcl:"sample_id"` // TODO: move the sample ID somewhere else?
-	Forward    bool    `hcl:"forward"`
-	StepVolume float64 `hcl:"step_volume"`
-	StepDelay  float64 `hcl:"step_delay"`
-	Steps      uint64  `hcl:"steps"`
+	SampleProjectID string  `hcl:"sample_project_id"` // TODO: move the project ID somewhere else?
+	SampleID        string  `hcl:"sample_id"`         // TODO: move the sample ID somewhere else?
+	Forward         bool    `hcl:"forward"`
+	StepVolume      float64 `hcl:"step_volume"`
+	StepDelay       float64 `hcl:"step_delay"`
+	Steps           uint64  `hcl:"steps"`
 }
 
 func (c *Client) RunImagingAction(ctx context.Context, p PlanktoscopeImagingParams) error {
-	token, err := c.SetMetadata(p.SampleID, time.Now())
+	token, err := c.SetMetadata(p.SampleProjectID, p.SampleID, time.Now())
 	if err != nil {
 		return err
 	}

internal/clients/planktoscope/metadata.go

@@ -2,15 +2,19 @@ package planktoscope
 
 import (
 	"encoding/json"
+	"fmt"
 	"time"
 
 	"github.com/eclipse/paho.mqtt.golang"
 )
 
 // Send Commands
 
-func (c *Client) SetMetadata(sampleID string, acquisitionTime time.Time) (mqtt.Token, error) {
+func (c *Client) SetMetadata(
+	sampleProjectID, sampleID string, acquisitionTime time.Time,
+) (mqtt.Token, error) {
 	type Metadata struct {
+		SampleProjectID      string `json:"sample_project"`
 		SampleID             string `json:"sample_id"`
 		SampleCollectionDate string `json:"object_date"`
 		SampleCollectionTime string `json:"object_time"`
@@ -22,7 +26,8 @@ func (c *Client) SetMetadata(sampleID string, acquisitionTime time.Time) (mqtt.T
 	}{
 		Action: "update_config",
 		Metadata: Metadata{
-			SampleID:             sampleID,
+			SampleProjectID:      sampleProjectID,
+			SampleID:             fmt.Sprintf("%s_%s", sampleProjectID, sampleID),
 			SampleCollectionDate: acquisitionTime.Format("2006-01-02"),
 			SampleCollectionTime: acquisitionTime.Format("15:04:05"),
 			AcquisitionID:        acquisitionTime.Format(time.RFC3339),

internal/clients/planktoscope/models.go

@@ -79,7 +79,7 @@ type ImagerSettings struct {
 }
 
 func DefaultImagerSettings() ImagerSettings {
-	const defaultStepVolume = 0.4
+	const defaultStepVolume = 0.04
 	const defaultStepDelay = 0.5
 	const defaultSteps = 100
 	return ImagerSettings{

tools/go.mod

@@ -1,11 +1,11 @@
-module github.com/sargassum-world/pslive/build
+module github.com/sargassum-world/pslive/tools
 
 go 1.19
 
 require (
 	github.com/deepmap/oapi-codegen v1.12.4
 	github.com/golangci/golangci-lint v1.52.2
-	github.com/goreleaser/goreleaser v1.16.2
+	github.com/goreleaser/goreleaser v1.17.2
 	github.com/hairyhenderson/gomplate/v3 v3.11.4
 	github.com/open-policy-agent/opa v0.51.0
 	mvdan.cc/gofumpt v0.5.0
@@ -101,7 +101,7 @@ require (
 	github.com/butuzov/ireturn v0.1.1 // indirect
 	github.com/bytecodealliance/wasmtime-go/v3 v3.0.2 // indirect
 	github.com/caarlos0/ctrlc v1.2.0 // indirect
-	github.com/caarlos0/env/v7 v7.0.0 // indirect
+	github.com/caarlos0/env/v8 v8.0.0 // indirect
 	github.com/caarlos0/go-reddit/v3 v3.0.1 // indirect
 	github.com/caarlos0/go-shellwords v1.0.12 // indirect
 	github.com/caarlos0/log v0.2.2 // indirect
@@ -196,12 +196,13 @@ require (
 	github.com/golangci/misspell v0.4.0 // indirect
 	github.com/golangci/revgrep v0.0.0-20220804021717-745bb2f7c2e6 // indirect
 	github.com/golangci/unconvert v0.0.0-20180507085042-28b1c447d1f4 // indirect
+	github.com/google/btree v1.1.2 // indirect
 	github.com/google/flatbuffers v22.11.23+incompatible // indirect
 	github.com/google/go-cmp v0.5.9 // indirect
 	github.com/google/go-containerregistry v0.14.0 // indirect
 	github.com/google/go-github/v50 v50.1.0 // indirect
 	github.com/google/go-querystring v1.1.0 // indirect
-	github.com/google/ko v0.12.0 // indirect
+	github.com/google/ko v0.13.0 // indirect
 	github.com/google/safetext v0.0.0-20220905092116-b49f7bc46da2 // indirect
 	github.com/google/uuid v1.3.0 // indirect
 	github.com/google/wire v0.5.0 // indirect
@@ -345,7 +346,7 @@ require (
 	github.com/securego/gosec/v2 v2.15.0 // indirect
 	github.com/sergi/go-diff v1.2.0 // indirect
 	github.com/shazow/go-diff v0.0.0-20160112020656-b6b7b6733b8c // indirect
-	github.com/sigstore/cosign v1.13.1 // indirect
+	github.com/sigstore/cosign/v2 v2.0.0 // indirect
 	github.com/sigstore/rekor v1.0.1 // indirect
 	github.com/sigstore/sigstore v1.5.1 // indirect
 	github.com/sirupsen/logrus v1.9.0 // indirect