Merge pull request #1 from sapiris/master

grim code

Author: mmaiers-nmdp

grim/CONTRIBUTING.md

@@ -0,0 +1,58 @@
+Contributing to graph-imputation-match
+===
+
+1) Log into Github web interface with your username-nmdp account
+
+2) Browse to the repo at https://github.com/nmdp-bioinformatics/graph-imputation-match, hit the Fork button
+
+3) Copy the clone URL from the Github web page for the fork (something like https://github.com/username-nmdp/graph-imputation-match.git)
+
+4) Clone the fork
+```bash
+$ git clone https://github.com/username-nmdp/graph-imputation-match.git
+$ cd graph-imputation-match
+```
+
+5) Add upstream as remote
+```bash
+$ git remote add upstream https://github.com/nmdp-bioinformatics/graph-imputation-match
+```
+
+6) Pull and merge latest changes from upstream master to your local master branch
+```bash
+$ git checkout master
+$ git pull upstream master
+$ git push
+```
+
+7) Create a new local feature branch
+```bash
+$ git checkout -b new-feature-branch
+```
+
+8) Edit files locally
+
+9) Commit changes to local feature branch
+```bash
+$ git commit -m "made changes"
+```
+
+10) Push changes from local feature branch to remote feature branch on your fork
+```bash
+$ git push origin new-feature-branch
+```
+
+11) Browse to the Github web page for your fork repo (something like https://github.com/username-nmdp/graph-imputation-match) and hit the new pull request button
+
+12) Edit the pull request description and hit save (or create or new, I can't remember) button
+
+13) Other contributors will review the changes in the pull request
+
+14) When the pull request looks good, it is merged into the upstream repo
+
+15) Hit the delete branch button to delete your remote feature branch (the commits have been merge upstream, so it is no longer necessary)
+
+16) Delete your local feature branch
+```bash
+$ git branch -d new-feature-branch
+```

grim/Dockerfile

@@ -0,0 +1,38 @@
+FROM python:3.8
+
+MAINTAINER "Pradeep Bashyal" [email protected]
+
+# Setup Repo for Neo4j version 3.5
+RUN wget -O - https://debian.neo4j.com/neotechnology.gpg.key | apt-key add - && \
+    echo 'deb https://debian.neo4j.com stable 3.5' | tee /etc/apt/sources.list.d/neo4j.list
+
+# Install neo4j and cpanm
+RUN apt-get update && \
+  apt-get -y install neo4j cpanminus && \
+  apt-get autoremove
+
+# Install the Perl libraries
+RUN cpanm install --auto-cleanup 0 --notest \
+    REST::Client JSON JSON::Parse Math::Round
+
+# Disable PIP Version check
+ENV PIP_DISABLE_PIP_VERSION_CHECK=1
+# Disable cache
+ENV PIP_NO_CACHE_DIR=1
+
+# Install Python libraries
+RUN pip install pandas==1.0.3 networkx==2.3 py2neo==4.3.0
+
+# Map cloned grimm directory to /grimm
+# -v $PWD:/grimm
+VOLUME /grimm
+WORKDIR /grimm
+
+# Setup env for Neo4J
+ENV NEO4J_HOME=/usr/share/neo4j
+ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
+
+COPY docker-entrypoint.sh /usr/local/bin/
+
+ENTRYPOINT ["/usr/local/bin/docker-entrypoint.sh"]
+

grim/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
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+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
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+Version".
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