diff --git a/.gitignore b/.gitignore
index d1678e0df6ff2617b3e5aa6ca3c79d21fb35e923..014eb23bc12a1a9d01367a132e2f8130f0e3cb0e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,159 +1,15 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
+*.egg-info/
+.ipynb_checkpoints/
dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-# Usually these files are written by a python script from a template
-# before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask instance folder
-instance/
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-docs/source/_static/embed-bundle.js
-docs/source/_static/embed-bundle.js.map
-
-# PyBuilder
-target/
-
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# dotenv
-.env
-
-# virtualenv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-
-# Rope project settings
-.ropeproject
-
-# =========================
-# Operating System Files
-# =========================
+build/
+*.py[cod]
+node_modules/
-# OSX
-# =========================
+# Compiled javascript
+dicom_upload/static/
+# OS X
.DS_Store
-.AppleDouble
-.LSOverride
-
-# Thumbnails
-._*
-
-# Files that might appear in the root of a volume
-.DocumentRevisions-V100
-.fseventsd
-.Spotlight-V100
-.TemporaryItems
-.Trashes
-.VolumeIcon.icns
-
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
-
-# Windows
-# =========================
-
-# Windows image file caches
-Thumbs.db
-ehthumbs.db
-
-# Folder config file
-Desktop.ini
-
-# Recycle Bin used on file shares
-$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
diff --git a/MANIFEST b/MANIFEST
deleted file mode 100644
index 05d4d105017082169159ac0ec5a02bb805aa56d8..0000000000000000000000000000000000000000
--- a/MANIFEST
+++ /dev/null
@@ -1,48 +0,0 @@
-# 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
diff --git a/MANIFEST.in b/MANIFEST.in
index cca0ee3270c6695e9686a83260276e67e383a171..fcb5c45216aba3a6b0232fc69bbe2b510324e68a 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,39 +1,2 @@
-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
diff --git a/README.md b/README.md
index 39ab7a09082aa2426792526e42742234e9ed07a7..a5c67efd33229c2f39b7cc63ac8afb9e96fbe611 100644
--- a/README.md
+++ b/README.md
@@ -1,37 +1,35 @@
-# dicom-upload
+dicom-upload
+===============================
-[](https://travis-ci.org/jsc/dicom_upload)
-[](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
-```
diff --git a/RELEASE.md b/RELEASE.md
new file mode 100644
index 0000000000000000000000000000000000000000..aad40c1125c6730f28db9a8ef3e9051bca8585db
--- /dev/null
+++ b/RELEASE.md
@@ -0,0 +1,22 @@
+- 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
diff --git a/dicom-upload.json b/dicom-upload.json
new file mode 100644
index 0000000000000000000000000000000000000000..b08c155d80937ee75a065787b096395ec4c34d93
--- /dev/null
+++ b/dicom-upload.json
@@ -0,0 +1,5 @@
+{
+ "load_extensions": {
+ "dicom-upload/extension": true
+ }
+}
diff --git a/dicom_upload.json b/dicom_upload.json
deleted file mode 100644
index da0c02f018b55a2a6ce466e9bd3bb46182db4a6f..0000000000000000000000000000000000000000
--- a/dicom_upload.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
- "load_extensions": {
- "dicom_upload/extension": true
- }
-}
diff --git a/dicom_upload/__init__.py b/dicom_upload/__init__.py
index 30766ea8054e1b7dd4cfd3d9814af086bc1c3693..bb6c2c3167002cb85a398643ded8c49d5229114c 100644
--- a/dicom_upload/__init__.py
+++ b/dicom_upload/__init__.py
@@ -1,10 +1,28 @@
-#!/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'
+ }]
diff --git a/dicom_upload/_frontend.py b/dicom_upload/_frontend.py
index 4c6cb8f6ea01842b50ad69b4e24f49a7f0441e57..a52119a27b7f145c720e303419dc930fb5b3a3cd 100644
--- a/dicom_upload/_frontend.py
+++ b/dicom_upload/_frontend.py
@@ -1,12 +1,6 @@
-#!/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"
diff --git a/dicom_upload/_version.py b/dicom_upload/_version.py
index ac15a29926e8c3e5d986e8f6c63e7056c7b1069d..f4cbb9d6b23e61e6d08070c6bb1541abcf977c2f 100644
--- a/dicom_upload/_version.py
+++ b/dicom_upload/_version.py
@@ -1,8 +1,9 @@
-#!/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]))
diff --git a/dicom_upload/nbextension/__init__.py b/dicom_upload/nbextension/__init__.py
deleted file mode 100644
index 5530d4df0b2721be1771fd436f56aefb785f050e..0000000000000000000000000000000000000000
--- a/dicom_upload/nbextension/__init__.py
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/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'
- }]
diff --git a/dicom_upload/nbextension/static/extension.js b/dicom_upload/nbextension/static/extension.js
deleted file mode 100644
index 2929289f82046abd8ea05de8604d974eafca8c1a..0000000000000000000000000000000000000000
--- a/dicom_upload/nbextension/static/extension.js
+++ /dev/null
@@ -1,17 +0,0 @@
-// 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() {}
- };
-});
diff --git a/dicom_upload/tests/__init__.py b/dicom_upload/tests/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/dicom_upload/tests/conftest.py b/dicom_upload/tests/conftest.py
deleted file mode 100644
index 20a88fb1eeaae59526ed78035c1c08ca41aace60..0000000000000000000000000000000000000000
--- a/dicom_upload/tests/conftest.py
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/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)
diff --git a/dicom_upload/tests/test_example.py b/dicom_upload/tests/test_example.py
deleted file mode 100644
index 49ce42dd844acccfa05e97eecca211df9d45ca98..0000000000000000000000000000000000000000
--- a/dicom_upload/tests/test_example.py
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/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'
diff --git a/dicom_upload/tests/test_nbextension_path.py b/dicom_upload/tests/test_nbextension_path.py
deleted file mode 100644
index 541cccf41af955b7a04a6059ffc61b60c8bb0c96..0000000000000000000000000000000000000000
--- a/dicom_upload/tests/test_nbextension_path.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/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)
diff --git a/dicom_upload/widget_upload.py b/dicom_upload/widget_upload.py
index 6a66aaa73027bf7ffd272074fa7237097c6d2346..35ab61cc2e6baf9d43b4feef5808f4784c72f192 100644
--- a/dicom_upload/widget_upload.py
+++ b/dicom_upload/widget_upload.py
@@ -20,11 +20,12 @@ from ipywidgets.widgets.widget_button import ButtonStyle
from ipywidgets.widgets.widget_description import DescriptionWidget
from traitlets import (
- default, Unicode, Dict, List, Int, Bool, Bytes, CaselessStrEnum
+ default, Unicode, Dict, List, Int, Bool, Bytes, CaselessStrEnum
)
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)
@@ -58,9 +62,9 @@ class Uploader(DescriptionWidget, ValueWidget):
# Needed for uploading using the Notebook Server RestAPI.
token = Unicode(help='Jupyter API token').tag(sync=True)
upload_url = Unicode('http://localhost:8888/api/contents/',
- help='http(s)://notebook_url/api/contents/').tag(sync=True)
- password = Unicode(None, allow_none=True,
- help="If set, encrypts DICOM files with the password.").tag(sync=True)
+ help='http(s)://notebook_url/api/contents/').tag(sync=True)
+ password = Unicode(None, allow_none=True,
+ help="If set, encrypts DICOM files with the password.").tag(sync=True)
# Variables set on the JavaScript side.
files = List().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.
@@ -85,4 +88,4 @@ class Uploader(DescriptionWidget, ValueWidget):
def upload(self):
"""Uploads file(s) via the JS fetch API."""
- self._upload = True
\ No newline at end of file
+ self._upload = True
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index e169612810c1777bab6614fe13b508fe4ee9986d..0000000000000000000000000000000000000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# 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)
diff --git a/docs/environment.yml b/docs/environment.yml
deleted file mode 100644
index cbb38d46e6c20d1ead98bafe24de2415bb77e8b0..0000000000000000000000000000000000000000
--- a/docs/environment.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-
-name: dicom_upload_docs
-channels:
- - conda-forge
-dependencies:
-- python=3.5
-- nodejs
-- numpy
-- sphinx
-- nbsphinx
-- jupyter_sphinx
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index d1fb5f7149d2ce263b909ad5c5786f310b5087e7..0000000000000000000000000000000000000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,36 +0,0 @@
-@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
diff --git a/docs/source/_static/helper.js b/docs/source/_static/helper.js
deleted file mode 100644
index cb2e2a819f59dba528c5830c315b3f617d62a429..0000000000000000000000000000000000000000
--- a/docs/source/_static/helper.js
+++ /dev/null
@@ -1,5 +0,0 @@
-var cache_require = window.require;
-
-window.addEventListener('load', function() {
- window.require = cache_require;
-});
diff --git a/docs/source/conf.py b/docs/source/conf.py
deleted file mode 100644
index f07c3f2b0b46c73fe5c0d6f337901e702061b0c6..0000000000000000000000000000000000000000
--- a/docs/source/conf.py
+++ /dev/null
@@ -1,208 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
-# dicom_upload documentation build configuration file
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.viewcode',
- 'sphinx.ext.intersphinx',
- 'sphinx.ext.napoleon',
- 'sphinx.ext.todo',
- 'nbsphinx',
- 'jupyter_sphinx.embed_widgets',
- 'nbsphinx_link',
-]
-
-# Ensure our extension is available:
-import sys
-from os.path import dirname, join as pjoin
-docs = dirname(dirname(__file__))
-root = dirname(docs)
-sys.path.insert(0, root)
-sys.path.insert(0, pjoin(docs, 'sphinxext'))
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = 'dicom_upload'
-copyright = '2019, Alice Grosch'
-author = 'Alice Grosch'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-
-
-# get version from python package:
-import os
-here = os.path.dirname(__file__)
-repo = os.path.join(here, '..', '..')
-_version_py = os.path.join(repo, 'dicom_upload', '_version.py')
-version_ns = {}
-with open(_version_py) as f:
- exec(f.read(), version_ns)
-
-# The short X.Y version.
-version = '%i.%i' % version_ns['version_info'][:2]
-# The full version, including alpha/beta/rc tags.
-release = version_ns['__version__']
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['**.ipynb_checkpoints']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-
-# -- Options for HTML output ----------------------------------------------
-
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'dicom_uploaddoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
- # The paper size ('letterpaper' or 'a4paper').
- #
- # 'papersize': 'letterpaper',
-
- # The font size ('10pt', '11pt' or '12pt').
- #
- # 'pointsize': '10pt',
-
- # Additional stuff for the LaTeX preamble.
- #
- # 'preamble': '',
-
- # Latex figure (float) alignment
- #
- # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-# author, documentclass [howto, manual, or own class]).
-latex_documents = [
- (master_doc, 'dicom_upload.tex', 'dicom_upload Documentation',
- 'Alice Grosch', 'manual'),
-]
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- (master_doc,
- 'dicom_upload',
- 'dicom_upload Documentation',
- [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- (master_doc,
- 'dicom_upload',
- 'dicom_upload Documentation',
- author,
- 'dicom_upload',
- 'Upload DICOM files with removed headers.',
- 'Miscellaneous'),
-]
-
-
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
-
-# Read The Docs
-# on_rtd is whether we are on readthedocs.org, this line of code grabbed from
-# docs.readthedocs.org
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-
-if not on_rtd: # only import and set the theme if we're building docs locally
- import sphinx_rtd_theme
- html_theme = 'sphinx_rtd_theme'
- html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-
-# otherwise, readthedocs.org uses their theme by default, so no need to specify it
-
-
-# Uncomment this line if you have know exceptions in your included notebooks
-# that nbsphinx complains about:
-#
-nbsphinx_allow_errors = True # exception ipstruct.py ipython_genutils
-
-
-def setup(app):
- app.setup_extension('jupyter_sphinx.embed_widgets')
- def add_scripts(app):
- for fname in ['helper.js', 'embed-bundle.js']:
- if not os.path.exists(os.path.join(here, '_static', fname)):
- app.warn('missing javascript file: %s' % fname)
- app.add_javascript(fname)
- app.connect('builder-inited', add_scripts)
diff --git a/docs/source/develop-install.rst b/docs/source/develop-install.rst
deleted file mode 100644
index 6893eb14db78a0a1aefaa916369c9f6fa8840a9b..0000000000000000000000000000000000000000
--- a/docs/source/develop-install.rst
+++ /dev/null
@@ -1,31 +0,0 @@
-
-Developer install
-=================
-
-
-To install a developer version of dicom_upload, you will first need to clone
-the repository::
-
- git clone https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload.git
- cd dicom-upload
-
-Next, install it with a develop install using pip::
-
- pip install -e .
-
-
-If you are planning on working on the JS/frontend code, you should also do
-a link installation of the extension::
-
- jupyter nbextension install [--sys-prefix / --user / --system] --symlink --py dicom_upload
-
- jupyter nbextension enable [--sys-prefix / --user / --system] --py dicom_upload
-
-with the `appropriate flag`_. Or, if you are using Jupyterlab::
-
- jupyter labextension install .
-
-
-.. links
-
-.. _`appropriate flag`: https://jupyter-notebook.readthedocs.io/en/stable/extending/frontend_extensions.html#installing-and-enabling-extensions
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
deleted file mode 100644
index 26b2bd282d251c000fd8ce348744939f2061d144..0000000000000000000000000000000000000000
--- a/docs/source/examples/index.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-
-Examples
-========
-
-This section contains several examples generated from Jupyter notebooks.
-The widgets have been embedded into the page for demonstrative pruposes.
-
-.. todo::
-
- Add links to notebooks in examples folder similar to the initial
- one. This is a manual step to ensure only those examples that
- are suited for inclusion are used.
-
-
-.. toctree::
- :glob:
-
- *
diff --git a/docs/source/examples/introduction.nblink b/docs/source/examples/introduction.nblink
deleted file mode 100644
index 258bb0f010ea5a1338ec4f11679f645f9fa7ccf3..0000000000000000000000000000000000000000
--- a/docs/source/examples/introduction.nblink
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "path": "../../../examples/introduction.ipynb"
-}
diff --git a/docs/source/index.rst b/docs/source/index.rst
deleted file mode 100644
index c172176864c57168b3054f6486f8661722a25cc3..0000000000000000000000000000000000000000
--- a/docs/source/index.rst
+++ /dev/null
@@ -1,49 +0,0 @@
-
-dicom_upload
-=====================================
-
-Version: |release|
-
-Upload DICOM files with removed headers.
-
-
-Quickstart
-----------
-
-To get started with dicom_upload, install with pip::
-
- pip install dicom_upload
-
-or with conda::
-
- conda install dicom_upload
-
-
-Contents
---------
-
-.. toctree::
- :maxdepth: 2
- :caption: Installation and usage
-
- installing
- introduction
-
-.. toctree::
- :maxdepth: 1
-
- examples/index
-
-
-.. toctree::
- :maxdepth: 2
- :caption: Development
-
- develop-install
-
-
-.. links
-
-.. _`Jupyter widgets`: https://jupyter.org/widgets.html
-
-.. _`notebook`: https://jupyter-notebook.readthedocs.io/en/latest/
diff --git a/docs/source/installing.rst b/docs/source/installing.rst
deleted file mode 100644
index 06fc02113f5a333b6e4905f291997a2ce07f30de..0000000000000000000000000000000000000000
--- a/docs/source/installing.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-
-.. _installation:
-
-Installation
-============
-
-
-The simplest way to install dicom_upload is via pip::
-
- pip install dicom_upload
-
-or via conda::
-
- conda install dicom_upload
-
-
-If you installed via pip, and notebook version < 5.3, you will also have to
-install / configure the front-end extension as well. If you are using classic
-notebook (as opposed to Jupyterlab), run::
-
- jupyter nbextension install [--sys-prefix / --user / --system] --py dicom_upload
-
- jupyter nbextension enable [--sys-prefix / --user / --system] --py dicom_upload
-
-with the `appropriate flag`_. If you are using Jupyterlab, install the extension
-with::
-
- jupyter labextension install dicom-upload
-
-If you are installing using conda, these commands should be unnecessary, but If
-you need to run them the commands should be the same (just make sure you choose the
-`--sys-prefix` flag).
-
-
-.. links
-
-.. _`appropriate flag`: https://jupyter-notebook.readthedocs.io/en/stable/extending/frontend_extensions.html#installing-and-enabling-extensions
diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst
deleted file mode 100644
index ad0edd44f2396d7e34696000ad052789ef187536..0000000000000000000000000000000000000000
--- a/docs/source/introduction.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-=============
-Introduction
-=============
-
-.. todo::
-
- add prose explaining project purpose and usage here
diff --git a/examples/introduction.ipynb b/examples/example.ipynb
similarity index 97%
rename from examples/introduction.ipynb
rename to examples/example.ipynb
index 0e495ff7be91284fb0c2e03f7a475f438404abed..c0bf0a67bea050c0b16613f496e6e941182f63bc 100644
--- a/examples/introduction.ipynb
+++ b/examples/example.ipynb
@@ -154,7 +154,7 @@
"metadata": {},
"outputs": [],
"source": [
- "!openssl aes-256-cbc -d -md md5 -in IM000001 -k $password | base64 -d > IM000001.decoded"
+ "!openssl aes-256-cbc -d -md md5 -in IM000001 -k \"$password\" | base64 -D > IM000001.decoded"
]
},
{
@@ -193,7 +193,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.9"
+ "version": "3.6.5"
}
},
"nbformat": 4,
diff --git a/js/README.md b/js/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..9faa6b6d594a57f7c415b9c5cb6ca275882babd6
--- /dev/null
+++ b/js/README.md
@@ -0,0 +1,11 @@
+Upload DICOM files with patient und study data removed from header
+
+Package Install
+---------------
+
+**Prerequisites**
+- [node](http://nodejs.org/)
+
+```bash
+npm install --save dicom-upload
+```
diff --git a/js/lib/embed.js b/js/lib/embed.js
new file mode 100644
index 0000000000000000000000000000000000000000..9d4f3fa6db94005e3f149e33e8c4b9ae29ba8cf2
--- /dev/null
+++ b/js/lib/embed.js
@@ -0,0 +1,9 @@
+// Entry point for the unpkg bundle containing custom model definitions.
+//
+// It differs from the notebook bundle in that it does not need to define a
+// dynamic baseURL for the static assets and may load some css that would
+// already be loaded by the notebook otherwise.
+
+// Export widget models and views, and the npm package version number.
+module.exports = require('./widget.js');
+module.exports['version'] = require('../package.json').version;
diff --git a/js/lib/extension.js b/js/lib/extension.js
new file mode 100644
index 0000000000000000000000000000000000000000..8990a5fd9060150421ca5f257a17e1db420171e7
--- /dev/null
+++ b/js/lib/extension.js
@@ -0,0 +1,25 @@
+// This file contains the javascript that is run when the notebook is loaded.
+// It contains some requirejs configuration and the `load_ipython_extension`
+// which is required for any notebook extension.
+//
+// Some static assets may be required by the custom widget javascript. The base
+// url for the notebook is not known at build time and is therefore computed
+// dynamically.
+__webpack_public_path__ = document.querySelector('body').getAttribute('data-base-url') + 'nbextensions/dicom-upload';
+
+
+// Configure requirejs
+if (window.require) {
+ window.require.config({
+ map: {
+ "*" : {
+ "dicom-upload": "nbextensions/dicom-upload/index",
+ }
+ }
+ });
+}
+
+// Export the required load_ipython_extension
+module.exports = {
+ load_ipython_extension: function() {}
+};
diff --git a/js/lib/index.js b/js/lib/index.js
new file mode 100644
index 0000000000000000000000000000000000000000..a51a33254d886940cd27f8decf49a95e0f0a2771
--- /dev/null
+++ b/js/lib/index.js
@@ -0,0 +1,3 @@
+// Export widget models and views, and the npm package version number.
+module.exports = require('./widget.js');
+module.exports['version'] = require('../package.json').version;
diff --git a/js/lib/labplugin.js b/js/lib/labplugin.js
new file mode 100644
index 0000000000000000000000000000000000000000..a5a71def20fb24d90484fe66100ce31fd55d99ca
--- /dev/null
+++ b/js/lib/labplugin.js
@@ -0,0 +1,16 @@
+var plugin = require('./index');
+var base = require('@jupyter-widgets/base');
+
+module.exports = {
+ id: 'dicom-upload',
+ requires: [base.IJupyterWidgetRegistry],
+ activate: function(app, widgets) {
+ widgets.registerWidget({
+ name: 'dicom-upload',
+ version: plugin.version,
+ exports: plugin
+ });
+ },
+ autoStart: true
+};
+
diff --git a/js/lib/widget.js b/js/lib/widget.js
new file mode 100644
index 0000000000000000000000000000000000000000..1d503c9a582d8613a2ce265578a14999a1c3ca7a
--- /dev/null
+++ b/js/lib/widget.js
@@ -0,0 +1,306 @@
+// Copyright (c) Juelich Supercomputing Centre (JSC)
+// Distributed under the terms of the Modified BSD License.
+
+var _ = require('lodash');
+var widgets = require('@jupyter-widgets/base');
+var CryptoJS = require('crypto-js');
+var SparkMD5 = require('spark-md5');
+
+import { parseDicom } from 'dicom-parser';
+import { clone } from 'underscore';
+
+export var UploaderModel = widgets.DOMWidgetModel.extend({
+ defaults: _.extend(widgets.DOMWidgetModel.prototype.defaults(), {
+ _model_name: 'UploaderModel',
+ _view_name: 'UploaderView',
+ _model_module: 'dicom-upload',
+ _view_module: 'dicom-upload',
+ _model_module_version: '0.1.3',
+ _view_module_version: '0.1.3',
+
+ accept: '',
+ description: 'Upload',
+ tooltip: '',
+ disabled: false,
+ icon: 'upload',
+ button_style: '',
+ multiple: false,
+ metadata: [],
+ style: null,
+
+ token: '',
+ upload_url: 'http://localhost:8888/api/contents/',
+ _upload: false,
+ hash: '',
+ files: [],
+ responses: [],
+ finished: false,
+ })
+});
+
+export var UploaderView = widgets.DOMWidgetView.extend({
+ render() {
+ this.el.classList.add('jupyter-widgets');
+ this.el.classList.add('widget-upload');
+ this.el.classList.add('jupyter-button');
+
+ this.fileInput = document.createElement('input');
+ this.fileInput.type = 'file';
+ this.fileInput.style.display = 'none';
+ this.el.appendChild(this.fileInput);
+
+ this.el.addEventListener('click', () => {
+ this.fileInput.click();
+ });
+
+ this.fileInput.addEventListener('click', () => {
+ this.fileInput.value = '';
+ });
+
+ this.fileInput.addEventListener('change', () => {
+ // Reset upload to `false` when new files are selected.
+ this.model.set('_upload', false);
+ this.model.set('finished', false);
+ this.model.set('hash', '');
+
+ let fileList = Array.from(this.fileInput.files)
+ this.model.set({
+ 'fileList': fileList
+ });
+
+ let files = [];
+ let responses = [];
+ fileList.forEach(file => {
+ files.push(file.name);
+ responses.push(null);
+ });
+ this.model.set({
+ 'files': files
+ });
+ this.model.set({
+ 'responses': responses
+ });
+ this.touch();
+ });
+
+ this.model.on('change:_upload', this.upload_files, this);
+ this.model.on('change:files', this.create_hash, this);
+
+ this.listenTo(this.model, 'change:button_style', this.update_button_style);
+ this.set_button_style();
+ this.update();
+ },
+
+ update() {
+ this.el.disabled = this.model.get('disabled');
+ this.el.setAttribute('title', this.model.get('tooltip'));
+
+ let description = `${this.model.get('description')}`
+ let icon = this.model.get('icon');
+ if (description.length || icon.length) {
+ this.el.textContent = '';
+ if (icon.length) {
+ let i = document.createElement('i');
+ i.classList.add('fa');
+ i.classList.add('fa-' + icon);
+ if (description.length === 0) {
+ i.classList.add('center');
+ }
+ this.el.appendChild(i);
+ }
+ this.el.appendChild(document.createTextNode(description));
+ }
+
+ this.fileInput.accept = this.model.get('accept');
+ this.fileInput.multiple = this.model.get('multiple');
+
+ // return super.update();
+ return widgets.DOMWidgetView.prototype.update();
+ },
+
+ update_button_style() {
+ let class_map = {
+ primary: ['mod-primary'],
+ success: ['mod-success'],
+ info: ['mod-info'],
+ warning: ['mod-warning'],
+ danger: ['mod-danger']
+ }
+ this.update_mapped_classes(class_map, 'button_style', this.el);
+ },
+
+ set_button_style() {
+ let class_map = {
+ primary: ['mod-primary'],
+ success: ['mod-success'],
+ info: ['mod-info'],
+ warning: ['mod-warning'],
+ danger: ['mod-danger']
+ }
+ this.set_mapped_classes(class_map, 'button_style', this.el);
+ },
+
+ create_hash() {
+ let fileList = this.model.get('fileList');
+ let hashList = Array(fileList.length);
+
+ let that = this;
+
+ fileList.forEach(function (file, index) {
+ let reader = new FileReader();
+ reader.onloadend = function (evt) {
+ hashList[index] = SparkMD5.ArrayBuffer.hash(reader.result);
+ if (index == fileList.length - 1) {
+ let spark = new SparkMD5();
+ hashList.forEach(function (hash) {
+ spark.append(hash);
+ })
+ let hexHash = spark.end();
+ console.log(hexHash);
+ that.model.set({
+ 'hash': hexHash,
+ });
+ that.touch();
+ }
+ }
+ reader.readAsArrayBuffer(file);
+ })
+ },
+
+ upload_files() {
+ if (this.model.get('_upload') == false) { return; }
+
+ let token = "token " + this.model.get('token');
+ let upload_url = this.model.get('upload_url');
+ let that = this;
+
+ function parseFile(file, index) {
+
+ function Uint8ToBase64(u8Arr) {
+ let CHUNK_SIZE = 0x8000; //arbitrary number
+ let index = 0;
+ let length = u8Arr.length;
+ let result = '';
+ while (index < length) {
+ let slice = u8Arr.subarray(index, Math.min(index + CHUNK_SIZE, length));
+ result += String.fromCharCode.apply(null, slice);
+ index += CHUNK_SIZE;
+ }
+ return btoa(result);
+ }
+
+ function removeHeader(arrayBuffer) {
+ let byteArray = new Uint8Array(arrayBuffer);
+ // Parse the arrayBuffer. Return null if the file is not a DICOM file.
+ try {
+ var dataSet = parseDicom(byteArray);
+ }
+ catch (e) {
+ return null;
+ }
+
+ // Slice the byteArray and remove elements of group 0008 and 0010
+ let tags = Object.keys(dataSet.elements);
+ let group8_first_tag = _.find(tags, (t) => {
+ return t.startsWith('x0008');
+ });
+ let group8_offset = dataSet.elements[group8_first_tag].dataOffset - 8;
+ let group10_last_tag = _.findLast(tags, (t) => {
+ return t.startsWith('x0010');
+ });
+ let group10_offset = dataSet.elements[group10_last_tag].dataOffset
+ + dataSet.elements[group10_last_tag].length;
+
+ let slice1 = byteArray.slice(0, group8_offset);
+ let slice2 = byteArray.slice(group10_offset);
+
+ // Create a new Uint8 array with the sliced parts of the original array.
+ let slicedByteArray = new Uint8Array(slice1.length + slice2.length);
+ slicedByteArray.set(slice1);
+ slicedByteArray.set(slice2, slice1.length);
+ return slicedByteArray;
+ }
+
+ let readEventHandler = function (evt) {
+ if (evt.target.error == null) {
+ let slicedByteArray = removeHeader(evt.target.result);
+ if (slicedByteArray == null) {
+ let responses = clone(that.model.get('responses'));
+ responses[index] = 'Not a dicom file';
+ that.model.set('responses', responses)
+
+ if (index == fileList.length - 1) {
+ that.model.set('finished', true);
+ }
+ that.touch();
+ return;
+ }
+ let b64String = Uint8ToBase64(slicedByteArray);
+
+ let model = { name: file.name, path: file.name }
+ model["type"] = 'file';
+ model["format"] = 'base64';
+ if (that.model.get('password') == null) {
+ model["content"] = b64String;
+ } else { // Encrypt
+ let key = that.model.get('password');
+ model["content"] = CryptoJS.AES.encrypt(b64String, key).toString();
+ }
+
+ fetch(upload_url + file.name, {
+ method: "PUT",
+ headers: {
+ "Authorization": token,
+ "Content-Type": "application/json",
+ },
+ body: JSON.stringify(model),
+ })
+ .then(function (response) {
+ if (!response.ok) {
+ throw response
+ }
+ return response.json()
+ })
+ .then(function (myJson) {
+ console.log(JSON.stringify(myJson));
+
+ let responses = clone(that.model.get('responses'));
+ responses[index] = 'ok';
+ that.model.set('responses', responses)
+
+ if (index == fileList.length - 1) {
+ that.model.set('finished', true);
+ }
+ that.touch()
+ return;
+ })
+ .catch(function (err) {
+ console.log(err);
+
+ let responses = clone(that.model.get('responses'));
+ responses[index] = err.status + ' ' + err.statusText;
+ that.model.set('responses', responses)
+
+ if (index == fileList.length - 1) {
+ that.model.set('finished', true);
+ }
+ that.touch();
+ })
+
+ } else {
+ console.log("Read error: " + evt.target.error);
+ return;
+ }
+ }
+
+ let reader = new FileReader();
+ reader.onload = readEventHandler;
+ reader.readAsArrayBuffer(file);
+ }
+
+ let fileList = this.model.get('fileList');
+ fileList.forEach(function (file, index) {
+ parseFile(file, index);
+ });
+ }
+});
\ No newline at end of file
diff --git a/js/package.json b/js/package.json
new file mode 100644
index 0000000000000000000000000000000000000000..595c763ef168adf0fbcac9623eca29fa30f7e886
--- /dev/null
+++ b/js/package.json
@@ -0,0 +1,52 @@
+{
+ "name": "dicom-upload",
+ "version": "0.1.3",
+ "description": "Upload DICOM files with patient und study data removed from header",
+ "keywords": [
+ "jupyter",
+ "widgets",
+ "ipython",
+ "ipywidgets",
+ "jupyterlab-extension"
+ ],
+ "files": [
+ "lib/**/*.js",
+ "dist/*.js"
+ ],
+ "homepage": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload",
+ "bugs": {
+ "url": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload/issues"
+ },
+ "license": "BSD-3-Clause",
+ "author": {
+ "name": "Alice Grosch",
+ "email": "a.grosch@fz-juelich.de"
+ },
+ "main": "lib/index.js",
+ "repository": {
+ "type": "git",
+ "url": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload"
+ },
+ "scripts": {
+ "clean": "rimraf dist/",
+ "prepublish": "webpack",
+ "build": "webpack",
+ "watch": "webpack --watch --mode=development",
+ "test": "echo \"Error: no test specified\" && exit 1"
+ },
+ "devDependencies": {
+ "webpack": "^3.5.5",
+ "rimraf": "^2.6.1"
+ },
+ "dependencies": {
+ "@jupyter-widgets/base": "^1.1 || ^2|| ^3",
+ "lodash": "^4.17.4",
+ "crypto-js": "^3.1.9-1",
+ "dicom-parser": "^1.8.4",
+ "spark-md5": "^3.0.0",
+ "underscore": "^1.9.1"
+ },
+ "jupyterlab": {
+ "extension": "lib/labplugin"
+ }
+}
\ No newline at end of file
diff --git a/js/webpack.config.js b/js/webpack.config.js
new file mode 100644
index 0000000000000000000000000000000000000000..a8259cae1a3330d67a9b9856e621026847e01f74
--- /dev/null
+++ b/js/webpack.config.js
@@ -0,0 +1,72 @@
+var path = require('path');
+var version = require('./package.json').version;
+
+// Custom webpack rules are generally the same for all webpack bundles, hence
+// stored in a separate local variable.
+var rules = [
+ { test: /\.css$/, use: ['style-loader', 'css-loader']}
+]
+
+
+module.exports = [
+ {// Notebook extension
+ //
+ // This bundle only contains the part of the JavaScript that is run on
+ // load of the notebook. This section generally only performs
+ // some configuration for requirejs, and provides the legacy
+ // "load_ipython_extension" function which is required for any notebook
+ // extension.
+ //
+ entry: './lib/extension.js',
+ output: {
+ filename: 'extension.js',
+ path: path.resolve(__dirname, '..', 'dicom_upload', 'static'),
+ libraryTarget: 'amd'
+ }
+ },
+ {// Bundle for the notebook containing the custom widget views and models
+ //
+ // This bundle contains the implementation for the custom widget views and
+ // custom widget.
+ // It must be an amd module
+ //
+ entry: './lib/index.js',
+ output: {
+ filename: 'index.js',
+ path: path.resolve(__dirname, '..', 'dicom_upload', 'static'),
+ libraryTarget: 'amd'
+ },
+ devtool: 'source-map',
+ module: {
+ rules: rules
+ },
+ externals: ['@jupyter-widgets/base']
+ },
+ {// Embeddable dicom-upload bundle
+ //
+ // This bundle is generally almost identical to the notebook bundle
+ // containing the custom widget views and models.
+ //
+ // The only difference is in the configuration of the webpack public path
+ // for the static assets.
+ //
+ // It will be automatically distributed by unpkg to work with the static
+ // widget embedder.
+ //
+ // The target bundle is always `dist/index.js`, which is the path required
+ // by the custom widget embedder.
+ //
+ entry: './lib/embed.js',
+ output: {
+ filename: 'index.js',
+ path: path.resolve(__dirname, 'dist'),
+ libraryTarget: 'amd',
+ publicPath: 'https://unpkg.com/dicom-upload@' + version + '/dist/'
+ },
+ devtool: 'source-map',
+ module: {
+ rules: rules
+ },
+ externals: ['@jupyter-widgets/base']
+ }
+];
diff --git a/js/yarn.lock b/js/yarn.lock
new file mode 100644
index 0000000000000000000000000000000000000000..49c996589ead22cf3c2903979ecbc46eedf090ab
--- /dev/null
+++ b/js/yarn.lock
@@ -0,0 +1,2852 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+"@jupyter-widgets/base@^1.1 || ^2|| ^3":
+ version "3.0.0"
+ resolved "https://registry.yarnpkg.com/@jupyter-widgets/base/-/base-3.0.0.tgz#3996d566cddb742d275b007e0713de1e17f55a44"
+ integrity sha512-un1ZTHALCwE/SAYk2gEaonYM1JoaFyhosN8a3y2bhl4N26yCB3dP1PqGHLsAFur6ZB7fwuWwBEkIZx+nOwstAQ==
+ dependencies:
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+ "@lumino/messaging" "^1.2.1"
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+ "@types/backbone" "^1.4.1"
+ "@types/lodash" "^4.14.134"
+ backbone "1.2.3"
+ base64-js "^1.2.1"
+ jquery "^3.1.1"
+ lodash "^4.17.4"
+
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+ version "4.1.0"
+ resolved "https://registry.yarnpkg.com/@jupyterlab/coreutils/-/coreutils-4.1.0.tgz#ac6cee0558b7c15786e0a210ac3b40a86aec8e84"
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+ moment "^2.24.0"
+ path-posix "~1.0.0"
+ url-parse "~1.4.7"
+
+"@jupyterlab/nbformat@^2.1.0":
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+ resolved "https://registry.yarnpkg.com/@jupyterlab/nbformat/-/nbformat-2.1.0.tgz#cff41b91c647d32c30f1587ff12e6a3ee6d91ba0"
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+ node-fetch "^2.6.0"
+ ws "^7.2.0"
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diff --git a/package-lock.json b/package-lock.json
deleted file mode 100644
index e20badd3f3a431477e974476871488ad30ab7843..0000000000000000000000000000000000000000
--- a/package-lock.json
+++ /dev/null
@@ -1,7089 +0,0 @@
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- },
- "xtend": {
- "version": "4.0.2",
- "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
- "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
- "dev": true
- },
- "y18n": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz",
- "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w==",
- "dev": true
- },
- "yallist": {
- "version": "2.1.2",
- "resolved": "https://registry.npmjs.org/yallist/-/yallist-2.1.2.tgz",
- "integrity": "sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI=",
- "dev": true
- },
- "yargs": {
- "version": "13.2.4",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.2.4.tgz",
- "integrity": "sha512-HG/DWAJa1PAnHT9JAhNa8AbAv3FPaiLzioSjCcmuXXhP8MlpHO5vwls4g4j6n30Z74GVQj8Xa62dWVx1QCGklg==",
- "dev": true,
- "requires": {
- "cliui": "^5.0.0",
- "find-up": "^3.0.0",
- "get-caller-file": "^2.0.1",
- "os-locale": "^3.1.0",
- "require-directory": "^2.1.1",
- "require-main-filename": "^2.0.0",
- "set-blocking": "^2.0.0",
- "string-width": "^3.0.0",
- "which-module": "^2.0.0",
- "y18n": "^4.0.0",
- "yargs-parser": "^13.1.0"
- },
- "dependencies": {
- "find-up": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/find-up/-/find-up-3.0.0.tgz",
- "integrity": "sha512-1yD6RmLI1XBfxugvORwlck6f75tYL+iR0jqwsOrOxMZyGYqUuDhJ0l4AXdO1iX/FTs9cBAMEk1gWSEx1kSbylg==",
- "dev": true,
- "requires": {
- "locate-path": "^3.0.0"
- }
- }
- }
- },
- "yargs-parser": {
- "version": "13.1.1",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.1.tgz",
- "integrity": "sha512-oVAVsHz6uFrg3XQheFII8ESO2ssAf9luWuAd6Wexsu4F3OtIW0o8IribPXYrD4WC24LWtPrJlGy87y5udK+dxQ==",
- "dev": true,
- "requires": {
- "camelcase": "^5.0.0",
- "decamelize": "^1.2.0"
- }
- },
- "yeast": {
- "version": "0.1.2",
- "resolved": "https://registry.npmjs.org/yeast/-/yeast-0.1.2.tgz",
- "integrity": "sha1-AI4G2AlDIMNy28L47XagymyKxBk=",
- "dev": true
- }
- }
-}
diff --git a/package.json b/package.json
deleted file mode 100644
index e92487b984e5f61f085bd115b62255ce8c115c40..0000000000000000000000000000000000000000
--- a/package.json
+++ /dev/null
@@ -1,89 +0,0 @@
-{
- "name": "dicom-upload",
- "version": "0.1.3",
- "description": "Upload DICOM files with removed headers.",
- "keywords": [
- "jupyter",
- "jupyterlab",
- "jupyterlab-extension",
- "widgets"
- ],
- "files": [
- "lib/**/*.js",
- "dist/*.js"
- ],
- "homepage": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload",
- "bugs": {
- "url": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload/issues"
- },
- "license": "BSD-3-Clause",
- "author": {
- "name": "Alice Grosch",
- "email": "a.grosch@fz-juelich.de"
- },
- "main": "lib/index.js",
- "types": "./lib/index.d.ts",
- "repository": {
- "type": "git",
- "url": "https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload"
- },
- "scripts": {
- "build": "npm run build:lib && npm run build:nbextension",
- "build:labextension": "npm run clean:labextension && mkdirp dicom_upload/labextension && cd dicom_upload/labextension && npm pack ../..",
- "build:lib": "tsc",
- "build:nbextension": "webpack -p",
- "build:all": "npm run build:labextension && npm run build:nbextension",
- "clean": "npm run clean:lib && npm run clean:nbextension",
- "clean:lib": "rimraf lib",
- "clean:labextension": "rimraf dicom_upload/labextension",
- "clean:nbextension": "rimraf dicom_upload/nbextension/static/index.js",
- "prepack": "npm run build:lib",
- "test": "npm run test:firefox",
- "test:chrome": "karma start --browsers=Chrome tests/karma.conf.js",
- "test:debug": "karma start --browsers=Chrome --singleRun=false --debug=true tests/karma.conf.js",
- "test:firefox": "karma start --browsers=Firefox tests/karma.conf.js",
- "test:ie": "karma start --browsers=IE tests/karma.conf.js",
- "watch": "npm-run-all -p watch:*",
- "watch:lib": "tsc -w",
- "watch:nbextension": "webpack --watch"
- },
- "dependencies": {
- "@jupyter-widgets/base": "^1.1.10 || ^2",
- "crypto-js": "^3.1.9-1",
- "dicom-parser": "^1.8.4",
- "lodash": "^4.17.15",
- "spark-md5": "^3.0.0",
- "underscore": "^1.9.1"
- },
- "devDependencies": {
- "@phosphor/application": "^1.6.0",
- "@phosphor/widgets": "^1.6.0",
- "@types/expect.js": "^0.3.29",
- "@types/mocha": "^5.2.5",
- "@types/node": "^10.11.6",
- "@types/webpack-env": "^1.13.6",
- "css-loader": "^3.2.0",
- "expect.js": "^0.3.1",
- "fs-extra": "^7.0.0",
- "karma": "^3.0.0",
- "karma-chrome-launcher": "^2.2.0",
- "karma-firefox-launcher": "^1.1.0",
- "karma-ie-launcher": "^1.0.0",
- "karma-mocha": "^1.3.0",
- "karma-mocha-reporter": "^2.2.5",
- "karma-typescript": "^3.0.13",
- "mkdirp": "^0.5.1",
- "mocha": "^5.2.0",
- "npm-run-all": "^4.1.3",
- "rimraf": "^2.6.2",
- "source-map-loader": "^0.2.4",
- "style-loader": "^1.0.0",
- "ts-loader": "^5.2.1",
- "typescript": "~3.1.2",
- "webpack": "^4.20.2",
- "webpack-cli": "^3.1.2"
- },
- "jupyterlab": {
- "extension": "lib/plugin"
- }
-}
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index 0dcd2d7f984d8b6989f16584b80a7ffa82069a25..0000000000000000000000000000000000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-[pytest]
-testpaths = dicom_upload/tests examples
-norecursedirs = node_modules .ipynb_checkpoints
-addopts = --nbval --current-env
diff --git a/readthedocs.yml b/readthedocs.yml
deleted file mode 100644
index c972d9ccf24afee0885a5bfb0ace67ebfdec6cda..0000000000000000000000000000000000000000
--- a/readthedocs.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-type: sphinx
-python:
- version: 3.5
- pip_install: true
- extra_requirements:
- - examples
- - docs
-conda:
- file: docs/environment.yml
diff --git a/setup.cfg b/setup.cfg
index d085b61a2332d435627d6be98b62b18018cbba65..3c6e79cf31da1c0433d2fa666bf50b53f6359f26 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,2 @@
[bdist_wheel]
universal=1
-
-[metadata]
-description-file = README.md
-license_file = LICENSE.txt
diff --git a/setup.py b/setup.py
index 47d2142b422d5f818c7913e2b097c53cd3fb68f4..14b464bcc4ad2835130aca6ee36cc645f77bd85f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,116 +1,178 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
from __future__ import print_function
-from glob import glob
-from os.path import join as pjoin
-
-
-from setupbase import (
- create_cmdclass, install_npm, ensure_targets,
- find_packages, combine_commands, ensure_python,
- get_version, HERE
-)
-
-from setuptools import setup
-
-
-# The name of the project
-name = 'dicom_upload'
-
-# Ensure a valid python version
-ensure_python('>=3.4')
-
-# Get our version
-version = get_version(pjoin(name, '_version.py'))
-
-nb_path = pjoin(HERE, name, 'nbextension', 'static')
-lab_path = pjoin(HERE, name, 'labextension')
-
-# Representative files that should exist after a successful build
-jstargets = [
- pjoin(nb_path, 'index.js'),
- pjoin(HERE, 'lib', 'plugin.js'),
-]
-
-package_data_spec = {
- name: [
- 'nbextension/static/*.*js*',
- 'labextension/*.tgz'
+from setuptools import setup, find_packages, Command
+from setuptools.command.sdist import sdist
+from setuptools.command.build_py import build_py
+from setuptools.command.egg_info import egg_info
+from subprocess import check_call
+import os
+import sys
+import platform
+
+here = os.path.dirname(os.path.abspath(__file__))
+node_root = os.path.join(here, 'js')
+is_repo = os.path.exists(os.path.join(here, '.git'))
+
+npm_path = os.pathsep.join([
+ os.path.join(node_root, 'node_modules', '.bin'),
+ os.environ.get('PATH', os.defpath),
+])
+
+from distutils import log
+log.set_verbosity(log.DEBUG)
+log.info('setup.py entered')
+log.info('$PATH=%s' % os.environ['PATH'])
+
+LONG_DESCRIPTION = 'Upload DICOM files with patient und study data removed from header'
+
+def js_prerelease(command, strict=False):
+ """decorator for building minified js/css prior to another command"""
+ class DecoratedCommand(command):
+ def run(self):
+ jsdeps = self.distribution.get_command_obj('jsdeps')
+ if not is_repo and all(os.path.exists(t) for t in jsdeps.targets):
+ # sdist, nothing to do
+ command.run(self)
+ return
+
+ try:
+ self.distribution.run_command('jsdeps')
+ except Exception as e:
+ missing = [t for t in jsdeps.targets if not os.path.exists(t)]
+ if strict or missing:
+ log.warn('rebuilding js and css failed')
+ if missing:
+ log.error('missing files: %s' % missing)
+ raise e
+ else:
+ log.warn('rebuilding js and css failed (not a problem)')
+ log.warn(str(e))
+ command.run(self)
+ update_package_data(self.distribution)
+ return DecoratedCommand
+
+def update_package_data(distribution):
+ """update package_data to catch changes during setup"""
+ build_py = distribution.get_command_obj('build_py')
+ # distribution.package_data = find_package_data()
+ # re-init build_py options which load package_data
+ build_py.finalize_options()
+
+
+class NPM(Command):
+ description = 'install package.json dependencies using npm'
+
+ user_options = []
+
+ node_modules = os.path.join(node_root, 'node_modules')
+
+ targets = [
+ os.path.join(here, 'dicom_upload', 'static', 'extension.js'),
+ os.path.join(here, 'dicom_upload', 'static', 'index.js')
]
-}
-data_files_spec = [
- ('share/jupyter/nbextensions/dicom_upload',
- nb_path, '*.js*'),
- ('share/jupyter/lab/extensions', lab_path, '*.tgz'),
- ('etc/jupyter/nbconfig/notebook.d' , HERE, 'dicom_upload.json')
-]
-
-
-cmdclass = create_cmdclass('jsdeps', package_data_spec=package_data_spec,
- data_files_spec=data_files_spec)
-cmdclass['jsdeps'] = combine_commands(
- install_npm(HERE, build_cmd='build:all'),
- ensure_targets(jstargets),
-)
-
-
-setup_args = dict(
- name = name,
- description = 'Upload DICOM files with removed headers.',
- version = version,
- scripts = glob(pjoin('scripts', '*')),
- cmdclass = cmdclass,
- packages = find_packages(),
- author = 'Alice Grosch',
- author_email = 'a.grosch@fz-juelich.de',
- url = 'https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_extras/dicom-upload',
- license = 'BSD',
- platforms = "Linux, Mac OS X, Windows",
- keywords = ['Jupyter', 'Widgets', 'IPython'],
- classifiers = [
+ def initialize_options(self):
+ pass
+
+ def finalize_options(self):
+ pass
+
+ def get_npm_name(self):
+ npmName = 'npm';
+ if platform.system() == 'Windows':
+ npmName = 'npm.cmd';
+
+ return npmName;
+
+ def has_npm(self):
+ npmName = self.get_npm_name();
+ try:
+ check_call([npmName, '--version'])
+ return True
+ except:
+ return False
+
+ def should_run_npm_install(self):
+ package_json = os.path.join(node_root, 'package.json')
+ node_modules_exists = os.path.exists(self.node_modules)
+ return self.has_npm()
+
+ def run(self):
+ has_npm = self.has_npm()
+ if not has_npm:
+ log.error("`npm` unavailable. If you're running this command using sudo, make sure `npm` is available to sudo")
+
+ env = os.environ.copy()
+ env['PATH'] = npm_path
+
+ if self.should_run_npm_install():
+ log.info("Installing build dependencies with npm. This may take a while...")
+ npmName = self.get_npm_name();
+ check_call([npmName, 'install'], cwd=node_root, stdout=sys.stdout, stderr=sys.stderr)
+ os.utime(self.node_modules, None)
+
+ for t in self.targets:
+ if not os.path.exists(t):
+ msg = 'Missing file: %s' % t
+ if not has_npm:
+ msg += '\nnpm is required to build a development version of a widget extension'
+ raise ValueError(msg)
+
+ # update package data in case this created new files
+ update_package_data(self.distribution)
+
+version_ns = {}
+with open(os.path.join(here, 'dicom_upload', '_version.py')) as f:
+ exec(f.read(), {}, version_ns)
+
+setup_args = {
+ 'name': 'dicom_upload',
+ 'version': version_ns['__version__'],
+ 'description': 'Upload DICOM files with patient und study data removed from header',
+ 'long_description': LONG_DESCRIPTION,
+ 'include_package_data': True,
+ 'data_files': [
+ ('share/jupyter/nbextensions/dicom-upload', [
+ 'dicom_upload/static/extension.js',
+ 'dicom_upload/static/index.js',
+ 'dicom_upload/static/index.js.map',
+ ],),
+ ('etc/jupyter/nbconfig/notebook.d' ,['dicom-upload.json'])
+ ],
+ 'install_requires': [
+ 'ipywidgets>=7.0.0',
+ ],
+ 'packages': find_packages(),
+ 'zip_safe': False,
+ 'cmdclass': {
+ 'build_py': js_prerelease(build_py),
+ 'egg_info': js_prerelease(egg_info),
+ 'sdist': js_prerelease(sdist, strict=True),
+ 'jsdeps': NPM,
+ },
+
+ 'author': 'Alice Grosch',
+ 'author_email': 'a.grosch@fz-juelich.de',
+ 'url': 'https://github.com/jsc/dicom-upload',
+ 'keywords': [
+ 'ipython',
+ 'jupyter',
+ 'widgets',
+ ],
+ 'classifiers': [
+ 'Development Status :: 4 - Beta',
+ 'Framework :: IPython',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
- 'License :: OSI Approved :: BSD License',
- 'Programming Language :: Python',
+ 'Topic :: Multimedia :: Graphics',
+ 'Programming Language :: Python :: 2',
+ 'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
+ 'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
- 'Framework :: Jupyter',
- ],
- include_package_data = True,
- install_requires = [
- 'ipywidgets>=7.0.0',
],
- extras_require = {
- 'test': [
- 'pytest>=3.6',
- 'pytest-cov',
- 'nbval',
- ],
- 'examples': [
- # Any requirements for the examples to run
- ],
- 'docs': [
- 'sphinx>=1.5',
- 'recommonmark',
- 'sphinx_rtd_theme',
- 'nbsphinx>=0.2.13,<0.4.0',
- 'jupyter_sphinx',
- 'nbsphinx-link',
- 'pytest_check_links',
- 'pypandoc',
- ],
- },
- entry_points = {
- },
-)
+}
-if __name__ == '__main__':
- setup(**setup_args)
+setup(**setup_args)
diff --git a/setupbase.py b/setupbase.py
deleted file mode 100644
index b0792eac4500112da6c82f852e57fe95d6268d0d..0000000000000000000000000000000000000000
--- a/setupbase.py
+++ /dev/null
@@ -1,718 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-"""
-This file originates from the 'jupyter-packaging' package, and
-contains a set of useful utilities for including npm packages
-within a Python package.
-"""
-from collections import defaultdict
-from os.path import join as pjoin
-import io
-import os
-import functools
-import pipes
-import re
-import shlex
-import subprocess
-import sys
-
-
-# BEFORE importing distutils, remove MANIFEST. distutils doesn't properly
-# update it when the contents of directories change.
-if os.path.exists('MANIFEST'): os.remove('MANIFEST')
-
-
-from distutils.cmd import Command
-from distutils.command.build_py import build_py
-from distutils.command.sdist import sdist
-from distutils import log
-
-from setuptools.command.develop import develop
-from setuptools.command.bdist_egg import bdist_egg
-
-try:
- from wheel.bdist_wheel import bdist_wheel
-except ImportError:
- bdist_wheel = None
-
-if sys.platform == 'win32':
- from subprocess import list2cmdline
-else:
- def list2cmdline(cmd_list):
- return ' '.join(map(pipes.quote, cmd_list))
-
-
-__version__ = '0.2.0'
-
-# ---------------------------------------------------------------------------
-# Top Level Variables
-# ---------------------------------------------------------------------------
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-is_repo = os.path.exists(pjoin(HERE, '.git'))
-node_modules = pjoin(HERE, 'node_modules')
-
-SEPARATORS = os.sep if os.altsep is None else os.sep + os.altsep
-
-npm_path = ':'.join([
- pjoin(HERE, 'node_modules', '.bin'),
- os.environ.get('PATH', os.defpath),
-])
-
-if "--skip-npm" in sys.argv:
- print("Skipping npm install as requested.")
- skip_npm = True
- sys.argv.remove("--skip-npm")
-else:
- skip_npm = False
-
-
-# ---------------------------------------------------------------------------
-# Public Functions
-# ---------------------------------------------------------------------------
-
-def get_version(file, name='__version__'):
- """Get the version of the package from the given file by
- executing it and extracting the given `name`.
- """
- path = os.path.realpath(file)
- version_ns = {}
- with io.open(path, encoding="utf8") as f:
- exec(f.read(), {}, version_ns)
- return version_ns[name]
-
-
-def ensure_python(specs):
- """Given a list of range specifiers for python, ensure compatibility.
- """
- if not isinstance(specs, (list, tuple)):
- specs = [specs]
- v = sys.version_info
- part = '%s.%s' % (v.major, v.minor)
- for spec in specs:
- if part == spec:
- return
- try:
- if eval(part + spec):
- return
- except SyntaxError:
- pass
- raise ValueError('Python version %s unsupported' % part)
-
-
-def find_packages(top=HERE):
- """
- Find all of the packages.
- """
- packages = []
- for d, dirs, _ in os.walk(top, followlinks=True):
- if os.path.exists(pjoin(d, '__init__.py')):
- packages.append(os.path.relpath(d, top).replace(os.path.sep, '.'))
- elif d != top:
- # Do not look for packages in subfolders if current is not a package
- dirs[:] = []
- return packages
-
-
-def update_package_data(distribution):
- """update build_py options to get package_data changes"""
- build_py = distribution.get_command_obj('build_py')
- build_py.finalize_options()
-
-
-class bdist_egg_disabled(bdist_egg):
- """Disabled version of bdist_egg
-
- Prevents setup.py install performing setuptools' default easy_install,
- which it should never ever do.
- """
- def run(self):
- sys.exit("Aborting implicit building of eggs. Use `pip install .` "
- " to install from source.")
-
-
-def create_cmdclass(prerelease_cmd=None, package_data_spec=None,
- data_files_spec=None):
- """Create a command class with the given optional prerelease class.
-
- Parameters
- ----------
- prerelease_cmd: (name, Command) tuple, optional
- The command to run before releasing.
- package_data_spec: dict, optional
- A dictionary whose keys are the dotted package names and
- whose values are a list of glob patterns.
- data_files_spec: list, optional
- A list of (path, dname, pattern) tuples where the path is the
- `data_files` install path, dname is the source directory, and the
- pattern is a glob pattern.
-
- Notes
- -----
- We use specs so that we can find the files *after* the build
- command has run.
-
- The package data glob patterns should be relative paths from the package
- folder containing the __init__.py file, which is given as the package
- name.
- e.g. `dict(foo=['./bar/*', './baz/**'])`
-
- The data files directories should be absolute paths or relative paths
- from the root directory of the repository. Data files are specified
- differently from `package_data` because we need a separate path entry
- for each nested folder in `data_files`, and this makes it easier to
- parse.
- e.g. `('share/foo/bar', 'pkgname/bizz, '*')`
- """
- wrapped = [prerelease_cmd] if prerelease_cmd else []
- if package_data_spec or data_files_spec:
- wrapped.append('handle_files')
- wrapper = functools.partial(_wrap_command, wrapped)
- handle_files = _get_file_handler(package_data_spec, data_files_spec)
-
- if 'bdist_egg' in sys.argv:
- egg = wrapper(bdist_egg, strict=True)
- else:
- egg = bdist_egg_disabled
-
- cmdclass = dict(
- build_py=wrapper(build_py, strict=is_repo),
- bdist_egg=egg,
- sdist=wrapper(sdist, strict=True),
- handle_files=handle_files,
- )
-
- if bdist_wheel:
- cmdclass['bdist_wheel'] = wrapper(bdist_wheel, strict=True)
-
- cmdclass['develop'] = wrapper(develop, strict=True)
- return cmdclass
-
-
-def command_for_func(func):
- """Create a command that calls the given function."""
-
- class FuncCommand(BaseCommand):
-
- def run(self):
- func()
- update_package_data(self.distribution)
-
- return FuncCommand
-
-
-def run(cmd, **kwargs):
- """Echo a command before running it. Defaults to repo as cwd"""
- log.info('> ' + list2cmdline(cmd))
- kwargs.setdefault('cwd', HERE)
- kwargs.setdefault('shell', os.name == 'nt')
- if not isinstance(cmd, (list, tuple)) and os.name != 'nt':
- cmd = shlex.split(cmd)
- cmd_path = which(cmd[0])
- if not cmd_path:
- sys.exit("Aborting. Could not find cmd (%s) in path. "
- "If command is not expected to be in user's path, "
- "use an absolute path." % cmd[0])
- cmd[0] = cmd_path
- return subprocess.check_call(cmd, **kwargs)
-
-
-def is_stale(target, source):
- """Test whether the target file/directory is stale based on the source
- file/directory.
- """
- if not os.path.exists(target):
- return True
- target_mtime = recursive_mtime(target) or 0
- return compare_recursive_mtime(source, cutoff=target_mtime)
-
-
-class BaseCommand(Command):
- """Empty command because Command needs subclasses to override too much"""
- user_options = []
-
- def initialize_options(self):
- pass
-
- def finalize_options(self):
- pass
-
- def get_inputs(self):
- return []
-
- def get_outputs(self):
- return []
-
-
-def combine_commands(*commands):
- """Return a Command that combines several commands."""
-
- class CombinedCommand(Command):
- user_options = []
-
- def initialize_options(self):
- self.commands = []
- for C in commands:
- self.commands.append(C(self.distribution))
- for c in self.commands:
- c.initialize_options()
-
- def finalize_options(self):
- for c in self.commands:
- c.finalize_options()
-
- def run(self):
- for c in self.commands:
- c.run()
- return CombinedCommand
-
-
-def compare_recursive_mtime(path, cutoff, newest=True):
- """Compare the newest/oldest mtime for all files in a directory.
-
- Cutoff should be another mtime to be compared against. If an mtime that is
- newer/older than the cutoff is found it will return True.
- E.g. if newest=True, and a file in path is newer than the cutoff, it will
- return True.
- """
- if os.path.isfile(path):
- mt = mtime(path)
- if newest:
- if mt > cutoff:
- return True
- elif mt < cutoff:
- return True
- for dirname, _, filenames in os.walk(path, topdown=False):
- for filename in filenames:
- mt = mtime(pjoin(dirname, filename))
- if newest: # Put outside of loop?
- if mt > cutoff:
- return True
- elif mt < cutoff:
- return True
- return False
-
-
-def recursive_mtime(path, newest=True):
- """Gets the newest/oldest mtime for all files in a directory."""
- if os.path.isfile(path):
- return mtime(path)
- current_extreme = None
- for dirname, dirnames, filenames in os.walk(path, topdown=False):
- for filename in filenames:
- mt = mtime(pjoin(dirname, filename))
- if newest: # Put outside of loop?
- if mt >= (current_extreme or mt):
- current_extreme = mt
- elif mt <= (current_extreme or mt):
- current_extreme = mt
- return current_extreme
-
-
-def mtime(path):
- """shorthand for mtime"""
- return os.stat(path).st_mtime
-
-
-def install_npm(path=None, build_dir=None, source_dir=None, build_cmd='build', force=False, npm=None):
- """Return a Command for managing an npm installation.
-
- Note: The command is skipped if the `--skip-npm` flag is used.
-
- Parameters
- ----------
- path: str, optional
- The base path of the node package. Defaults to the repo root.
- build_dir: str, optional
- The target build directory. If this and source_dir are given,
- the JavaScript will only be build if necessary.
- source_dir: str, optional
- The source code directory.
- build_cmd: str, optional
- The npm command to build assets to the build_dir.
- npm: str or list, optional.
- The npm executable name, or a tuple of ['node', executable].
- """
-
- class NPM(BaseCommand):
- description = 'install package.json dependencies using npm'
-
- def run(self):
- if skip_npm:
- log.info('Skipping npm-installation')
- return
- node_package = path or HERE
- node_modules = pjoin(node_package, 'node_modules')
- is_yarn = os.path.exists(pjoin(node_package, 'yarn.lock'))
-
- npm_cmd = npm
-
- if npm is None:
- if is_yarn:
- npm_cmd = ['yarn']
- else:
- npm_cmd = ['npm']
-
- if not which(npm_cmd[0]):
- log.error("`{0}` unavailable. If you're running this command "
- "using sudo, make sure `{0}` is available to sudo"
- .format(npm_cmd[0]))
- return
-
- if force or is_stale(node_modules, pjoin(node_package, 'package.json')):
- log.info('Installing build dependencies with npm. This may '
- 'take a while...')
- run(npm_cmd + ['install'], cwd=node_package)
- if build_dir and source_dir and not force:
- should_build = is_stale(build_dir, source_dir)
- else:
- should_build = True
- if should_build:
- run(npm_cmd + ['run', build_cmd], cwd=node_package)
-
- return NPM
-
-
-def ensure_targets(targets):
- """Return a Command that checks that certain files exist.
-
- Raises a ValueError if any of the files are missing.
-
- Note: The check is skipped if the `--skip-npm` flag is used.
- """
-
- class TargetsCheck(BaseCommand):
- def run(self):
- if skip_npm:
- log.info('Skipping target checks')
- return
- missing = [t for t in targets if not os.path.exists(t)]
- if missing:
- raise ValueError(('missing files: %s' % missing))
-
- return TargetsCheck
-
-
-# `shutils.which` function copied verbatim from the Python-3.3 source.
-def which(cmd, mode=os.F_OK | os.X_OK, path=None):
- """Given a command, mode, and a PATH string, return the path which
- conforms to the given mode on the PATH, or None if there is no such
- file.
- `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
- of os.environ.get("PATH"), or can be overridden with a custom search
- path.
- """
-
- # Check that a given file can be accessed with the correct mode.
- # Additionally check that `file` is not a directory, as on Windows
- # directories pass the os.access check.
- def _access_check(fn, mode):
- return (os.path.exists(fn) and os.access(fn, mode) and
- not os.path.isdir(fn))
-
- # Short circuit. If we're given a full path which matches the mode
- # and it exists, we're done here.
- if _access_check(cmd, mode):
- return cmd
-
- path = (path or os.environ.get("PATH", os.defpath)).split(os.pathsep)
-
- if sys.platform == "win32":
- # The current directory takes precedence on Windows.
- if os.curdir not in path:
- path.insert(0, os.curdir)
-
- # PATHEXT is necessary to check on Windows.
- pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
- # See if the given file matches any of the expected path extensions.
- # This will allow us to short circuit when given "python.exe".
- matches = [cmd for ext in pathext if cmd.lower().endswith(ext.lower())]
- # If it does match, only test that one, otherwise we have to try
- # others.
- files = [cmd] if matches else [cmd + ext.lower() for ext in pathext]
- else:
- # On other platforms you don't have things like PATHEXT to tell you
- # what file suffixes are executable, so just pass on cmd as-is.
- files = [cmd]
-
- seen = set()
- for dir in path:
- dir = os.path.normcase(dir)
- if dir not in seen:
- seen.add(dir)
- for thefile in files:
- name = os.path.join(dir, thefile)
- if _access_check(name, mode):
- return name
- return None
-
-
-# ---------------------------------------------------------------------------
-# Private Functions
-# ---------------------------------------------------------------------------
-
-
-def _wrap_command(cmds, cls, strict=True):
- """Wrap a setup command
-
- Parameters
- ----------
- cmds: list(str)
- The names of the other commands to run prior to the command.
- strict: boolean, optional
- Wether to raise errors when a pre-command fails.
- """
- class WrappedCommand(cls):
-
- def run(self):
- if not getattr(self, 'uninstall', None):
- try:
- [self.run_command(cmd) for cmd in cmds]
- except Exception:
- if strict:
- raise
- else:
- pass
- # update package data
- update_package_data(self.distribution)
-
- result = cls.run(self)
- return result
- return WrappedCommand
-
-
-def _get_file_handler(package_data_spec, data_files_spec):
- """Get a package_data and data_files handler command.
- """
- class FileHandler(BaseCommand):
-
- def run(self):
- package_data = self.distribution.package_data
- package_spec = package_data_spec or dict()
-
- for (key, patterns) in package_spec.items():
- package_data[key] = _get_package_data(key, patterns)
-
- self.distribution.data_files = _get_data_files(
- data_files_spec, self.distribution.data_files
- )
-
- return FileHandler
-
-
-def _glob_pjoin(*parts):
- """Join paths for glob processing"""
- if parts[0] in ('.', ''):
- parts = parts[1:]
- return pjoin(*parts).replace(os.sep, '/')
-
-
-def _get_data_files(data_specs, existing, top=HERE):
- """Expand data file specs into valid data files metadata.
-
- Parameters
- ----------
- data_specs: list of tuples
- See [create_cmdclass] for description.
- existing: list of tuples
- The existing distrubution data_files metadata.
-
- Returns
- -------
- A valid list of data_files items.
- """
- # Extract the existing data files into a staging object.
- file_data = defaultdict(list)
- for (path, files) in existing or []:
- file_data[path] = files
-
- # Extract the files and assign them to the proper data
- # files path.
- for (path, dname, pattern) in data_specs or []:
- if os.path.isabs(dname):
- dname = os.path.relpath(dname, top)
- dname = dname.replace(os.sep, '/')
- offset = 0 if dname in ('.', '') else len(dname) + 1
- files = _get_files(_glob_pjoin(dname, pattern), top=top)
- for fname in files:
- # Normalize the path.
- root = os.path.dirname(fname)
- full_path = _glob_pjoin(path, root[offset:])
- print(dname, root, full_path, offset)
- if full_path.endswith('/'):
- full_path = full_path[:-1]
- file_data[full_path].append(fname)
-
- # Construct the data files spec.
- data_files = []
- for (path, files) in file_data.items():
- data_files.append((path, files))
- return data_files
-
-
-def _get_files(file_patterns, top=HERE):
- """Expand file patterns to a list of paths.
-
- Parameters
- -----------
- file_patterns: list or str
- A list of glob patterns for the data file locations.
- The globs can be recursive if they include a `**`.
- They should be relative paths from the top directory or
- absolute paths.
- top: str
- the directory to consider for data files
-
- Note:
- Files in `node_modules` are ignored.
- """
- if not isinstance(file_patterns, (list, tuple)):
- file_patterns = [file_patterns]
-
- for i, p in enumerate(file_patterns):
- if os.path.isabs(p):
- file_patterns[i] = os.path.relpath(p, top)
-
- matchers = [_compile_pattern(p) for p in file_patterns]
-
- files = set()
-
- for root, dirnames, filenames in os.walk(top):
- # Don't recurse into node_modules
- if 'node_modules' in dirnames:
- dirnames.remove('node_modules')
- for m in matchers:
- for filename in filenames:
- fn = os.path.relpath(_glob_pjoin(root, filename), top)
- fn = fn.replace(os.sep, '/')
- if m(fn):
- files.add(fn.replace(os.sep, '/'))
-
- return list(files)
-
-
-def _get_package_data(root, file_patterns=None):
- """Expand file patterns to a list of `package_data` paths.
-
- Parameters
- -----------
- root: str
- The relative path to the package root from `HERE`.
- file_patterns: list or str, optional
- A list of glob patterns for the data file locations.
- The globs can be recursive if they include a `**`.
- They should be relative paths from the root or
- absolute paths. If not given, all files will be used.
-
- Note:
- Files in `node_modules` are ignored.
- """
- if file_patterns is None:
- file_patterns = ['*']
- return _get_files(file_patterns, _glob_pjoin(HERE, root))
-
-
-def _compile_pattern(pat, ignore_case=True):
- """Translate and compile a glob pattern to a regular expression matcher."""
- if isinstance(pat, bytes):
- pat_str = pat.decode('ISO-8859-1')
- res_str = _translate_glob(pat_str)
- res = res_str.encode('ISO-8859-1')
- else:
- res = _translate_glob(pat)
- flags = re.IGNORECASE if ignore_case else 0
- return re.compile(res, flags=flags).match
-
-
-def _iexplode_path(path):
- """Iterate over all the parts of a path.
-
- Splits path recursively with os.path.split().
- """
- (head, tail) = os.path.split(path)
- if not head or (not tail and head == path):
- if head:
- yield head
- if tail or not head:
- yield tail
- return
- for p in _iexplode_path(head):
- yield p
- yield tail
-
-
-def _translate_glob(pat):
- """Translate a glob PATTERN to a regular expression."""
- translated_parts = []
- for part in _iexplode_path(pat):
- translated_parts.append(_translate_glob_part(part))
- os_sep_class = '[%s]' % re.escape(SEPARATORS)
- res = _join_translated(translated_parts, os_sep_class)
- return '{res}\\Z(?ms)'.format(res=res)
-
-
-def _join_translated(translated_parts, os_sep_class):
- """Join translated glob pattern parts.
-
- This is different from a simple join, as care need to be taken
- to allow ** to match ZERO or more directories.
- """
- res = ''
- for part in translated_parts[:-1]:
- if part == '.*':
- # drop separator, since it is optional
- # (** matches ZERO or more dirs)
- res += part
- else:
- res += part + os_sep_class
-
- if translated_parts[-1] == '.*':
- # Final part is **
- res += '.+'
- # Follow stdlib/git convention of matching all sub files/directories:
- res += '({os_sep_class}?.*)?'.format(os_sep_class=os_sep_class)
- else:
- res += translated_parts[-1]
- return res
-
-
-def _translate_glob_part(pat):
- """Translate a glob PATTERN PART to a regular expression."""
- # Code modified from Python 3 standard lib fnmatch:
- if pat == '**':
- return '.*'
- i, n = 0, len(pat)
- res = []
- while i < n:
- c = pat[i]
- i = i + 1
- if c == '*':
- # Match anything but path separators:
- res.append('[^%s]*' % SEPARATORS)
- elif c == '?':
- res.append('[^%s]?' % SEPARATORS)
- elif c == '[':
- j = i
- if j < n and pat[j] == '!':
- j = j + 1
- if j < n and pat[j] == ']':
- j = j + 1
- while j < n and pat[j] != ']':
- j = j + 1
- if j >= n:
- res.append('\\[')
- else:
- stuff = pat[i:j].replace('\\', '\\\\')
- i = j + 1
- if stuff[0] == '!':
- stuff = '^' + stuff[1:]
- elif stuff[0] == '^':
- stuff = '\\' + stuff
- res.append('[%s]' % stuff)
- else:
- res.append(re.escape(c))
- return ''.join(res)
diff --git a/src/extension.ts b/src/extension.ts
deleted file mode 100644
index 046197954268f43d66fea6757070b0cda04f7d38..0000000000000000000000000000000000000000
--- a/src/extension.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-// Copyright (c) Jupyter Development Team.
-// Distributed under the terms of the Modified BSD License.
-
-// Entry point for the notebook bundle containing custom model definitions.
-//
-// Setup notebook base URL
-//
-// Some static assets may be required by the custom widget javascript. The base
-// url for the notebook is not known at build time and is therefore computed
-// dynamically.
-(window as any).__webpack_public_path__ = document.querySelector('body')!.getAttribute('data-base-url') + 'nbextensions/dicom_upload';
-
-export * from './index';
diff --git a/src/index.ts b/src/index.ts
deleted file mode 100644
index 54535d2cdd7cddb820acaf036512b136569e513c..0000000000000000000000000000000000000000
--- a/src/index.ts
+++ /dev/null
@@ -1,5 +0,0 @@
-// Copyright (c) Alice Grosch
-// Distributed under the terms of the Modified BSD License.
-
-export * from './version';
-export * from './widget';
diff --git a/src/plugin.ts b/src/plugin.ts
deleted file mode 100644
index 0ce3f1ff2e82706dc16c285c308072dfd678b7e4..0000000000000000000000000000000000000000
--- a/src/plugin.ts
+++ /dev/null
@@ -1,46 +0,0 @@
-// Copyright (c) Alice Grosch
-// Distributed under the terms of the Modified BSD License.
-
-import {
- Application, IPlugin
-} from '@phosphor/application';
-
-import {
- Widget
-} from '@phosphor/widgets';
-
-import {
- IJupyterWidgetRegistry
- } from '@jupyter-widgets/base';
-
-import * as widgetExports from './widget';
-
-import {
- MODULE_NAME, MODULE_VERSION
-} from './version';
-
-const EXTENSION_ID = 'dicom-upload:plugin';
-
-/**
- * The example plugin.
- */
-const examplePlugin: IPlugin<Application<Widget>, void> = {
- id: EXTENSION_ID,
- requires: [IJupyterWidgetRegistry],
- activate: activateWidgetExtension,
- autoStart: true
-};
-
-export default examplePlugin;
-
-
-/**
- * Activate the widget extension.
- */
-function activateWidgetExtension(app: Application<Widget>, registry: IJupyterWidgetRegistry): void {
- registry.registerWidget({
- name: MODULE_NAME,
- version: MODULE_VERSION,
- exports: widgetExports,
- });
-}
diff --git a/src/version.ts b/src/version.ts
deleted file mode 100644
index d8fc73bb899053f46f735119db8a7c3f4b6e38fa..0000000000000000000000000000000000000000
--- a/src/version.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-// Copyright (c) Alice Grosch
-// Distributed under the terms of the Modified BSD License.
-
-const data = require('../package.json');
-
-/**
- * The _model_module_version/_view_module_version this package implements.
- *
- * The html widget manager assumes that this is the same as the npm package
- * version number.
- */
-export const MODULE_VERSION = data.version;
-
-/*
- * The current package name.
- */
-export const MODULE_NAME = data.name;
diff --git a/src/widget.ts b/src/widget.ts
deleted file mode 100644
index 3d89ef6485e84cc8b81cff8c37921aa7848dec55..0000000000000000000000000000000000000000
--- a/src/widget.ts
+++ /dev/null
@@ -1,329 +0,0 @@
-// Copyright (c) Juelich Supercomputing Centre (JSC)
-// Distributed under the terms of the Modified BSD License.
-
-import {
- DOMWidgetModel, DOMWidgetView, ISerializers
-} from '@jupyter-widgets/base';
-
-import {
- MODULE_NAME, MODULE_VERSION
-} from './version';
-
-import * as _ from 'lodash';
-import { parseDicom } from 'dicom-parser';
-import { clone } from 'underscore';
-
-import CryptoJS = require('crypto-js');
-import SparkMD5 = require('spark-md5');
-
-export
-class UploaderModel extends DOMWidgetModel {
- defaults() {
- return {...super.defaults(),
- _model_name: UploaderModel.model_name,
- _model_module: UploaderModel.model_module,
- _model_module_version: UploaderModel.model_module_version,
- _view_name: UploaderModel.view_name,
- _view_module: UploaderModel.view_module,
- _view_module_version: UploaderModel.view_module_version,
-
- accept: '',
- description: 'Upload',
- tooltip: '',
- disabled: false,
- icon: 'upload',
- button_style: '',
- multiple: false,
- metadata: [],
- style: null,
-
- token:'',
- upload_url: 'http://localhost:8888/api/contents/',
- _upload: false,
- hash: '',
- files: [],
- responses: [],
- finished: false,
- };
- }
-
- static serializers: ISerializers = {
- ...DOMWidgetModel.serializers,
- }
-
- static model_name = 'UploaderModel';
- static model_module = MODULE_NAME;
- static model_module_version = MODULE_VERSION;
- static view_name = 'UploaderView';
- static view_module = MODULE_NAME;
- static view_module_version = MODULE_VERSION;
-}
-
-
-export
-class UploaderView extends DOMWidgetView {
-
- el: HTMLButtonElement;
- fileInput: HTMLInputElement;
-
- render() {
- super.render();
-
- this.el.classList.add('jupyter-widgets');
- this.el.classList.add('widget-upload');
- this.el.classList.add('jupyter-button');
-
- this.fileInput = document.createElement('input');
- this.fileInput.type = 'file';
- this.fileInput.style.display = 'none';
- this.el.appendChild(this.fileInput);
-
- this.el.addEventListener('click', () => {
- this.fileInput.click();
- });
-
- this.fileInput.addEventListener('click', () => {
- this.fileInput.value = '';
- });
-
- this.fileInput.addEventListener('change', () => {
- // Reset upload to `false` when new files are selected.
- this.model.set('_upload', false);
- this.model.set('finished', false);
- this.model.set('hash', '');
-
- let fileList = Array.from(this.fileInput.files)
- this.model.set({
- 'fileList': fileList
- });
-
- let files = [];
- let responses = [];
- fileList.forEach(file => {
- files.push(file.name);
- responses.push(null);
- });
- this.model.set({
- 'files': files
- });
- this.model.set({
- 'responses': responses
- });
- this.touch();
- });
-
- this.model.on('change:_upload', this.upload_files, this);
- this.model.on('change:files', this.create_hash, this);
-
- this.listenTo(this.model, 'change:button_style', this.update_button_style);
- this.set_button_style();
- this.update();
- }
-
- update() {
- this.el.disabled = this.model.get('disabled');
- this.el.setAttribute('title', this.model.get('tooltip'));
-
- let description = `${this.model.get('description')}`
- let icon = this.model.get('icon');
- if (description.length || icon.length) {
- this.el.textContent = '';
- if (icon.length) {
- let i = document.createElement('i');
- i.classList.add('fa');
- i.classList.add('fa-' + icon);
- if (description.length === 0) {
- i.classList.add('center');
- }
- this.el.appendChild(i);
- }
- this.el.appendChild(document.createTextNode(description));
- }
-
- this.fileInput.accept = this.model.get('accept');
- this.fileInput.multiple = this.model.get('multiple');
-
- return super.update();
- }
-
- update_button_style() {
- this.update_mapped_classes(UploaderView.class_map, 'button_style', this.el);
- }
-
- set_button_style() {
- this.set_mapped_classes(UploaderView.class_map, 'button_style', this.el);
- }
-
- create_hash() {
- let fileList = this.model.get('fileList');
- let hashList = Array(fileList.length);
-
- let that = this;
-
- fileList.forEach(function (file, index) {
- let reader = new FileReader();
- reader.onloadend = function(evt) {
- hashList[index] = SparkMD5.ArrayBuffer.hash(reader.result);
- if (index == fileList.length - 1) {
- let spark = new SparkMD5();
- hashList.forEach(function (hash) {
- spark.append(hash);
- })
- let hexHash = spark.end();
- console.log(hexHash);
- that.model.set({
- 'hash': hexHash,
- });
- that.touch();
- }
- }
- reader.readAsArrayBuffer(file);
- })
- }
-
- upload_files() {
- if (this.model.get('_upload') == false) { return; }
-
- let token = "token " + this.model.get('token');
- let upload_url = this.model.get('upload_url');
- let that = this;
-
- function parseFile(file, index) {
-
- function Uint8ToBase64(u8Arr){
- let CHUNK_SIZE = 0x8000; //arbitrary number
- let index = 0;
- let length = u8Arr.length;
- let result = '';
- while (index < length) {
- let slice = u8Arr.subarray(index, Math.min(index + CHUNK_SIZE, length));
- result += String.fromCharCode.apply(null, slice);
- index += CHUNK_SIZE;
- }
- return btoa(result);
- }
-
- function removeHeader(arrayBuffer) {
- let byteArray = new Uint8Array(arrayBuffer);
- // Parse the arrayBuffer. Return null if the file is not a DICOM file.
- try {
- var dataSet = parseDicom(byteArray);
- }
- catch (e) {
- return null;
- }
-
- // Slice the byteArray and remove elements of group 0008 and 0010
- let tags = Object.keys(dataSet.elements);
- let group8_first_tag = _.find(tags, (t) => {
- return t.startsWith('x0008');
- });
- let group8_offset = dataSet.elements[group8_first_tag].dataOffset - 8;
- let group10_last_tag = _.findLast(tags, (t) => {
- return t.startsWith('x0010');
- });
- let group10_offset = dataSet.elements[group10_last_tag].dataOffset
- + dataSet.elements[group10_last_tag].length;
-
- let slice1 = byteArray.slice(0, group8_offset);
- let slice2 = byteArray.slice(group10_offset);
-
- // Create a new Uint8 array with the sliced parts of the original array.
- let slicedByteArray = new Uint8Array(slice1.length + slice2.length);
- slicedByteArray.set(slice1);
- slicedByteArray.set(slice2, slice1.length);
- return slicedByteArray;
- }
-
- let readEventHandler = function (evt) {
- if (evt.target.error == null) {
- let slicedByteArray = removeHeader(evt.target.result);
- if (slicedByteArray == null) {
- let responses = clone(that.model.get('responses'));
- responses[index] = 'Not a dicom file';
- that.model.set('responses', responses)
-
- if (index == fileList.length - 1) {
- that.model.set('finished', true);
- }
- that.touch();
- return;
- }
- let b64String = Uint8ToBase64(slicedByteArray);
-
- let model = { name: file.name, path: file.name }
- model["type"] = 'file';
- model["format"] = 'base64';
- if (that.model.get('password') == null) {
- model["content"] = b64String;
- } else { // Encrypt
- let key = that.model.get('password');
- model["content"] = CryptoJS.AES.encrypt(b64String, key).toString();
- }
-
- fetch(upload_url + file.name, {
- method: "PUT",
- headers: {
- "Authorization": token,
- "Content-Type": "application/json",
- },
- body: JSON.stringify(model),
- })
- .then(function (response) {
- if (!response.ok) {
- throw response
- }
- return response.json()
- })
- .then(function (myJson) {
- console.log(JSON.stringify(myJson));
-
- let responses = clone(that.model.get('responses'));
- responses[index] = 'ok';
- that.model.set('responses', responses)
-
- if (index == fileList.length - 1) {
- that.model.set('finished', true);
- }
- that.touch()
- return;
- })
- .catch(function (err) {
- console.log(err);
-
- let responses = clone(that.model.get('responses'));
- responses[index] = err.status + ' ' + err.statusText;
- that.model.set('responses', responses)
-
- if (index == fileList.length - 1) {
- that.model.set('finished', true);
- }
- that.touch();
- })
-
- } else {
- console.log("Read error: " + evt.target.error);
- return;
- }
- }
-
- let reader = new FileReader();
- reader.onload = readEventHandler;
- reader.readAsArrayBuffer(file);
-
- }
-
- let fileList = this.model.get('fileList');
- fileList.forEach(function (file, index) {
- parseFile(file, index);
- });
- }
-
- static class_map = {
- primary: ['mod-primary'],
- success: ['mod-success'],
- info: ['mod-info'],
- warning: ['mod-warning'],
- danger: ['mod-danger']
- };
-}
diff --git a/tests/karma.conf.js b/tests/karma.conf.js
deleted file mode 100644
index e9bb736108ab87d2ec17aebb5c3b6fb1a03a4ed7..0000000000000000000000000000000000000000
--- a/tests/karma.conf.js
+++ /dev/null
@@ -1,41 +0,0 @@
-module.exports = function (config) {
- config.set({
- basePath: '..',
- frameworks: ['mocha', 'karma-typescript'],
- reporters: ['mocha', 'karma-typescript'],
- client: {
- mocha: {
- timeout : 10000, // 10 seconds - upped from 2 seconds
- retries: 3 // Allow for slow server on CI.
- }
- },
- files: [
- { pattern: "tests/src/**/*.ts" },
- { pattern: "src/**/*.ts" },
- ],
- exclude: [
- "src/extension.ts",
- ],
- preprocessors: {
- '**/*.ts': ['karma-typescript']
- },
- browserNoActivityTimeout: 31000, // 31 seconds - upped from 10 seconds
- port: 9876,
- colors: true,
- singleRun: true,
- logLevel: config.LOG_INFO,
-
-
- karmaTypescriptConfig: {
- tsconfig: 'tests/tsconfig.json',
- reports: {
- "text-summary": "",
- "html": "coverage",
- "lcovonly": {
- "directory": "coverage",
- "filename": "coverage.lcov"
- }
- }
- }
- });
-};
diff --git a/tests/src/index.spec.ts b/tests/src/index.spec.ts
deleted file mode 100644
index efd598cd676aa9fa2c3b6003e7be2aed9a2b85d8..0000000000000000000000000000000000000000
--- a/tests/src/index.spec.ts
+++ /dev/null
@@ -1,38 +0,0 @@
-// Copyright (c) Jupyter Development Team.
-// Distributed under the terms of the Modified BSD License.
-
-import expect = require('expect.js');
-
-import {
- // Add any needed widget imports here (or from controls)
-} from '@jupyter-widgets/base';
-
-import {
- createTestModel
-} from './utils.spec';
-
-import {
- ExampleModel, ExampleView
-} from '../../src/'
-
-
-describe('Example', () => {
-
- describe('ExampleModel', () => {
-
- it('should be createable', () => {
- let model = createTestModel(ExampleModel);
- expect(model).to.be.an(ExampleModel);
- expect(model.get('value')).to.be('Hello World');
- });
-
- it('should be createable with a value', () => {
- let state = { value: 'Foo Bar!' }
- let model = createTestModel(ExampleModel, state);
- expect(model).to.be.an(ExampleModel);
- expect(model.get('value')).to.be('Foo Bar!');
- });
-
- });
-
-});
diff --git a/tests/src/utils.spec.ts b/tests/src/utils.spec.ts
deleted file mode 100644
index edf744b36069600aa84f34edc736ce2e0f564ca2..0000000000000000000000000000000000000000
--- a/tests/src/utils.spec.ts
+++ /dev/null
@@ -1,113 +0,0 @@
-// Copyright (c) Jupyter Development Team.
-// Distributed under the terms of the Modified BSD License.
-
-import * as widgets from '@jupyter-widgets/base';
-import * as services from '@jupyterlab/services';
-import * as Backbone from 'backbone';
-
-let numComms = 0;
-
-export
-class MockComm {
- target_name = 'dummy';
-
- constructor() {
- this.comm_id = `mock-comm-id-${numComms}`;
- numComms += 1;
- }
- on_close(fn: Function | null) {
- this._on_close = fn;
- }
- on_msg(fn: Function | null) {
- this._on_msg = fn;
- }
- _process_msg(msg: services.KernelMessage.ICommMsg) {
- if (this._on_msg) {
- return this._on_msg(msg);
- } else {
- return Promise.resolve();
- }
- }
- close(): string {
- if (this._on_close) {
- this._on_close();
- }
- return 'dummy';
- }
- send(): string {
- return 'dummy';
- }
-
- open(): string {
- return 'dummy';
- }
- comm_id: string;
- _on_msg: Function | null = null;
- _on_close: Function | null = null;
-}
-
-export
-class DummyManager extends widgets.ManagerBase<HTMLElement> {
- constructor() {
- super();
- this.el = window.document.createElement('div');
- }
-
- display_view(msg: services.KernelMessage.IMessage, view: Backbone.View<Backbone.Model>, options: any) {
- // TODO: make this a spy
- // TODO: return an html element
- return Promise.resolve(view).then(view => {
- this.el.appendChild(view.el);
- view.on('remove', () => console.log('view removed', view));
- return view.el;
- });
- }
-
- protected loadClass(className: string, moduleName: string, moduleVersion: string): Promise<any> {
- if (moduleName === '@jupyter-widgets/base') {
- if ((widgets as any)[className]) {
- return Promise.resolve((widgets as any)[className]);
- } else {
- return Promise.reject(`Cannot find class ${className}`)
- }
- } else if (moduleName === 'jupyter-datawidgets') {
- if (this.testClasses[className]) {
- return Promise.resolve(this.testClasses[className]);
- } else {
- return Promise.reject(`Cannot find class ${className}`)
- }
- } else {
- return Promise.reject(`Cannot find module ${moduleName}`);
- }
- }
-
- _get_comm_info() {
- return Promise.resolve({});
- }
-
- _create_comm() {
- return Promise.resolve(new MockComm());
- }
-
- el: HTMLElement;
-
- testClasses: { [key: string]: any } = {};
-}
-
-
-export
-interface Constructor<T> {
- new (attributes?: any, options?: any): T;
-}
-
-export
-function createTestModel<T extends widgets.WidgetModel>(constructor: Constructor<T>, attributes?: any): T {
- let id = widgets.uuid();
- let widget_manager = new DummyManager();
- let modelOptions = {
- widget_manager: widget_manager,
- model_id: id,
- }
-
- return new constructor(attributes, modelOptions);
-}
diff --git a/tests/tsconfig.json b/tests/tsconfig.json
deleted file mode 100644
index b9259012eb6e7c8413c337c67c6448aeeb6d1cf1..0000000000000000000000000000000000000000
--- a/tests/tsconfig.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "compilerOptions": {
- "declaration": true,
- "noImplicitAny": true,
- "lib": ["dom", "es5", "es2015.promise", "es2015.iterable"],
- "noEmitOnError": true,
- "strictNullChecks": true,
- "module": "commonjs",
- "moduleResolution": "node",
- "target": "ES5",
- "outDir": "build",
- "skipLibCheck": true,
- "sourceMap": true
- },
- "include": [
- "src/*.ts",
- "../src/**/*.ts"
- ]
-}
diff --git a/tsconfig.json b/tsconfig.json
deleted file mode 100644
index 573496c34e55ed97f1131e32b3e72f00bcf6f31d..0000000000000000000000000000000000000000
--- a/tsconfig.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
- "compilerOptions": {
- "declaration": true,
- "esModuleInterop":true,
- "lib": ["es2015", "dom"],
- "module": "commonjs",
- "moduleResolution": "node",
- "noEmitOnError": true,
- "noUnusedLocals": true,
- "outDir": "lib",
- "resolveJsonModule": true,
- "rootDir": "src",
- "skipLibCheck": true,
- "sourceMap": true,
- "strict": false,
- "target": "es2015"
- },
- "include": [
- "src/**/*.ts",
- "src/**/*.tsx",
- ]
-}
diff --git a/webpack.config.js b/webpack.config.js
deleted file mode 100644
index e02c96da360697997aa139273d66e90c3fc10239..0000000000000000000000000000000000000000
--- a/webpack.config.js
+++ /dev/null
@@ -1,90 +0,0 @@
-const path = require('path');
-const version = require('./package.json').version;
-
-// Custom webpack rules
-const rules = [
- { test: /\.ts$/, loader: 'ts-loader' },
- { test: /\.js$/, loader: 'source-map-loader' },
- { test: /\.css$/, use: ['style-loader', 'css-loader']}
-];
-
-// Packages that shouldn't be bundled but loaded at runtime
-const externals = ['@jupyter-widgets/base'];
-
-const resolve = {
- // Add '.ts' and '.tsx' as resolvable extensions.
- extensions: [".webpack.js", ".web.js", ".ts", ".js"]
-};
-
-module.exports = [
- /**
- * Notebook extension
- *
- * This bundle only contains the part of the JavaScript that is run on load of
- * the notebook.
- */
- {
- entry: './src/extension.ts',
- output: {
- filename: 'index.js',
- path: path.resolve(__dirname, 'dicom_upload', 'nbextension', 'static'),
- libraryTarget: 'amd'
- },
- module: {
- rules: rules
- },
- devtool: 'source-map',
- externals,
- resolve,
- },
-
- /**
- * Embeddable dicom-upload bundle
- *
- * This bundle is almost identical to the notebook extension bundle. The only
- * difference is in the configuration of the webpack public path for the
- * static assets.
- *
- * The target bundle is always `dist/index.js`, which is the path required by
- * the custom widget embedder.
- */
- {
- entry: './src/index.ts',
- output: {
- filename: 'index.js',
- path: path.resolve(__dirname, 'dist'),
- libraryTarget: 'amd',
- library: "dicom-upload",
- publicPath: 'https://unpkg.com/dicom-upload@' + version + '/dist/'
- },
- devtool: 'source-map',
- module: {
- rules: rules
- },
- externals,
- resolve,
- },
-
-
- /**
- * Documentation widget bundle
- *
- * This bundle is used to embed widgets in the package documentation.
- */
- {
- entry: './src/index.ts',
- output: {
- filename: 'embed-bundle.js',
- path: path.resolve(__dirname, 'docs', 'source', '_static'),
- library: "dicom-upload",
- libraryTarget: 'amd'
- },
- module: {
- rules: rules
- },
- devtool: 'source-map',
- externals,
- resolve,
- }
-
-];