Add webanno tool to SABER repository

saber/webanno/.gitignore

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+.venv
+
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+# End of https://www.gitignore.io/api/code,python,macos

saber/webanno/README.md

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+# webanno
+
+A human-facing web annotation tool for different flavors of data.
+
+
+
+## Overview
+
+The `webanno` tool runs a Python process that exposes a web server with a single user-facing web-page which holds developer-defined data to annotate (perhaps it's text, perhaps it's a webform, perhaps it's imagery...). Once the data are annotated and submitted, the web server shuts down gracefully (exitcode 0), which means you can use the output data in a SABER workflow.
+
+### Why not a conventional web app?
+
+A conventional web application process does not stop once the data are annotated, which means you cannot run it "in-line" with the rest of a SABER workflow.
+
+## How do I pick the data to annotate?
+
+`webanno` uses a plugin architecture system: A plugin defines both the HTML of the page as well as what to do with the data when annotation is over.
+
+There are many already-existing annotation plugins:
+
+### `ButtonPressPlugin`
+
+This plugin is the simplest (and a good example to learn from!), and just monitors when a button is pressed.
+
+### `FormInputPlugin`
+
+This plugin lets you create a custom form in HTML for a user to fill out.
+
+### `CentroidsPlugin`
+
+This plugin lets a user place points in a 2D image, and returns a JSON file of the coordinates of those clicks.
+
+### `BossVolumePlugin`
+
+This plugin lets a user place points in a 3D volume downloaded from BossDB.
+
+
+## Installation
+
+To get started, you need only pip-install this package and its dependencies:
+
+```shell
+pip3 install -r requirements.txt
+pip3 install -e .
+```
+
+## Usage
+
+Use the `webanno` tool from the command-line:
+
+```shell
+webanno examples/example_centroids_image.json
+```
+
+Results will be stored in `results.json` in PWD. If you would like to store them elsewhere, set `json_file_output` in any config file (all plugins accept this config value).

saber/webanno/examples/example_basic.json

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+{
+    "plugin": "webanno.plugins.ButtonPressPlugin",
+    "config": {}
+}

saber/webanno/examples/example_boss_centroids.json

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+{
+    "plugin": "webanno.plugins.BossVolumePlugin",
+    "config": {
+        "boss_uri": "bossdb://https://api.bossdb.io/wilson2019/P7/em",
+        "start": [
+            32820,
+            26731,
+            32
+        ],
+        "stop": [
+            33616,
+            27500,
+            46
+        ],
+        "res": 0,
+        "dot_color": [
+            255,
+            0,
+            255
+        ]
+    }
+}

saber/webanno/examples/example_centroids_image.json

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+{
+    "plugin": "webanno.plugins.CentroidsPlugin",
+    "config": {
+        "max_count": 5,
+        "prompt": "<b>Click on the eyes.</b>",
+        "image_url": "http://www.fillmurray.com/600/600/"
+    }
+}

saber/webanno/examples/example_form_input.json

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+{
+    "plugin": "webanno.plugins.FormInputPlugin",
+    "config": {
+        "fields": [
+            {
+                "name": "name",
+                "type": "text"
+            },
+            {
+                "name": "age",
+                "type": "number"
+            },
+            {
+                "name": "todays_date",
+                "type": "time",
+                "label": "When did you wake up today?"
+            }
+        ]
+    }
+}

saber/webanno/requirements.txt

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+flask
+flask_cors
+pillow
+intern
+numpy

saber/webanno/scripts/webanno

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+#!/usr/bin/env python3
+
+from webanno import run
+
+run()

saber/webanno/setup.py

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+import os
+from distutils.core import setup
+
+"""
+git tag {VERSION}
+git push --tags
+python setup.py sdist upload -r pypi
+"""
+
+VERSION = "0.1.0"
+
+setup(
+    name="webanno",
+    version=VERSION,
+    author="Jordan Matelsky",
+    author_email="j6k4m8@gmail.com",
+    description=("Web annotation plugin platform"),
+    license="Apache 2.0",
+    keywords=[
+    ],
+    url="https://github.com/aplbrain/webanno/tarball/" + VERSION,
+    packages=['webanno'],
+    scripts=[
+        'scripts/webanno'
+    ],
+    classifiers=[],
+    install_requires=[
+        'flask', 'flask_cors'
+    ],
+)

saber/webanno/webanno/__init__.py

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+import sys
+import importlib
+import json
+from flask import Flask, request, render_template
+from flask_cors import CORS
+
+
+from webanno.plugins import Plugin
+
+
+def shutdown_server():
+    func = request.environ.get("werkzeug.server.shutdown")
+    if func is None:
+        raise RuntimeError("Not running with the Werkzeug Server")
+    func()
+
+
+def attach_plugin(plugin: Plugin, app: Flask):
+    CORS(app)
+
+    def _prompt():
+        return plugin.prompt().replace("[[SUBMIT_URL]]", "http://localhost:5000/submit")
+
+    def _submit():
+        plugin.collect(request.json, request)
+        shutdown_server()
+        return "ok"
+
+    for path, route_fn in plugin.routes().items():
+        app.add_url_rule("/plugin/" + path.lstrip("/"), path, route_fn)
+
+    app.add_url_rule("/", "prompt", _prompt)
+    app.add_url_rule("/submit", "submit", _submit, methods=["POST"])
+
+
+def run():
+    APP = Flask(__name__)
+    config = json.load(open(sys.argv[1], "r"))
+    plugin = importlib.import_module(config["plugin"])
+    attach_plugin(plugin._Plugin(config["config"]), APP)
+    APP.run(debug=True)