Merge pull request #43 from aplbrain/development

Development

.gitignore

@@ -0,0 +1,14 @@
+#Ignore cache and DS_Store files
+*.DS_Store
+*.pyc
+
+#ignore notebooks
+*.ipynb
+
+#Ignore all local volume and test files
+volumes/
+
+#ignore DAGs except template
+conduit/dags
+!conduit/dags/__init__.py
+!conduit/dags/template_dag

conduit/CWLDockerfile → CWLDockerfile

@@ -15,7 +15,7 @@
 #### CWL parser dockerfile ####
 
 FROM python:3.6-slim
-ARG AIRFLOW_VERSION=1.10.0
+ARG AIRFLOW_VERSION=1.10.4
 ENV SLUGIFY_USES_TEXT_UNIDECODE=yes
 RUN set -ex \
     && buildDeps=' \
@@ -36,13 +36,13 @@ RUN set -ex \
         $buildDeps \
         python3-pip \
         python3-requests \
-        mysql-client \
-        mysql-server \
         default-libmysqlclient-dev \
         apt-utils \
         curl \
         rsync \
         netcat \
+        default-mysql-server \
+        default-mysql-client \
         locales
 RUN apt-get update \
   && apt-get install -y python3-pip python3-dev \
@@ -51,9 +51,6 @@ RUN apt-get update \
 
 RUN pip3 install apache-airflow==$AIRFLOW_VERSION 
 RUN pip install apache-airflow==$AIRFLOW_VERSION 
-COPY requirements.txt /
-RUN pip install -r /requirements.txt
-RUN pip3 install -r /requirements.txt
 # COPY awsbatch_operator.py \
 #     cwl-to-dag.py \
 #     create_job_definitions.py \
@@ -63,4 +60,7 @@ RUN pip3 install -r /requirements.txt
     # s3wrap \
     # cwl_monitor /scripts/
 # ENTRYPOINT [ "cwl_monitor" ]
+COPY ./conduit /conduit
+COPY ./setup.py /
+RUN pip install -e /
 ENV PATH="/conduit:${PATH}"

Contributing.md

@@ -0,0 +1,89 @@
+# Contributing
+
+When contributing to SABER, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build. Pin versions where appropriate.
+2. Update the README.md in the appropriate folder with details of changes to the interface or tools.
+3. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

README.md

@@ -23,9 +23,9 @@ Please see our [wiki](https://github.com/aplbrain/saber/wiki/Data-Access) for mo
 
 ## Legal
 
-Use or redistribution of the Boss system in source and/or binary forms, with or without modification, are permitted provided that the following conditions are met:
+Use or redistribution of the SABER system in source and/or binary forms, with or without modification, are permitted provided that the following conditions are met:
 
 1. Redistributions of source code or binary forms must adhere to the terms and conditions of any applicable software licenses.
-2. End-user documentation or notices, whether included as part of a redistribution or disseminated as part of a legal or scientific disclosure (e.g. publication) or advertisement, must include the following acknowledgement:  The Boss software system was designed and developed by the Johns Hopkins University Applied Physics Laboratory (JHU/APL). 
-3. The names "The Boss", "JHU/APL", "Johns Hopkins University", "Applied Physics Laboratory", "MICrONS", or "IARPA" must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact [email protected].
+2. End-user documentation or notices, whether included as part of a redistribution or disseminated as part of a legal or scientific disclosure (e.g. publication) or advertisement, must include the following acknowledgement:  The SABER software system was designed and developed by the Johns Hopkins University Applied Physics Laboratory (JHU/APL). 
+3. The names "SABER", "JHU/APL", "Johns Hopkins University", "Applied Physics Laboratory" must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact [email protected].
 4. This source code and library is distributed in the hope that it will be useful, but is provided without any warranty of any kind.

conduit/WebDockerfile → WebDockerfile

@@ -9,7 +9,7 @@ ENV DEBIAN_FRONTEND noninteractive
 ENV TERM linux
 
 # Airflow
-ARG AIRFLOW_VERSION=1.10.0
+ARG AIRFLOW_VERSION=1.10.4
 ARG AIRFLOW_HOME=/root
 
 # Define en_US.
@@ -38,31 +38,29 @@ RUN set -ex \
         $buildDeps \
         python3-pip \
         python3-requests \
-        mysql-client \
-        mysql-server \
         default-libmysqlclient-dev \
         apt-utils \
         curl \
         rsync \
         netcat \
         locales \
+        default-mysql-server \
+        default-mysql-client \
     && apt-get install -y git \
     && sed -i 's/^# en_US.UTF-8 UTF-8$/en_US.UTF-8 UTF-8/g' /etc/locale.gen \
     && locale-gen \
     && update-locale LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 \
     && useradd -ms /bin/bash -d ${AIRFLOW_HOME} airflow \
     && pip install -U pip setuptools wheel \
+    && pip install werkzeug==0.16.0 \
+    && pip install SQLAlchemy==1.3.15 \
     && pip install Cython \
     && pip install pytz \
     && pip install pyOpenSSL \
     && pip install ndg-httpsclient \
     && pip install pyasn1 \
     && pip install apache-airflow[crypto,celery,postgres,hive,jdbc,mysql]==$AIRFLOW_VERSION \
-    && pip install celery[redis]==4.1.1 \
-    && pip install boto3==1.9.79 \
-    && pip install datajoint==0.11.1 \ 
-    && pip install parse==1.9.0 \
-    && pip install docker==3.7.0
+    && pip install celery[redis]==4.1.1 
     # && apt-get purge --auto-remove -yqq $buildDeps \
     # && apt-get autoremove -yqq --purge \
     # && apt-get clean \
@@ -74,13 +72,13 @@ RUN set -ex \
     #     /usr/share/doc \
     #     /usr/share/doc-base
 
-RUN git clone https://github.com/aplbrain/cwl-airflow-parser.git \
-    && cd cwl-airflow-parser \
-    && pip install -U . \
-    && cd ../
+# RUN git clone https://github.com/aplbrain/cwl-airflow-parser.git \
+#     && cd cwl-airflow-parser \
+#     && pip install -U . \
+#     && cd ../
 
-COPY ./scripts/entrypoint.sh /entrypoint.sh
-COPY ./config/airflow.cfg ${AIRFLOW_HOME}/airflow.cfg
+COPY ./conduit/scripts/entrypoint.sh /entrypoint.sh
+COPY ./conduit/config/airflow.cfg ${AIRFLOW_HOME}/airflow.cfg
 
 RUN chown -R airflow: ${AIRFLOW_HOME}
 
@@ -89,4 +87,6 @@ EXPOSE 8080 5555 8793
 # USER airflow
 WORKDIR /home
 ENTRYPOINT ["/entrypoint.sh"]
-CMD ["webserver"] # set default arg for entrypoint
+COPY ./conduit /conduit
+COPY ./setup.py /
+RUN pip install -e /