Merge branch 'master' of https://gitlab.com/openflexure/openflexure-microscope-server

docs/source/extensions/marshaling.rst

@@ -37,8 +37,8 @@ For example, if you are creating an API route, in which you expect parameters ``
 
 .. code-block:: python
 
-    from labthings.server.schema import Schema
+    from labthings.schema import Schema
-    from labthings.server import fields
+    from labthings import fields
 
     class UserSchema(Schema):
         name = fields.String(required=True)

docs/source/extensions/structure.rst

@@ -1,10 +1,10 @@
 Basic extension structure
 =========================
 
-An extension starts as a simple instance of :py:class:`labthings.server.extensions.BaseExtension`. 
+An extension starts as a simple instance of :py:class:`labthings.extensions.BaseExtension`. 
 Each extension is described by a single ``BaseExtension`` instance, containing any number of methods, API views, and additional hardware components. 
 
-In order to access the currently running microscope object, use the :py:func:`labthings.server.find.find_component` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above.
+In order to access the currently running microscope object, use the :py:func:`labthings.find_component` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above.
 
 A simple extension file, with no API views but application-available methods may look like:
 
@@ -15,7 +15,7 @@ Once this extension is loaded, any other extensions will have access to your met
 
 .. code-block:: python
 
-    from labthings.server.find import find_extension
+    from labthings import find_extension
 
     def test_extension_method():
         # Find your extension. Returns None if it hasn't been found.
@@ -29,7 +29,7 @@ Once this extension is loaded, any other extensions will have access to your met
 Subclassing ``BaseExtension``
 -------------------------------
 
-The syntax used above allows novice programmers to easily start building extensions, without having to deal with subclassing. However, for more complex extensions which require persistent state, subclassing :py:class:`labthings.server.extensions.BaseExtension` is recommended.
+The syntax used above allows novice programmers to easily start building extensions, without having to deal with subclassing. However, for more complex extensions which require persistent state, subclassing :py:class:`labthings.extensions.BaseExtension` is recommended.
 
 The same simple extension as seen above can be written using subclassing:
 

docs/source/extensions/tasks_locks.rst

@@ -32,7 +32,7 @@ An example of a long running task may look like:
 .. code-block:: python
 
     ...
-    from labthings.server.view import ActionView
+    from labthings import ActionView
 
     class SlowAPI(ActionView):
         def post(self):

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -47,7 +47,8 @@ class ZipObjectDescription:
     def close(self):
         logging.debug(self.fp.name)
         self.fp.close()
-        os.unlink(self.fp.name)
+        if os.path.exists(self.fp.name):
+            os.unlink(self.fp.name)
 
         assert not os.path.exists(self.fp.name)
 

openflexure_microscope/api/static/src/components/genericComponents/taskProgress.vue

@@ -1,209 +0,0 @@
-<template>
-  <div>
-    <div
-      class="progress uk-margin-top uk-margin-horizontal-remove uk-padding-remove"
-    >
-      <div
-        v-if="progress"
-        class="determinate"
-        :style="barWidthFromProgress"
-      ></div>
-      <div v-else class="indeterminate"></div>
-    </div>
-
-    <button
-      type="button"
-      class="uk-button uk-button-danger uk-form-small uk-float-right uk-width-1-1"
-      @click="terminateTask()"
-    >
-      Terminate
-    </button>
-  </div>
-</template>
-
-<script>
-import axios from "axios";
-
-export default {
-  name: "TaskProgress",
-
-  props: {
-    taskId: {
-      type: String,
-      required: true
-    },
-    pollInterval: {
-      type: Number,
-      required: false,
-      default: 500
-    }
-  },
-
-  data: function() {
-    return {
-      polling: null,
-      progress: null
-    };
-  },
-
-  computed: {
-    barWidthFromProgress: function() {
-      var progress = this.progress <= 100 ? this.progress : 100;
-      var styleString = `width: ${progress}%`;
-      return styleString;
-    }
-  },
-
-  created() {
-    this.polling = setInterval(() => {
-      this.pollProgress();
-    }, this.pollInterval);
-  },
-
-  beforeDestroy() {
-    clearInterval(this.polling);
-  },
-
-  methods: {
-    pollProgress: function() {
-      console.log("Starting progress polling");
-      axios
-        .get(`${this.$store.getters.uriV2}/tasks/${this.taskId}`)
-        .then(response => {
-          console.log("PROGRESS RESPONSE: ", response.data.progress);
-          this.progress = response.data.progress;
-        });
-    },
-
-    terminateTask: function() {
-      axios
-        .delete(`${this.$store.getters.uriV2}/tasks/${this.taskId}`)
-        .then(response => {
-          console.log("TERMINATION RESPONSE: ", response.data);
-        });
-    }
-  }
-};
-</script>
-
-<style lang="less" scoped>
-@import "../../assets/less/theme.less";
-
-.progress {
-  position: relative;
-  height: 5px;
-  display: block;
-  width: 100%;
-  background-color: rgba(180, 180, 180, 0.15);
-  border-radius: 2px;
-  background-clip: padding-box;
-  margin: 0.5rem 0 1rem 0;
-  overflow: hidden;
-}
-
-.progress .determinate {
-  position: absolute;
-  background-color: inherit;
-  top: 0;
-  bottom: 0;
-  transition: width 0.3s linear;
-}
-
-.progress .indeterminate,
-.progress .determinate {
-  background-color: @global-primary-background;
-}
-
-.hook-inverse() {
-  .progress .indeterminate,
-  .progress .determinate {
-    background-color: @inverse-primary-muted-color;
-  }
-}
-
-.progress .indeterminate:before {
-  content: "";
-  position: absolute;
-  background-color: inherit;
-  top: 0;
-  left: 0;
-  bottom: 0;
-  will-change: left, right;
-  -webkit-animation: indeterminate 2.1s cubic-bezier(0.65, 0.815, 0.735, 0.395)
-    infinite;
-  animation: indeterminate 2.1s cubic-bezier(0.65, 0.815, 0.735, 0.395) infinite;
-}
-
-.progress .indeterminate:after {
-  content: "";
-  position: absolute;
-  background-color: inherit;
-  top: 0;
-  left: 0;
-  bottom: 0;
-  will-change: left, right;
-  -webkit-animation: indeterminate-short 2.1s cubic-bezier(0.165, 0.84, 0.44, 1)
-    infinite;
-  animation: indeterminate-short 2.1s cubic-bezier(0.165, 0.84, 0.44, 1)
-    infinite;
-  -webkit-animation-delay: 1.15s;
-  animation-delay: 1.15s;
-}
-
-@-webkit-keyframes indeterminate {
-  0% {
-    left: -35%;
-    right: 100%;
-  }
-  60% {
-    left: 100%;
-    right: -90%;
-  }
-  100% {
-    left: 100%;
-    right: -90%;
-  }
-}
-@keyframes indeterminate {
-  0% {
-    left: -35%;
-    right: 100%;
-  }
-  60% {
-    left: 100%;
-    right: -90%;
-  }
-  100% {
-    left: 100%;
-    right: -90%;
-  }
-}
-@-webkit-keyframes indeterminate-short {
-  0% {
-    left: -200%;
-    right: 100%;
-  }
-  60% {
-    left: 107%;
-    right: -8%;
-  }
-  100% {
-    left: 107%;
-    right: -8%;
-  }
-}
-@keyframes indeterminate-short {
-  0% {
-    left: -200%;
-    right: 100%;
-  }
-  60% {
-    left: 107%;
-    right: -8%;
-  }
-  100% {
-    left: 107%;
-    right: -8%;
-  }
-}
-</style>

openflexure_microscope/api/static/src/components/genericComponents/taskSubmitter.vue

@@ -90,6 +90,7 @@ export default {
   data: function() {
     return {
       taskId: null,
+      taskUrl: null,
       polling: null,
       progress: null,
       taskStarted: false,
@@ -150,6 +151,7 @@ export default {
           // Fetch the task ID
           console.log("Task ID: " + response.data.id);
           this.taskId = response.data.id;
+          this.taskUrl = response.data.href;
           // Start the store polling TaskId for success
           this.taskRunning = true;
           this.$emit("taskRunning", this.taskId);
@@ -192,12 +194,12 @@ export default {
       var checkCondition = (resolve, reject) => {
         // If the condition is met, we're done!
         axios
-          .get(`${this.$store.getters.uriV2}/tasks/${taskId}`)
+          .get(this.taskUrl)
           .then(response => {
             console.log(response.data.status);
             var result = response.data.status;
             // If the task ends with success
-            if (result == "success") {
+            if (result == "completed") {
               resolve(response.data);
             }
             // If task ends with an error
@@ -206,16 +208,10 @@ export default {
               reject(new Error(response.data.return));
             }
             // If task ends with termination
-            else if (result == "terminated") {
+            else if (result == "cancelled") {
               // Pass a generic termination error back with reject
-              reject(new Error("Task terminated"));
+              reject(new Error("Task cancelled"));
             }
-            // If task ends in any other way
-            else if (result != "running") {
-              // Pass status string as error
-              reject(new Error(result));
-            }
-            // Didn't match and too much time, reject!
             else {
               // Since the task is still running, we can update the progress bar
               this.progress = response.data.progress;
@@ -232,7 +228,7 @@ export default {
       console.log("Starting progress polling");
 
       axios
-        .get(`${this.$store.getters.uriV2}/tasks/${this.taskId}`)
+        .get(this.taskUrl)
         .then(response => {
           console.log("PROGRESS RESPONSE: ", response.data.progress);
           this.progress = response.data.progress;
@@ -241,7 +237,7 @@ export default {
 
     terminateTask: function() {
       axios
-        .delete(`${this.$store.getters.uriV2}/tasks/${this.taskId}`)
+        .delete(this.taskUrl)
         .then(response => {
           console.log("TERMINATION RESPONSE: ", response.data);
         });

openflexure_microscope/api/static/src/components/viewComponents/galleryComponents/zipDownloader.vue

@@ -166,7 +166,7 @@ export default {
     },
 
     onResponse: function(response) {
-      this.lastSessionId = response.return.id;
+      this.lastSessionId = response.output.id;
       this.downloadUrl = `${this.zipGetterUri}/${this.lastSessionId}`;
       this.downloadReady = true;
     },

openflexure_microscope/camera/mock.py

@@ -204,6 +204,8 @@ class MissingCamera(BaseCamera):
 
             if isinstance(output, str):
                 output.close()
+            else:
+                output.flush()
 
     # HANDLE STREAM FRAMES
 

openflexure_microscope/captures/capture.py

@@ -129,7 +129,7 @@ class CaptureObject(object):
 
         # Store a nice ID
         self.id = uuid.uuid4()  #: str: Unique capture ID
-        logging.debug("Created StreamObject {}".format(self.id))
+        logging.debug("Created CaptureObject {}".format(self.id))
         self.datetime = datetime.datetime.now()
 
         # Create file name. Default to UUID
@@ -151,6 +151,7 @@ class CaptureObject(object):
         self.thumb_bytes = None
 
     def write(self, s):
+        logging.debug(f"Writing to {self}")
         self.stream.write(s)
 
     def flush(self):

openflexure_microscope/microscope.py

@@ -354,7 +354,8 @@ class Microscope:
             )
 
             # Capture to output object
-            logging.info(f"Starting microscope capture {filename}")
+            logging.info(f"Starting microscope capture {output.file}")
+            print(output)
             self.camera.capture(
                 output,
                 use_video_port=use_video_port,