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Preparing E-Health/drishti for FHIR DevDays

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@dermatologist
dermatologist / doit.sh
Created Sep 1, 2019 — forked from charlesreid1/doit.sh
Download the Large-scale CelebFaces Attributes (CelebA) Dataset from their Google Drive link
View doit.sh
#!/bin/bash
#
# Download the Large-scale CelebFaces Attributes (CelebA) Dataset
# from their Google Drive link.
#
# CelebA: http://mmlab.ie.cuhk.edu.hk/projects/CelebA.html
#
# Google Drive: https://drive.google.com/drive/folders/0B7EVK8r0v71pWEZsZE9oNnFzTm8
python3 get_drive_file.py 0B7EVK8r0v71pZjFTYXZWM3FlRnM celebA.zip
@dermatologist
dermatologist / Dockerfile
Created Aug 14, 2019 — forked from orenitamar/Dockerfile
Installing numpy, scipy, pandas and matplotlib in Alpine (Docker)
View Dockerfile
# Below are the dependencies required for installing the common combination of numpy, scipy, pandas and matplotlib
# in an Alpine based Docker image.
FROM alpine:3.4
RUN echo "http://dl-8.alpinelinux.org/alpine/edge/community" >> /etc/apk/repositories
RUN apk --no-cache --update-cache add gcc gfortran python python-dev py-pip build-base wget freetype-dev libpng-dev openblas-dev
RUN ln -s /usr/include/locale.h /usr/include/xlocale.h
RUN pip install numpy scipy pandas matplotlib
@dermatologist
dermatologist / cui2vec2word2vec.py
Last active Aug 13, 2019
Convert pre-trained cui2vec to Glove and word2vec
View cui2vec2word2vec.py
import os
from gensim.models import KeyedVectors
from gensim.scripts.glove2word2vec import glove2word2vec
if os.path.exists('cui2vec_w.txt'):
wv_from_text = KeyedVectors.load_word2vec_format('cui2vec_w.txt', unicode_errors='ignore')
print(wv_from_text.most_similar("C0000052", topn=2))
wv_from_text.save_word2vec_format('cui2vec_w.bin', binary=True)
else:
with open("cui2vec_pretrained.csv",'r') as f:
@dermatologist
dermatologist / docker-compose-backup.sh
Created Aug 3, 2019 — forked from pirate/docker-compose-backup.sh
Backup a docker-compose project, including all images, named and unnamed volumes, container filesystems, config, logs, and databases.
View docker-compose-backup.sh
#!/usr/bin/env bash
# Fully backup a docker-compose project, including all images, named and unnamed volumes, container filesystems, config, logs, and databases.
project_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && cd .. && pwd )"
cd "$project_dir"
project_name=$(basename "$project_dir")
backup_time=$(date +"%Y-%m-%d_%H-%M")
backup_dir="$project_dir/data/backups/$backup_time"
View Singularity cheat sheet
// Create a Singularity image from a Docker image that is in the Docker hub
// where /tmp/ is the folder where the image will be created and ubuntu:14.04
// is the docker image used to convert to the Singularity image
docker run \
-v /var/run/docker.sock:/var/run/docker.sock \
-v /tmp/:/output \
--privileged -t --rm \
singularityware/docker2singularity \
ubuntu:14.04
//
@dermatologist
dermatologist / NLP_Demo.py
Created Feb 11, 2019 — forked from narulkargunjan/NLP_Demo.py
Topic Modeling (LDA/Word2Vec) with Spacy
View NLP_Demo.py
import os
import codecs
data_directory = os.path.join('..', 'data',
'yelp_dataset_challenge_academic_dataset')
businesses_filepath = os.path.join(data_directory,
'yelp_academic_dataset_business.json')
with codecs.open(businesses_filepath, encoding='utf_8') as f:
@dermatologist
dermatologist / install.sh
Created Feb 10, 2019 — forked from cwant/install.sh
This is a script that takes a fresh Compute Canada Ubuntu 16.04 cloud instance, installs docker, docker-compose, ruby, grabs avalon source, and starts services
View install.sh
#!/bin/bash
BIND_NETWORK='192.168'
RUBY_VERSION='2.4'
BUNDLER_VERSION='1.14'
AVALON_REPO='https://github.com/cwant/avalon'
AVALON_BRANCH='cwant/docker-refactor'
SRC_DIR=$HOME/gitwork
AVALON_DIR=$SRC_DIR/avalon
View citing-github-repo.bib
@misc{Eapen2016,
author = {Eapen, BR.},
title = {Behavioural Research support tools in Python including Grounded Theory Dictionary Generator.},
year = {2016},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/dermatologist/nlp-qrmine}},
commit = {4f57d6a0e4c030202a07a60bc1bb1ed1544bf679}
}
@dermatologist
dermatologist / FileUpload.cs
Created Jul 24, 2017
ASP.Net Core Upload Multiple Files , Zip and Save as a byte array in database
View FileUpload.cs
using System;
using System.Collections.Generic;
using System.Linq;
using System.Threading.Tasks;
using Microsoft.AspNetCore.Http;
using System.IO;
using System.IO.Compression;
namespace MyNameSpace
{
@dermatologist
dermatologist / camel-raw-oauth.java
Created Nov 5, 2018 — forked from rafaeltuelho/camel-raw-oauth.java
camel snippet using oauth to get an auth token and use it to request a secured rest service
View camel-raw-oauth.java
from("timer://scheduler?period=30s")
.log("get access token")
.to("direct:authService");
from("direct:authService").tracing()
.setHeader(Exchange.HTTP_PATH)
.simple("<auth service context>/oauth2/token")
.setHeader("CamelHttpMethod")
.simple("POST")
.setHeader("Content-Type")
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