Merge branch 'develop' of https://github.com/CenterForOpenScience/modular-file-renderer into feature/markdown-upgrade

Author: AddisonSchiller

.dockerignore

@@ -1,3 +1,4 @@
 .git
 *.pyc
 **/*.pyc
+Dockerfile

.travis.yml

@@ -2,6 +2,7 @@ language: python
 
 python:
   - "3.5"
+  - "3.6"
 
 sudo: false
 
@@ -35,3 +36,6 @@ before_cache:
 
 notifications:
   flowdock: 0221882cdda034c0e9ac2a0e766053dd
+
+after_success:
+  coveralls

AUTHORS.rst

@@ -30,3 +30,4 @@ Contributors
 - Rafael de Lucena Valle `@rafaeldelucena <https://github.com/rafaeldelucena>`_
 - Matthew Keitelman `@zamattiac <https://github.com/zamattiac>`_
 - John Tordoff `@Johnetordoff <https://github.com/Johnetordoff>`_
+- Addison Schiller `@AddisonSchiller <https://github.com/AddisonSchiller>`_

CHANGELOG

@@ -2,6 +2,25 @@
 ChangeLog
 *********
 
+0.22.0 (2017-10-10)
+===================
+- Feature: Added support for rendering ~50 new plain-text file types via codepygments, including
+FASTA files, ImageJ macros, and Turtle files. (thanks, @AddisonSchiller!)
+- Feature: Add a unique request ID to MFR's response headers to help with tracking down errors.
+- Feature: Add a new task to clean the export and render caches. (thanks, @icereval!)
+- Fix: Error more gracefully when missing required query parameters.
+- Fix: Make scrollbars visible on IE11 when content overflows the iframe.
+- Fix: Fix ALLOWED_PROVIDER_DOMAINS example in MFR docs. (thanks, @jonathon-love for reporting!)
+- Code: Teach MFR to listen for a SIGTERM signal and exit immediately upon receiving it. This
+bypasses the 10 second wait for shutdown when running it in Docker.
+- Code: Add code-coverage checking via coveralls.io. (thanks, @abought!)
+- Code: Add Python 3.6 to travis testing matrix. (thanks, @abought!)
+- Code: Add a Pull Request template for GitHub. (thanks, @cslzchen!)
+
+0.21.2 (2017-09-13)
+===================
+- Fix: Update jQuery onload invocation to be compatible with jQuery 3.  (thanks, @sloria!)
+
 0.21.1 (2017-07-20)
 ===================
 - Fix: Quiet some overly-verbose error logging.

CONTRIBUTING.rst

@@ -8,6 +8,7 @@ In general
 - `PEP 8`_, when sensible.
 - Test ruthlessly. Write docs for new features.
 - Even more important than Test-Driven Development--*Human-Driven Development*.
+- If you add an extension to setup.py, add it to supportedextensions.md.
 - Please update AUTHORS.rst when you contribute.
 
 .. _`PEP 8`: http://www.python.org/dev/peps/pep-0008/
@@ -107,14 +108,12 @@ Manual Local Testing
 
 To make sure a new renderer is functioning properly, it's recommended that you try to render a file of that type locally. 
 
-First, change the default provider to HTTP (in `/mfr/server/settings.py`) and update the provider domain whitelist:
+First, change the default provider to HTTP (in `/mfr/server/settings.py`), then update the provider domain in the ``ALLOWED_PROVIDER_DOMAINS`` whitelist (a space-separated string):
 
 .. code-block:: python
 
     PROVIDER_NAME = config.get('PROVIDER_NAME', 'http')
-    ALLOWED_PROVIDER_DOMAINS = config.get('ALLOWED_PROVIDER_DOMAINS', ['http://localhost:8000/'])
-
-	
+    ALLOWED_PROVIDER_DOMAINS = config.get('ALLOWED_PROVIDER_DOMAINS', 'http://localhost:8000/')
 
 Because the MFR is passed a url to render, you also need to be running an http server.
 
@@ -130,15 +129,13 @@ Or for python 3
 
     python3 -m http.server 8000
 
-With both the SimpleHTTPServer the MFR server running, go to 
+With both the SimpleHTTPServer and the MFR server running, go to
 
 .. code-block:: bash
 
 	http://localhost:7778/render?url=http://localhost:8000/[filename].[ext]
 
 
-
-
 Writing A File Format Package
 -----------------------------
 

Dockerfile

@@ -1,8 +1,11 @@
 FROM python:3.5-slim
 
-RUN usermod -d /home www-data && chown www-data:www-data /home
+# ensure unoconv can locate the uno library
+ENV PYTHONPATH=/usr/lib/python3/dist-packages
 
-RUN apt-get update \
+RUN usermod -d /home www-data \
+    && chown www-data:www-data /home \
+    && apt-get update \
     # mfr dependencies
     && apt-get install -y \
         git \
@@ -19,49 +22,39 @@ RUN apt-get update \
         libxml2-dev \
         libxslt1-dev \
         zlib1g-dev \
-    # unoconv dependencies
-    && apt-get install -y \
+        # unoconv dependencies
         unoconv \
-    # pspp dependencies
-    && apt-get install -y \
+        # pspp dependencies
         pspp \
-    && apt-get clean \
-    && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/*
-
-# grab gosu for easy step-down from root
-ENV GOSU_VERSION 1.4
-RUN apt-get update \
-    && apt-get install -y \
+        # gosu dependencies
         curl \
+    # gosu
+    && export GOSU_VERSION='1.10' \
     && gpg --keyserver pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 \
     && curl -o /usr/local/bin/gosu -SL "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture)" \
   	&& curl -o /usr/local/bin/gosu.asc -SL "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture).asc" \
   	&& gpg --verify /usr/local/bin/gosu.asc \
   	&& rm /usr/local/bin/gosu.asc \
   	&& chmod +x /usr/local/bin/gosu \
+    # /gosu
     && apt-get clean \
     && apt-get autoremove -y \
         curl \
-    && rm -rf /var/lib/apt/lists/*
-
-# ensure unoconv can locate the uno library
-ENV PYTHONPATH=/usr/lib/python3/dist-packages
+    && rm -rf /var/lib/apt/lists/* \
+    && pip install -U pip \
+    && pip uninstall -y setuptools \
+    && rm -f /usr/local/lib/python3.5/site-packages/mfr-nspkg.pth \
+    && pip install setuptools==30.4.0 \
+    && mkdir -p /code
 
-RUN mkdir -p /code
 WORKDIR /code
 
-RUN pip install -U pip
-RUN pip uninstall -y setuptools
-RUN rm -f /usr/local/lib/python3.5/site-packages/mfr-nspkg.pth
-RUN pip install setuptools==30.4.0
-
-COPY ./requirements.txt /code/
+COPY ./requirements.txt ./
 
-RUN pip install --no-cache-dir -r /code/requirements.txt
+RUN pip install --no-cache-dir -r ./requirements.txt
 
 # Copy the rest of the code over
-COPY ./ /code/
+COPY ./ ./
 
 ARG GIT_COMMIT=
 ENV GIT_COMMIT ${GIT_COMMIT}
@@ -70,4 +63,4 @@ RUN python setup.py develop
 
 EXPOSE 7778
 
-CMD ["gosu", "nobody", "invoke", "server"]
+CMD ["gosu", "www-data", "invoke", "server"]

PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,40 @@
+<!-- Use the following format for the title of the Pull Request:
+
+    [Status] [Ticket] Title
+
+    - For PR ready for review, no need for status
+    - For PR in progress, use [WIP]
+    - For PR on hold, use [HOLD]
+-->
+
+<!-- Before submit your Pull Request, make sure you picked the right branch:
+
+    - For hotfixes, select "master" as the target branch
+    - For new features and improvements, select "develop" as the target branch
+-->
+
+<!-- For security related tickets, talk with the team lead before submit your PR -->
+
+## Ticket
+
+<!-- Link to JIRA ticket, if applicable e.g. https://openscience.atlassian.net/browse/SVCS-1234 -->
+
+## Purpose
+
+<!-- Describe the purpose of your changes -->
+
+## Changes
+
+<!-- Briefly describe or list your changes  -->
+
+## Side effects
+
+<!-- Any possible side effects? -->
+
+## QA Notes
+
+<!-- If applicable, briefly describe how QA should test this ticket/PR -->
+
+## Deployment Notes
+
+<!-- Any special configurations for deployment? -->

README.md

@@ -4,6 +4,8 @@
 
 `develop` Build Status: [![Build Status](https://travis-ci.org/CenterForOpenScience/modular-file-renderer.svg?branch=develop)](https://travis-ci.org/CenterForOpenScience/modular-file-renderer)
 
+[![Coverage Status](https://coveralls.io/repos/github/CenterForOpenScience/modular-file-renderer/badge.svg)](https://coveralls.io/github/CenterForOpenScience/modular-file-renderer)
+
 A Python package for rendering files to HTML via an embeddable iframe.
 
 ### Compatibility
@@ -53,12 +55,12 @@ MFR configuration is done through a JSON file (`mfr-test.json`) that lives in th
 mkdir ~/.cos
 ```
 
-The defaults should suffice for most local testing.  If you're running the OSF on something other than `http://localhost:5000/`, you'll need to update the `ALLOWED_PROVIDER_DOMAINS` settings value:
+The defaults should suffice for most local testing.  If you're running the OSF or WaterButler on something other than `http://localhost:5000/` and `http://localhost:7777/`, you'll need to update the `ALLOWED_PROVIDER_DOMAINS` settings value. `ALLOWED_PROVIDER_DOMAINS` is a list formatted as a space-separated string.  This allows MFR to be configured via an environment variable (which are always strings), as is done in the OSF's `.docker-compose.mfr.env`.  Example of customized domains:
 
 ```json
 {
   "SERVER_CONFIG": {
-    "ALLOWED_PROVIDER_DOMAINS": ["http://localhost:9999/"]
+    "ALLOWED_PROVIDER_DOMAINS": "http://my_osf:5001/ http://my_wb:23405/"
   }
 }
 ```

constraints.txt

@@ -0,0 +1,7 @@
+## Constraints file for resolving conflicts across packages. Used to resolve issues with sub-dependencies of an actual requirement.
+##  (eg when python-coveralls indirectly requires a version of requests)
+## "Constraints files are requirements files that only control which version of a requirement is installed, not whether it is installed or not."
+##     See https://pip-python3.readthedocs.org/en/latest/user_guide.html#constraints-files
+
+# Newer version of requests throw an error when using the version of chardet we pin to; this causes issues for python-coveralls
+requests==2.14.2

dev-requirements.txt

@@ -1,6 +1,7 @@
 -r requirements.txt
 
 -e git+https://github.com/centerforopenscience/aiohttpretty.git@0.0.2#egg=aiohttpretty
+beautifulsoup4
 colorlog==2.5.0
 flake8==3.0.4
 ipdb
@@ -9,4 +10,5 @@ pydevd==0.0.6
 pyflakes
 pytest==2.8.2
 pytest-cov==2.2.0
+python-coveralls==2.9.1
 pyzmq==14.4.1