Refactor export_annotations command. Update changelog. Add util command documentation.

CHANGELOG.md

@@ -5,6 +5,10 @@
 
 ### Fixed
 
+
+## [2.1.1] 2023-10-02
+
+### Important Notice!
 In versions from 0.2.0 to 2.1.0 inclusive the default `docker-compose.yml` file fails to back up the database, due to a mismatch between the version of the database server and the version of the backup client.  This is now fixed, but in order to create a proper database backup before attempting to upgrade you will need to manually edit your `docker-compose.yml` file and change
 
 ```yaml
@@ -27,10 +31,24 @@ docker compose run --rm -it pgbackups /backup.sh
 
 (or `docker-compose` if your version of Docker does not support compose v2).
 
-## [2.1.1] 2023-10-02
-
 ### Added 
-- Script for extracting annotations without web UI
+- Script for extracting annotations without web UI ([#386](https://github.com/GateNLP/gate-teamware/pull/386))
+- Support upgrades as well as fresh installs for get-teamware.sh script ([#383](https://github.com/GateNLP/gate-teamware/pull/383))
+- Add transition effect when document changes ([#367](https://github.com/GateNLP/gate-teamware/pull/367))
+- Implement conditional widgets ([#350](https://github.com/GateNLP/gate-teamware/pull/350))
+
+### Changed
+- Attempt to spread documents more evenly across annotators ([#384](https://github.com/GateNLP/gate-teamware/pull/384))
+- Upgrade postgres-backup-local to version 14 ([#382](https://github.com/GateNLP/gate-teamware/pull/382))
+- enable version.py update to take version number as argument ([#365](https://github.com/GateNLP/gate-teamware/pull/365))
+
+### Fixed
+- Correct error in navbar property setting ([#376](https://github.com/GateNLP/gate-teamware/pull/376))
+- User-level DB lock in get_annotator_task to avoid race condition #375 ([#376](https://github.com/GateNLP/gate-teamware/pull/376))
+- Better frontend error page when backend is down ([#368](https://github.com/GateNLP/gate-teamware/pull/368))
+- Correct DOI ([#364](https://github.com/GateNLP/gate-teamware/pull/364))
+- Clear pending annotations when rejecting a user from a project ([#362](https://github.com/GateNLP/gate-teamware/pull/362))
+
 
 
 ## [2.1.0] 2023-05-03

backend/management/commands/download_annotations.py → backend/management/commands/export_annotations.py

@@ -7,34 +7,45 @@
 
 class Command(BaseCommand):
 
-    help = "Download annotation data"
-
-
+    help = "Export zipped annotation data to an file."
 
     def add_arguments(self, parser):
         parser.add_argument("output_path", type=str, help="Path of file output")
         parser.add_argument("project_id", type=str, help="ID of the project")
-        parser.add_argument("doc_type", type=str, help="Document type all, training, test, or annotation")
-        parser.add_argument("export_type", type=str, help="Type of export json, jsonl or csv")
-        parser.add_argument("anonymize", type=self.str2bool, help="Data should be anonymized or not ")
-        parser.add_argument("-j", "--json_format", type=str, help="Type of json format: raw (default) or gate ")
-        parser.add_argument("-n", "--num_entries_per_file", type=int, help="Number of entries to generate per file, default 500")
+        parser.add_argument("-d", "--document_type",
+                            type=str,
+                            help="Document type of either all, training, test, or annotation. Defaults to all.",
+                            choices=["all", "training", "test", "annotation"],
+                            default="all",
+                            metavar="DOCUMENT_TYPE")
+        parser.add_argument("-e", "--export_type",
+                            type=str,
+                            help="Type of export json, jsonl or csv. Defaults to json.",
+                            choices=["json", "jsonl", "csv"],
+                            default="json",
+                            metavar="EXPORT_TYPE")
+        parser.add_argument("-a", "--anonymize", type=self.str2bool, default=True,
+                            help="Anonymize data if true. Defaults to true.")
+        parser.add_argument("-j", "--json_format", type=str, default="raw",
+                            help="Type of json format, raw or gate. Defaults to raw.")
+        parser.add_argument("-n", "--num_entries_per_file", type=int, default=500,
+                            help="Number of entries to generate per file. Defaults to 500.")
 
 
-    def handle(self, *args, **options):
 
-        annotations_downloader = DownloadAnnotationsView()
+    def handle(self, *args, **options):
 
         output_path = options["output_path"]
         project_id = options["project_id"]
-        doc_type = options["doc_type"]
+        doc_type = options["document_type"]
         export_type = options["export_type"]
         anonymize = options["anonymize"]
-        json_format = options["json_format"] if options["json_format"] else "raw"
-        num_entries_per_file = options["num_entries_per_file"] if options["num_entries_per_file"] else 500
+        json_format = options["json_format"]
+        num_entries_per_file = options["num_entries_per_file"]
 
-        print(f"Writing annotations to {output_path} \n Project: {project_id}\n Document type: {doc_type}\n Export type: {export_type} \n Anonymized: {anonymize} \n Json format:  {json_format} \n Num entries per file: {num_entries_per_file}\n")
+        print(f"Writing annotations to: {output_path} \n Project id: {project_id}\n Document type: {doc_type}\n Export type: {export_type} \n Anonymized: {anonymize} \n Json format:  {json_format} \n Num entries per file: {num_entries_per_file}\n")
 
+        annotations_downloader = DownloadAnnotationsView()
         with open(output_path, "wb") as z:
             annotations_downloader.write_zip_to_file(file_stream=z,
                                                      project_id=project_id,

docs/docs/.vuepress/config.js

@@ -26,6 +26,7 @@ module.exports = context => ({
                 'releases',
                 'documentation',
                 "api_docs",
+                'commands'
 
             ],
         },

docs/docs/.vuepress/versions.json

@@ -18,6 +18,10 @@
    "text": "2.1.0",
    "value": "/gate-teamware/2.1.0/"
   },
+  {
+   "text": "2.1.1",
+   "value": "/gate-teamware/2.1.1/"
+  },
   {
    "text": "development",
    "value": "/gate-teamware/development/"

docs/docs/developerguide/commands.md

@@ -0,0 +1,28 @@
+# Utility commands
+Django provides various [built-in utility functions](https://docs.djangoproject.com/en/4.2/ref/django-admin/) that can 
+be accessed from `manage.py` script at the root of the project. A few teamware-specific utility commands have been added
+in order to assist with management and development of the application.
+
+To use the custom utility commands, navigate to the app's root folder (with the file `manage.py`) and 
+run `./manage.py command_name` where `command_name` is the command that you'd like to run. Adding a `-h` argument
+prints out the description and all possible options for the command e.g.:
+
+```
+./manage.py export_annotations -h
+```
+
+## Available commands
+
+### General Usage
+- **export_annotations** - Manually export annotations belonging to a project and save it to a zipped file.
+
+### Development
+<span style="color:red">**Warning, use of the following functions will modify or reset your database! Ensure your database is backed up
+before using them outside of development.**</span> 
+
+- **load_test_fixture** -  The command loads a pre-defined test fixture. Use without any arguments to see all 
+  available fixtures.
+- **check_create_superuser** - Checks whether there's a superuser in the database and creates one if none exists. The 
+  username, password and email are obtained from environment variables `SUPERUSER_USERNAME`, `SUPERUSER_PASSWORD` and
+  `SUPERUSER_EMAIL` respectively.
+

docs/versioned/0.3.0/.vuepress/versions.json

@@ -18,6 +18,10 @@
    "text": "2.1.0",
    "value": "/gate-teamware/2.1.0/"
   },
+  {
+   "text": "2.1.1",
+   "value": "/gate-teamware/2.1.1/"
+  },
   {
    "text": "development",
    "value": "/gate-teamware/development/"

docs/versioned/0.4.0/.vuepress/versions.json

@@ -18,6 +18,10 @@
    "text": "2.1.0",
    "value": "/gate-teamware/2.1.0/"
   },
+  {
+   "text": "2.1.1",
+   "value": "/gate-teamware/2.1.1/"
+  },
   {
    "text": "development",
    "value": "/gate-teamware/development/"

docs/versioned/2.0.0/.vuepress/versions.json

@@ -18,6 +18,10 @@
    "text": "2.1.0",
    "value": "/gate-teamware/2.1.0/"
   },
+  {
+   "text": "2.1.1",
+   "value": "/gate-teamware/2.1.1/"
+  },
   {
    "text": "development",
    "value": "/gate-teamware/development/"

docs/versioned/2.1.0/.vuepress/versions.json

@@ -18,6 +18,10 @@
    "text": "2.1.0",
    "value": "/gate-teamware/2.1.0/"
   },
+  {
+   "text": "2.1.1",
+   "value": "/gate-teamware/2.1.1/"
+  },
   {
    "text": "development",
    "value": "/gate-teamware/development/"

docs/versioned/2.1.1/.vuepress/components/AnnotationRendererPreview.vue

@@ -0,0 +1,107 @@
+<template>
+  <div>
+    <b-tabs>
+      <b-tab title="Code">
+
+      <slot></slot>
+
+      </b-tab>
+      <b-tab title="Preview">
+        <p v-if="documents.length > 1">Document {{documentIndex + 1}} of {{documents.length}}</p>
+        <b-card class="mb-2 mt-2">
+          <AnnotationRenderer ref="annotationRenderer"
+                              :config="config"
+                              :document="currentDocument" :allow_document_reject="true"
+                              v-model="annotationOutput"
+                              :doc_preannotation_field="preAnnotation"
+                              @submit="nextDocument()"
+                              @reject="nextDocument()"
+          ></AnnotationRenderer>
+        </b-card>
+        <b-card class="mb-2 mt-2">
+          <p><strong>Annotation output:</strong></p>
+          {{annotationOutput}}
+        </b-card>
+      </b-tab>
+
+    </b-tabs>
+  </div>
+
+</template>
+
+<script>
+import AnnotationRenderer from '@/components/AnnotationRenderer';
+
+export default {
+  name: "AnnotationRendererPreview",
+  components: {
+    AnnotationRenderer
+  },
+  data(){
+    return {
+      annotationOutput: {},
+      documentIndex: 0
+    }
+
+  },
+  computed: {
+    documents() {
+      if(Array.isArray(this.document)) {
+        return this.document
+      } else {
+        return [this.document]
+      }
+    },
+    currentDocument() {
+      return this.documents[this.documentIndex]
+    }
+  },
+  props: {
+    preAnnotation: {
+      default(){
+        return ""
+      }
+    },
+    document: {
+      default(){
+        return {text: "Sometext with <strong>html</strong>"}
+      }
+    },
+    config: {
+      default() {
+        return [
+            {
+              "name": "htmldisplay",
+              "type": "html",
+              "text": "{{{text}}}"
+            },
+            {
+              "name": "sentiment",
+              "type": "radio",
+              "title": "Sentiment",
+              "description": "Please select a sentiment of the text above.",
+              "options": {
+                "negative": "Negative",
+                "neutral": "Neutral",
+                "positive": "Positive"
+
+              }
+            }
+          ]
+      }
+    },
+  },
+  methods: {
+    nextDocument() {
+      this.documentIndex = (this.documentIndex + 1) % this.documents.length;
+      this.$refs.annotationRenderer.clearForm()
+    }
+  }
+}
+</script>
+
+<style>
+legend {
+font-weight: bold;
+}
+</style>

docs/versioned/2.1.1/.vuepress/components/DisplayVersion.vue

@@ -0,0 +1,21 @@
+<template>
+<span>{{version_name}}</span>
+</template>
+
+<script>
+import versionData from "../versions.json"
+export default {
+  name: "DisplayVersion",
+  computed: {
+    version_name(){
+      return versionData.current
+    }
+  }
+
+
+}
+</script>
+
+<style scoped>
+
+</style>

docs/versioned/2.1.1/.vuepress/config.js

@@ -0,0 +1,43 @@
+const versionData = require("./versions.json")
+const path = require("path");
+module.exports = context => ({
+    title: 'GATE Teamware Documentation',
+    description: 'Documentation for GATE Teamware',
+    base: versionData.base,
+    themeConfig: {
+        nav: [
+            {text: 'Home', link: '/'},
+            {text: 'Annotators', link: '/annotatorguide/'},
+            {text: 'Managers & Admins', link: '/manageradminguide/'},
+            {text: 'Developer', link: '/developerguide/'}
+        ],
+        sidebar: {
+            '/manageradminguide/': [
+                "",
+                "project_management",
+                "project_config",
+                "documents_annotations_management",
+                "annotators_management"
+            ],
+            '/developerguide/': [
+                '',
+                'frontend',
+                'testing',
+                'releases',
+                'documentation',
+                "api_docs",
+                'commands'
+
+            ],
+        },
+    },
+    configureWebpack: {
+        resolve: {
+            alias: {
+                '@': path.resolve(__dirname, versionData.frontendSource)
+            }
+        }
+    },
+
+
+})

docs/versioned/2.1.1/.vuepress/enhanceApp.js

@@ -0,0 +1,17 @@
+import Vue from 'vue'
+import {BootstrapVue, BootstrapVueIcons, IconsPlugin} from 'bootstrap-vue'
+
+import 'bootstrap/dist/css/bootstrap.css'
+import 'bootstrap-vue/dist/bootstrap-vue.css'
+
+Vue.use(BootstrapVue)
+Vue.use(BootstrapVueIcons)
+
+export default ({
+  Vue, // the version of Vue being used in the VuePress app
+  options, // the options for the root Vue instance
+  router, // the router instance for the app
+  siteData // site metadata
+}) => {
+
+}