Support JupyterLab 2.x

.gitignore

-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
 *.egg-info/                                                                                                                                                                                                 
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask instance folder
-instance/
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-docs/source/_static/embed-bundle.js
-docs/source/_static/embed-bundle.js.map
-
-# PyBuilder
-target/
-
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# dotenv
-.env
-
-# virtualenv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-
-# Rope project settings
-.ropeproject
+.ipynb_checkpoints/
+dist/
+build/
+*.py[cod]
+node_modules/
 
-# =========================
-# Operating System Files
-# =========================
+# Compiled javascript
+dicom_upload/static/
 
 # OS X
-# =========================
-
 .DS_Store
-.AppleDouble
-.LSOverride
-
-# Thumbnails
-._*
-
-# Files that might appear in the root of a volume
-.DocumentRevisions-V100
-.fseventsd
-.Spotlight-V100
-.TemporaryItems
-.Trashes
-.VolumeIcon.icns
-
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
-
-# Windows
-# =========================
-
-# Windows image file caches
-Thumbs.db
-ehthumbs.db
-
-# Folder config file
-Desktop.ini
-
-# Recycle Bin used on file shares
-$RECYCLE.BIN/
-
-# Windows Installer files
-*.cab
-*.msi
-*.msm
-*.msp
-
-# Windows shortcuts
-*.lnk
-
-
-# NPM
-# ----
-
-**/node_modules/
-dicom_upload/nbextension/static/index.*
-dicom_upload/labextension/*.tgz
-
-# Coverage data
-# -------------
-**/coverage/
-
-# Packed lab extensions
-dicom_upload/labextension
 
-# vscode
-.vscode/
+# VS Code
+*.vscode

MANIFEST

-# file GENERATED by distutils, do NOT edit
-LICENSE.txt
-README.md
-dicom_upload.json
-package.json
-pytest.ini
-setup.cfg
-setup.py
-setupbase.py
-tsconfig.json
-webpack.config.js
-dicom_upload/__init__.py
-dicom_upload/_frontend.py
-dicom_upload/_version.py
-dicom_upload/widget_upload.py
-dicom_upload/labextension/dicom-upload-0.1.2.tgz
-dicom_upload/nbextension/__init__.py
-dicom_upload/nbextension/static/extension.js
-dicom_upload/nbextension/static/index.js
-dicom_upload/nbextension/static/index.js.map
-dicom_upload/tests/__init__.py
-dicom_upload/tests/conftest.py
-dicom_upload/tests/test_example.py
-dicom_upload/tests/test_nbextension_path.py
-docs/Makefile
-docs/environment.yml
-docs/make.bat
-docs/source/conf.py
-docs/source/develop-install.rst
-docs/source/index.rst
-docs/source/installing.rst
-docs/source/introduction.rst
-docs/source/_static/embed-bundle.js
-docs/source/_static/embed-bundle.js.map
-docs/source/_static/helper.js
-docs/source/examples/index.rst
-docs/source/examples/introduction.nblink
-examples/introduction.ipynb
-examples/.ipynb_checkpoints/introduction-checkpoint.ipynb
-src/extension.ts
-src/index.ts
-src/plugin.ts
-src/version.ts
-src/widget.ts
-tests/karma.conf.js
-tests/tsconfig.json
-tests/src/index.spec.ts
-tests/src/utils.spec.ts

MANIFEST.in

-include LICENSE.txt
-include README.md
-
-include setupbase.py
-include pytest.ini
-include .coverage.rc
-
-include tsconfig.json
-include package.json
-include webpack.config.js
-include dicom_upload/labextension/*.tgz
-
-# Documentation
-graft docs
-exclude docs/\#*
-prune docs/build
-prune docs/gh-pages
-prune docs/dist
-
-# Examples
-graft examples
-
-# Tests
-graft tests
-prune tests/build
-
-# Javascript files
-graft dicom_upload/nbextension
-graft src
-prune **/node_modules
-prune coverage
-prune lib
-
-# Patterns to exclude from any directory
-global-exclude *~
-global-exclude *.pyc
-global-exclude *.pyo
-global-exclude .git
-global-exclude .ipynb_checkpoints
+recursive-include dicom_upload/static *.*
+include dicom-upload.json

README.md

-# dicom-upload
+dicom-upload
+===============================
 
-[![Build Status](https://travis-ci.org/jsc/dicom-upload.svg?branch=master)](https://travis-ci.org/jsc/dicom_upload)
-[![codecov](https://codecov.io/gh/jsc/dicom-upload/branch/master/graph/badge.svg)](https://codecov.io/gh/jsc/dicom-upload)
+Upload DICOM files with patient und study data removed from header
 
+Installation
+------------
 
-FileUpload Widget using the Jupyter Notebook Server RestAPI.
-Uploads DICOM files with anonymized headers, i.d. the 0004 and 
-0010 tags are removed on JS side before the upload.
+To install use pip:
 
-Can handle large files by uploading files in chunks.
+    $ pip install dicom_upload
+    $ jupyter nbextension enable --py --sys-prefix dicom_upload
 
-## Installation
+To install for jupyterlab
 
-You can install using `pip`:
+    $ jupyter labextension install dicom_upload
 
-```bash
-pip install dicom_upload
-```
-or from this GitLab directly
+For a development installation (requires npm),
 
-```bash
-pip install git+https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload.git
-```
+    $ git clone https://github.com/jsc/dicom-upload.git
+    $ cd dicom-upload
+    $ pip install -e .
+    $ jupyter nbextension install --py --symlink --sys-prefix dicom_upload
+    $ jupyter nbextension enable --py --sys-prefix dicom_upload
+    $ jupyter labextension install js
 
-Or if you use jupyterlab:
+When actively developing your extension, build Jupyter Lab with the command:
 
-```bash
-pip install dicom_upload
-jupyter labextension install @jupyter-widgets/jupyterlab-manager
-```
+    $ jupyter lab --watch
+
+This take a minute or so to get started, but then allows you to hot-reload your javascript extension.
+To see a change, save your javascript, watch the terminal for an update.
+
+Note on first `jupyter lab --watch`, you may need to touch a file to get Jupyter Lab to open.
 
-If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable
-the nbextension:
-```bash
-jupyter nbextension enable --py [--sys-prefix|--user|--system] dicom_upload
-```

RELEASE.md

+- To release a new version of dicom_upload on PyPI:
+
+Update _version.py (set release version, remove 'dev')
+git add the _version.py file and git commit
+`python setup.py sdist upload`
+`python setup.py bdist_wheel upload`
+`git tag -a X.X.X -m 'comment'`
+Update _version.py (add 'dev' and increment minor)
+git add and git commit
+git push
+git push --tags
+
+- To release a new version of dicom-upload on NPM:
+
+Update `js/package.json` with new npm package version
+
+```
+# clean out the `dist` and `node_modules` directories
+git clean -fdx
+npm install
+npm publish
+```
\ No newline at end of file

dicom_upload.json → dicom-upload.json

 {
   "load_extensions": {
-    "dicom_upload/extension": true
+    "dicom-upload/extension": true
   }
 }

dicom_upload/__init__.py

-#!/usr/bin/env python
-# coding: utf-8
+from ._version import version_info, __version__
 
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
+from .widget_upload import *
 
-from .widget_upload import Uploader
-from ._version import __version__, version_info
 
-from .nbextension import _jupyter_nbextension_paths
+def _jupyter_nbextension_paths():
+    """Called by Jupyter Notebook Server to detect if it is a valid nbextension and
+    to install the widget
+
+    Returns
+    =======
+    section: The section of the Jupyter Notebook Server to change.
+        Must be 'notebook' for widget extensions
+    src: Source directory name to copy files from. Webpack outputs generated files
+        into this directory and Jupyter Notebook copies from this directory during
+        widget installation
+    dest: Destination directory name to install widget files to. Jupyter Notebook copies
+        from `src` directory into <jupyter path>/nbextensions/<dest> directory
+        during widget installation
+    require: Path to importable AMD Javascript module inside the
+        <jupyter path>/nbextensions/<dest> directory
+    """
+    return [{
+        'section': 'notebook',
+        'src': 'static',
+        'dest': 'dicom-upload',
+        'require': 'dicom-upload/extension'
+    }]

dicom_upload/_frontend.py

-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
-
 """
 Information about the frontend package of the widgets.
 """
 
 module_name = "dicom-upload"
-module_version = "^0.1.0"
+module_version = "0.1.3"

dicom_upload/_version.py

-#!/usr/bin/env python
-# coding: utf-8
+# Module version
+version_info = (0, 1, 3, 'final', 0)
 
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
+# Module version stage suffix map
+_specifier_ = {'alpha': 'a', 'beta': 'b', 'candidate': 'rc', 'final': ''}
 
-version_info = (0, 1, 3, 'dev')
-__version__ = ".".join(map(str, version_info))
+# Module version accessible using dicom_upload.__version__
+__version__ = '%s.%s.%s%s' % (version_info[0], version_info[1], version_info[2],
+                              '' if version_info[3] == 'final' else _specifier_[version_info[3]]+str(version_info[4]))

dicom_upload/nbextension/__init__.py

-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Alice Grosch
-# Distributed under the terms of the Modified BSD License.
-
-def _jupyter_nbextension_paths():
-    return [{
-        'section': 'notebook',
-        'src': 'nbextension/static',
-        'dest': 'dicom_upload',
-        'require': 'dicom_upload/extension'
-    }]

dicom_upload/nbextension/static/extension.js

-// Entry point for the notebook bundle containing custom model definitions.
-//
-define(function() {
-    "use strict";
-
-    window['requirejs'].config({
-        map: {
-            '*': {
-                'dicom-upload': 'nbextensions/dicom_upload/index',
-            },
-        }
-    });
-    // Export the required load_ipython_extension function
-    return {
-        load_ipython_extension : function() {}
-    };
-});

dicom_upload/tests/conftest.py

-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
-
-import pytest
-
-from ipykernel.comm import Comm
-from ipywidgets import Widget
-
-class MockComm(Comm):
-    """A mock Comm object.
-
-    Can be used to inspect calls to Comm's open/send/close methods.
-    """
-    comm_id = 'a-b-c-d'
-    kernel = 'Truthy'
-
-    def __init__(self, *args, **kwargs):
-        self.log_open = []
-        self.log_send = []
-        self.log_close = []
-        super(MockComm, self).__init__(*args, **kwargs)
-
-    def open(self, *args, **kwargs):
-        self.log_open.append((args, kwargs))
-
-    def send(self, *args, **kwargs):
-        self.log_send.append((args, kwargs))
-
-    def close(self, *args, **kwargs):
-        self.log_close.append((args, kwargs))
-
-_widget_attrs = {}
-undefined = object()
-
-
-@pytest.fixture
-def mock_comm():
-    _widget_attrs['_comm_default'] = getattr(Widget, '_comm_default', undefined)
-    Widget._comm_default = lambda self: MockComm()
-    _widget_attrs['_ipython_display_'] = Widget._ipython_display_
-    def raise_not_implemented(*args, **kwargs):
-        raise NotImplementedError()
-    Widget._ipython_display_ = raise_not_implemented
-
-    yield MockComm()
-
-    for attr, value in _widget_attrs.items():
-        if value is undefined:
-            delattr(Widget, attr)
-        else:
-            setattr(Widget, attr, value)

dicom_upload/tests/test_example.py

-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
-
-import pytest
-
-from ..example import ExampleWidget
-
-
-def test_example_creation_blank():
-    w = ExampleWidget()
-    assert w.value == 'Hello World'

dicom_upload/tests/test_nbextension_path.py

-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Alice Grosch.
-# Distributed under the terms of the Modified BSD License.
-
-
-def test_nbextension_path():
-    # Check that magic function can be imported from package root:
-    from dicom_upload import _jupyter_nbextension_paths
-    # Ensure that it can be called without incident:
-    path = _jupyter_nbextension_paths()
-    # Some sanity checks:
-    assert len(path) == 1
-    assert isinstance(path[0], dict)

dicom_upload/widget_upload.py

@@ -25,6 +25,7 @@ from traitlets import (
 from ._frontend import module_name, module_version
 
 
+@register
 class Uploader(DescriptionWidget, ValueWidget):
     """Upload Widget. 
 
@@ -45,10 +46,13 @@ class Uploader(DescriptionWidget, ValueWidget):
     _view_module = Unicode(module_name).tag(sync=True)
     _view_module_version = Unicode(module_version).tag(sync=True)
 
-    accept = Unicode(help='File types to accept, empty string for all').tag(sync=True)
-    multiple = Bool(help='If True, allow for multiple files upload').tag(sync=True)
+    accept = Unicode(
+        help='File types to accept, empty string for all').tag(sync=True)
+    multiple = Bool(
+        help='If True, allow for multiple files upload').tag(sync=True)
     disabled = Bool(help='Enable or disable button').tag(sync=True)
-    icon = Unicode('upload', help="Font-awesome icon name, without the 'fa-' prefix.").tag(sync=True)
+    icon = Unicode(
+        'upload', help="Font-awesome icon name, without the 'fa-' prefix.").tag(sync=True)
     button_style = CaselessStrEnum(
         values=['primary', 'success', 'info', 'warning', 'danger', ''], default_value='',
         help="""Use a predefined styling for the button.""").tag(sync=True)
@@ -69,7 +73,6 @@ class Uploader(DescriptionWidget, ValueWidget):
     hash = Unicode().tag(sync=True)
     _upload = Bool(False).tag(sync=True)
 
-    
     def __init__(self, upload_url='http://localhost:8888/api/contents/', token='', *args, **kwargs):
         """Args:
             upload_url (str): Jupyter notebook URL appended by api/contents/<path>/. Directories on <path> must already exist.

docs/Makefile

-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = dicom_upload
-SOURCEDIR     = source
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/environment.yml

-
-name: dicom_upload_docs
-channels:
-  - conda-forge
-dependencies:
-- python=3.5
-- nodejs
-- numpy
-- sphinx
-- nbsphinx
-- jupyter_sphinx

docs/make.bat

-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=dicom_upload
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd

docs/source/_static/helper.js

-var cache_require = window.require;
-
-window.addEventListener('load', function() {
-  window.require = cache_require;
-});