From b9ae730c733165ae6d57518a8cf4a6a29f19c9ad Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 17:53:14 +0000
Subject: [PATCH] Updated to new metadata semantics

---
 .../controlComponents/paneCapture.vue         | 14 ++---
 .../controlComponents/paneNavigate.vue        |  2 +-
 .../controlComponents/paneStatus.vue          | 30 +++++-----
 .../settingsComponents/cameraSettings.vue     | 32 +++++-----
 .../settingsComponents/microscopeSettings.vue | 12 ++--
 .../viewComponents/connectDisplay.vue         |  4 +-
 .../galleryComponents/captureCard.vue         | 58 +++++++++----------
 .../galleryComponents/scanCard.vue            | 24 +++-----
 .../viewComponents/galleryDisplay.vue         | 44 +++++++-------
 .../viewComponents/streamDisplay.vue          |  2 +-
 10 files changed, 106 insertions(+), 116 deletions(-)

diff --git a/src/components/controlComponents/paneCapture.vue b/src/components/controlComponents/paneCapture.vue
index 864c6cb1..0eb6102e 100644
--- a/src/components/controlComponents/paneCapture.vue
+++ b/src/components/controlComponents/paneCapture.vue
@@ -84,9 +84,9 @@
       </li>
 
       <li>
-        <a class="uk-accordion-title" href="#">Metadata</a>
+        <a class="uk-accordion-title" href="#">Annotations</a>
         <div class="uk-accordion-content">
-          <keyvalList v-model="metadata" />
+          <keyvalList v-model="annotations" />
         </div>
       </li>
 
@@ -296,7 +296,7 @@ export default {
       },
       resizeDims: [640, 480],
       tags: [],
-      metadata: {
+      annotations: {
         Client: `${process.env.PACKAGE.name}.${process.env.PACKAGE.version}`
       },
       scanUri: null
@@ -316,7 +316,7 @@ export default {
       return `${this.$store.getters.baseUri}/api/v2/extensions`;
     },
     settingsFovUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/settings/fov`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings/fov`;
     },
     basePayload: function() {
       var payload = {};
@@ -339,13 +339,13 @@ export default {
         };
       }
 
-      // Additional metadata
-      payload.metadata = this.metadata;
+      // Additional annotations
+      payload.annotations = this.annotations;
       payload.tags = this.tags;
 
       // Attach notes
       if (this.captureNotes) {
-        payload.metadata["Notes"] = this.captureNotes;
+        payload.annotations["Notes"] = this.captureNotes;
       }
 
       return payload;
diff --git a/src/components/controlComponents/paneNavigate.vue b/src/components/controlComponents/paneNavigate.vue
index ce656103..d821a4e7 100644
--- a/src/components/controlComponents/paneNavigate.vue
+++ b/src/components/controlComponents/paneNavigate.vue
@@ -193,7 +193,7 @@ export default {
       return `${this.$store.getters.baseUri}/api/v2/actions/stage/zero`;
     },
     positionStatusUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/status/stage/position`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/state/stage/position`;
     },
     pluginsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/extensions`;
diff --git a/src/components/controlComponents/paneStatus.vue b/src/components/controlComponents/paneStatus.vue
index 500e5a3c..e45879eb 100644
--- a/src/components/controlComponents/paneStatus.vue
+++ b/src/components/controlComponents/paneStatus.vue
@@ -1,6 +1,6 @@
 <template>
   <div class="host-input">
-    <div v-if="status && $store.getters.ready">
+    <div v-if="configuration && $store.getters.ready">
       <div>
         <div class="uk-margin-small-bottom">
           <b>Host:</b>
@@ -17,7 +17,7 @@
       </div>
       <div>
         <b>Server version:</b> <br />
-        {{ status.version }}
+        {{ configuration.application.version }}
       </div>
 
       <hr />
@@ -25,16 +25,16 @@
       <div class="uk-margin-small-bottom">
         <b>Camera:</b>
         <br />
-        <div v-if="status.camera.board">
-          {{ status.camera.board }}
+        <div v-if="configuration.camera.type != 'MissingCamera'">
+          {{ configuration.camera.type }}
         </div>
         <div v-else class="uk-text-danger"><b>No camera connected</b></div>
       </div>
       <div>
         <b>Stage:</b>
         <br />
-        <div v-if="status.stage.board">
-          {{ status.stage.board }}
+        <div v-if="configuration.stage.type != 'MissingStage'">
+          {{ configuration.stage.type }}
         </div>
         <div v-else class="uk-text-danger"><b>No stage connected</b></div>
       </div>
@@ -86,7 +86,7 @@ export default {
 
   data: function() {
     return {
-      status: null,
+      configuration: null,
       settings: null,
       systemActionLinks: {}
     };
@@ -94,10 +94,10 @@ export default {
 
   computed: {
     settingsUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/settings`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
     },
-    statusUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/status`;
+    configurationUri: function() {
+      return `${this.$store.getters.baseUri}/api/v2/instrument/configuration`;
     },
     actionsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/actions`;
@@ -105,13 +105,13 @@ export default {
   },
 
   created: function() {
-    // Watch for host 'ready', then update status
+    // Watch for host 'ready', then update configuration
     this.$store.watch(
       (state, getters) => {
         return getters.ready;
       },
       () => {
-        this.updateStatus();
+        this.updateConfiguration();
         this.updateSettings();
         this.updateSystemActions();
       }
@@ -119,11 +119,11 @@ export default {
   },
 
   methods: {
-    updateStatus: function() {
+    updateConfiguration: function() {
       axios
-        .get(this.statusUri)
+        .get(this.configurationUri)
         .then(response => {
-          this.status = response.data;
+          this.configuration = response.data;
         })
         .catch(error => {
           this.modalError(error); // Let mixin handle error
diff --git a/src/components/controlComponents/settingsComponents/cameraSettings.vue b/src/components/controlComponents/settingsComponents/cameraSettings.vue
index 6b5192f9..6d4bd61d 100644
--- a/src/components/controlComponents/settingsComponents/cameraSettings.vue
+++ b/src/components/controlComponents/settingsComponents/cameraSettings.vue
@@ -1,28 +1,28 @@
 <template>
-  <div v-if="camera_settings" id="cameraSettings">
+  <div v-if="settings" id="cameraSettings">
     <form @submit.prevent="applyConfigRequest">
-      <div v-if="camera_settings.picamera_settings">
+      <div v-if="settings.picamera">
         <!--PiCamera settings block-->
-        <div v-if="camera_settings.picamera_settings.shutter_speed">
+        <div v-if="settings.picamera.shutter_speed">
           <label class="uk-form-label" for="form-stacked-text"
             >Exposure time</label
           >
           <div class="uk-form-controls">
             <input
-              v-model="camera_settings.picamera_settings.shutter_speed"
+              v-model="settings.picamera.shutter_speed"
               class="uk-input uk-form-small"
               type="number"
             />
           </div>
         </div>
 
-        <div v-if="camera_settings.picamera_settings.analog_gain">
+        <div v-if="settings.picamera.analog_gain">
           <label class="uk-form-label" for="form-stacked-text"
             >Analogue gain</label
           >
           <div class="uk-form-controls">
             <input
-              v-model="camera_settings.picamera_settings.analog_gain"
+              v-model="settings.picamera.analog_gain"
               class="uk-input uk-form-small"
               type="number"
               step="0.000001"
@@ -30,13 +30,13 @@
           </div>
         </div>
 
-        <div v-if="camera_settings.picamera_settings.digital_gain">
+        <div v-if="settings.picamera.digital_gain">
           <label class="uk-form-label" for="form-stacked-text"
             >Digital gain</label
           >
           <div class="uk-form-controls">
             <input
-              v-model="camera_settings.picamera_settings.digital_gain"
+              v-model="settings.picamera.digital_gain"
               class="uk-input uk-form-small"
               type="number"
               step="0.000001"
@@ -85,7 +85,7 @@ export default {
 
   data: function() {
     return {
-      camera_settings: null,
+      settings: null,
       recalibrationUri: null,
       isCalibrating: false
     };
@@ -93,7 +93,7 @@ export default {
 
   computed: {
     settingsUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/settings`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
     },
     pluginsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/extensions`;
@@ -110,7 +110,7 @@ export default {
       axios
         .get(this.settingsUri)
         .then(response => {
-          this.camera_settings = response.data.camera_settings;
+          this.settings = response.data.camera;
         })
         .catch(error => {
           this.modalError(error); // Let mixin handle error
@@ -139,11 +139,11 @@ export default {
     applyConfigRequest: function() {
       console.log("Applying config to the microscope");
       var payload = {
-        camera_settings: {
-          picamera_settings: {
-            shutter_speed: this.camera_settings.picamera_settings.shutter_speed,
-            analog_gain: this.camera_settings.picamera_settings.analog_gain,
-            digital_gain: this.camera_settings.picamera_settings.digital_gain
+        camera: {
+          picamera: {
+            shutter_speed: this.settings.picamera.shutter_speed,
+            analog_gain: this.settings.picamera.analog_gain,
+            digital_gain: this.settings.picamera.digital_gain
           }
         }
       };
diff --git a/src/components/controlComponents/settingsComponents/microscopeSettings.vue b/src/components/controlComponents/settingsComponents/microscopeSettings.vue
index 9998f194..601df633 100644
--- a/src/components/controlComponents/settingsComponents/microscopeSettings.vue
+++ b/src/components/controlComponents/settingsComponents/microscopeSettings.vue
@@ -11,7 +11,7 @@
           <label class="uk-form-label" for="form-stacked-text">x</label>
           <div class="uk-form-controls">
             <input
-              v-model="settings.stage_settings.backlash.x"
+              v-model="settings.stage.backlash.x"
               class="uk-input uk-form-small"
               type="number"
             />
@@ -22,7 +22,7 @@
           <label class="uk-form-label" for="form-stacked-text">y</label>
           <div class="uk-form-controls">
             <input
-              v-model="settings.stage_settings.backlash.y"
+              v-model="settings.stage.backlash.y"
               class="uk-input uk-form-small"
               type="number"
             />
@@ -33,7 +33,7 @@
           <label class="uk-form-label" for="form-stacked-text">z</label>
           <div class="uk-form-controls">
             <input
-              v-model="settings.stage_settings.backlash.z"
+              v-model="settings.stage.backlash.z"
               class="uk-input uk-form-small"
               type="number"
             />
@@ -80,7 +80,7 @@ export default {
 
   computed: {
     settingsUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/settings`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
     }
   },
 
@@ -103,8 +103,8 @@ export default {
     applyConfigRequest: function() {
       var payload = {
         name: this.settings.name,
-        stage_settings: {
-          backlash: this.settings.stage_settings.backlash
+        stage: {
+          backlash: this.settings.stage.backlash
         }
       };
 
diff --git a/src/components/viewComponents/connectDisplay.vue b/src/components/viewComponents/connectDisplay.vue
index 9df6ef7a..94f8a0a2 100644
--- a/src/components/viewComponents/connectDisplay.vue
+++ b/src/components/viewComponents/connectDisplay.vue
@@ -326,7 +326,7 @@ export default {
     },
 
     checkServerVersion: function() {
-      var versionUri = `${this.$store.getters.baseUri}/api/v2/status/version`;
+      var versionUri = `${this.$store.getters.baseUri}/api/v2/instrument/configuration/application/version`;
       axios
         .get(versionUri)
         .then(response => {
@@ -383,7 +383,7 @@ export default {
 
     saveHost: function() {
       // URI to get hostname directly from settings
-      var hostnameUri = `${this.$store.getters.baseUri}/api/v2/settings/name`;
+      var hostnameUri = `${this.$store.getters.baseUri}/api/v2/instrument/settings/name`;
       axios
         .get(hostnameUri)
         .then(response => {
diff --git a/src/components/viewComponents/galleryComponents/captureCard.vue b/src/components/viewComponents/galleryComponents/captureCard.vue
index 47ef95a1..91e34139 100644
--- a/src/components/viewComponents/galleryComponents/captureCard.vue
+++ b/src/components/viewComponents/galleryComponents/captureCard.vue
@@ -8,7 +8,7 @@
         <img
           class="uk-width-1-1"
           :data-src="thumbURL"
-          :alt="captureState.metadata.id"
+          :alt="captureState.metadata.image.id"
           width="300"
           height="225"
           uk-img
@@ -34,7 +34,7 @@
       <div
         class="uk-text-meta uk-margin-remove-top uk-padding-remove uk-width-expand"
       >
-        <time>{{ betterTimestring }}</time>
+        <time>{{ captureState.metadata.image.acquisitionDate }}</time>
       </div>
       <div
         class="uk-text-meta uk-margin-remove-top uk-padding-remove uk-width-auto"
@@ -77,13 +77,13 @@
         <button class="uk-modal-close-default" type="button" uk-close></button>
         <h2 class="uk-modal-title">{{ fileName }}</h2>
         <p><b>Path: </b>{{ captureState.path }}</p>
-        <p><b>Time: </b>{{ betterTimestring }}</p>
-        <p><b>ID: </b>{{ captureState.metadata.id }}</p>
-        <p><b>Format: </b>{{ captureState.metadata.format }}</p>
+        <p><b>Time: </b>{{ captureState.metadata.image.acquisitionDate }}</p>
+        <p><b>ID: </b>{{ captureState.metadata.image.id }}</p>
+        <p><b>Format: </b>{{ captureState.metadata.image.format }}</p>
 
         <hr />
 
-        <div v-for="(value, key) in customMetadata" :key="key">
+        <div v-for="(value, key) in annotations" :key="key">
           <p>
             <b>{{ key }}: </b>{{ value }}
           </p>
@@ -93,14 +93,14 @@
 
         <div class="uk-flex-bottom" uk-grid>
           <div class="uk-width-2-3">
-            <keyvalList v-model="newCustomMetadata" />
+            <keyvalList v-model="newAnnotations" />
           </div>
           <div class="uk-width-1-3">
             <button
               class="uk-button uk-button-primary uk-form-small uk-width-1-1"
-              @click="handleMetadataSubmit()"
+              @click="handleAnnotationsSubmit()"
             >
-              Add metadata
+              Add annotation
             </button>
           </div>
         </div>
@@ -171,15 +171,15 @@ export default {
     return {
       tags: [],
       newTag: "",
-      customMetadata: {},
-      newCustomMetadata: {}
+      annotations: {},
+      newAnnotations: {}
     };
   },
 
   computed: {
     fileName: function() {
-      return this.captureState.filename // If this.captureState.filename exists
-        ? this.captureState.filename // Use this.captureState.filename
+      return this.captureState.name // If this.captureState.filename exists
+        ? this.captureState.name // Use this.captureState.filename
         : this.captureState.metadata.filename; // Otherwise use old this.captureState.metadata.filename
     },
     tagModalID: function() {
@@ -203,23 +203,17 @@ export default {
     tagsURL: function() {
       return this.captureState.links.tags.href;
     },
-    metadataURL: function() {
-      return this.captureState.links.metadata.href;
+    annotationsURL: function() {
+      return this.captureState.links.annotations.href;
     },
     captureURL: function() {
       return this.captureState.links.self.href;
-    },
-    betterTimestring: function() {
-      var dtSplit = this.captureState.metadata.time.split("_");
-      var date = dtSplit[0];
-      var time = dtSplit[1].replace(/-/g, ":");
-      return date + " " + time;
     }
   },
 
   created: function() {
     this.getTagRequest();
-    this.getMetadataRequest();
+    this.getAnnotationsRequest();
   },
 
   methods: {
@@ -231,9 +225,9 @@ export default {
       UIkit.modal(event.target.parentNode).hide();
     },
 
-    handleMetadataSubmit: function() {
-      this.putMetadataRequest(this.newCustomMetadata);
-      this.newCustomMetadata = {};
+    handleAnnotationsSubmit: function() {
+      this.putAnnotationsRequest(this.newAnnotations);
+      this.newAnnotations = {};
     },
 
     delCaptureConfirm: function() {
@@ -269,13 +263,13 @@ export default {
         });
     },
 
-    putMetadataRequest: function(metadataObject) {
+    putAnnotationsRequest: function(annotationsObject) {
       // Send metadata PUT request
       axios
-        .put(this.metadataURL, metadataObject)
+        .put(this.annotationsURL, annotationsObject)
         .then(() => {
           // Update metadata object
-          this.getMetadataRequest();
+          this.getAnnotationsRequest();
         })
         .catch(error => {
           this.modalError(error); // Let mixin handle error
@@ -315,12 +309,12 @@ export default {
         });
     },
 
-    getMetadataRequest: function() {
+    getAnnotationsRequest: function() {
       // Send tag request
       axios
-        .get(this.metadataURL)
+        .get(this.annotationsURL)
         .then(response => {
-          this.customMetadata = response.data.custom;
+          this.annotations = response.data;
         })
         .catch(error => {
           this.modalError(error); // Let mixin handle error
@@ -328,7 +322,7 @@ export default {
     },
 
     makeModalName: function(prefix) {
-      return prefix + this.captureState.metadata.id;
+      return prefix + this.captureState.metadata.image.id;
     }
   }
 };
diff --git a/src/components/viewComponents/galleryComponents/scanCard.vue b/src/components/viewComponents/galleryComponents/scanCard.vue
index bcc75794..6fd5d1a1 100644
--- a/src/components/viewComponents/galleryComponents/scanCard.vue
+++ b/src/components/viewComponents/galleryComponents/scanCard.vue
@@ -7,13 +7,11 @@
         <img
           class="uk-width-1-1"
           :data-src="thumbnail"
-          :alt="metadata.scan_id"
+          :alt="metadata.id"
           width="300"
           height="225"
           uk-img
-          @click="
-            $root.$emit('globalUpdateCaptureFolder', metadata.custom.scan_id)
-          "
+          @click="$root.$emit('globalUpdateCaptureFolder', metadata.id)"
         />
       </a>
     </div>
@@ -24,14 +22,14 @@
         uk-grid
       >
         <div class="uk-margin-remove-top uk-padding-remove uk-width-expand">
-          <b>Scan:</b> {{ metadata.custom.basename }}
+          <b>{{ metadata.type || "Dataset" }}: </b> {{ metadata.name }}
         </div>
       </div>
 
       <div
         class="uk-text-meta uk-margin-remove-top uk-padding-remove uk-width-expand"
       >
-        <time>{{ betterTimestring }}</time>
+        <time>{{ metadata.acquisitionDate }}</time>
       </div>
       <div
         class="uk-text-meta uk-margin-remove-top uk-padding-remove uk-width-auto"
@@ -54,10 +52,12 @@
       <div class="uk-modal-dialog uk-modal-body">
         <button class="uk-modal-close-default" type="button" uk-close></button>
         <h2 class="uk-modal-title">{{ metadata.basename }}</h2>
-        <p><b>Time: </b>{{ betterTimestring }}</p>
-        <p><b>Scan ID: </b>{{ metadata.custom.scan_id }}</p>
+        <p><b>Time: </b>{{ metadata.acquisitionDate }}</p>
+        <p><b>ID: </b>{{ metadata.id }}</p>
 
-        <div v-for="(value, key) in metadata.custom" :key="key">
+        <hr />
+
+        <div v-for="(value, key) in metadata.annotations" :key="key">
           <p>
             <b>{{ key }}: </b>{{ value }}
           </p>
@@ -95,12 +95,6 @@ export default {
     },
     metadataModalTarget: function() {
       return "#" + this.metadataModalID;
-    },
-    betterTimestring: function() {
-      var dtSplit = this.metadata.custom.time.split("_");
-      var date = dtSplit[0];
-      var time = dtSplit[1].replace(/-/g, ":");
-      return date + " " + time;
     }
   },
 
diff --git a/src/components/viewComponents/galleryDisplay.vue b/src/components/viewComponents/galleryDisplay.vue
index 877a121d..053f1154 100644
--- a/src/components/viewComponents/galleryDisplay.vue
+++ b/src/components/viewComponents/galleryDisplay.vue
@@ -127,7 +127,7 @@ export default {
       // Return an array of unique tags across all captures
       var tags = [];
       for (var capture of this.captures) {
-        for (var tag of capture.metadata.tags) {
+        for (var tag of capture.metadata.image.tags) {
           if (!tags.includes(tag)) {
             tags.push(tag);
           }
@@ -140,11 +140,8 @@ export default {
       // List of captures that are not part of a scan
       var captures = [];
       for (var capture of this.captures) {
-        // Filter by selected tags
-        var tags = capture.metadata.tags;
-
         // Add to capture list if matched
-        if (!tags.includes(this.scanTag)) {
+        if (!capture.metadata.dataset) {
           captures.push(capture);
         }
       }
@@ -157,11 +154,12 @@ export default {
       var scans = {};
 
       for (var capture of this.captures) {
-        var custom = capture.metadata.custom;
-        var tags = capture.metadata.tags;
+        var annotations = capture.metadata.image.annotations;
+        var tags = capture.metadata.image.tags;
+        var dataset = capture.metadata.dataset;
 
-        if ("scan_id" in custom) {
-          var id = custom["scan_id"];
+        if (dataset) {
+          var id = dataset["id"];
 
           // If this scan ID hasn't been seen before
           if (!(id in scans)) {
@@ -169,21 +167,22 @@ export default {
             scans[id].isScan = true;
             scans[id].captures = [];
             scans[id].metadata = {
-              filename: custom.basename,
-              time: custom.time,
-              id: custom.scan_id
+              name: dataset.name,
+              acquisitionDate: dataset.acquisitionDate,
+              id: dataset.id,
+              type: dataset.type
             };
             scans[id].metadata.tags = [];
-            scans[id].metadata.custom = {};
+            scans[id].metadata.annotations = {};
           }
 
           // Add the capture object to the scan
           scans[id].captures.push(capture);
 
           // Add missing scan metadata, prioritising first capture
-          for (var key of Object.keys(custom)) {
-            if (!(key in scans[id].metadata.custom)) {
-              scans[id].metadata.custom[key] = custom[key];
+          for (var key of Object.keys(annotations)) {
+            if (!(key in scans[id].metadata.annotations)) {
+              scans[id].metadata.annotations[key] = annotations[key];
             }
           }
 
@@ -196,9 +195,9 @@ export default {
 
           // Create a preview thumbnail
           if (!("thumbnail" in scans[id])) {
-            scans[id].thumbnail = `${
-              capture.links.download.href
-            }?thumbnail=true`;
+            scans[
+              id
+            ].thumbnail = `${capture.links.download.href}?thumbnail=true`;
           }
         }
       }
@@ -231,12 +230,15 @@ export default {
       var captures = {};
 
       for (var item of this.filteredItems) {
+        // If it's a dataset
         if ("captures" in item) {
           for (var capture of item.captures) {
-            captures[capture.metadata.id] = capture;
+            // Get the ID of each capture in the set
+            captures[capture.metadata.image.id] = capture;
           }
         } else {
-          captures[item.metadata.id] = item;
+          // If it's a single capture, get the ID of the capture
+          captures[item.metadata.image.id] = item;
         }
       }
 
diff --git a/src/components/viewComponents/streamDisplay.vue b/src/components/viewComponents/streamDisplay.vue
index 915dcf47..251d6fec 100644
--- a/src/components/viewComponents/streamDisplay.vue
+++ b/src/components/viewComponents/streamDisplay.vue
@@ -70,7 +70,7 @@ export default {
       }/api/v2/actions/camera/preview/stop`;
     },
     settingsUri: function() {
-      return `${this.$store.getters.baseUri}/api/v2/settings`;
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
     }
   },