move from private repo

.gitignore

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+.DS_Store
+.Rproj.user
+*.Rproj
+app_key_dir
+app_vault_dir
+.deploy_vars
+.configs
+decode.sh
+.devcontainer/
+.bash_history
+.local/
+.rstudio/
+.dockerignore

Dockerfile

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+# syntax = docker/dockerfile:1.0-experimental # https://docs.docker.com/develop/develop-images/build_enhancements/
+FROM rocker/r-ver:4.0.3
+
+RUN export DEBIAN_FRONTEND=noninteractive && apt-get -y update \
+  && apt-get install -y \
+  alien \
+  bzip2 \
+  cmake \
+  curl \
+  file \
+  gdal-bin \
+  gnupg2 \
+  libaio1 \
+  libapparmor1 \
+  libcairo2 \
+  libcairo2-dev \
+  libcurl4-openssl-dev \
+  libedit2 \
+  libgdal-dev \
+  libglpk-dev \
+  libpoppler-cpp-dev \
+  libproj-dev \
+  libsqliteodbc \
+  libssl-dev \
+  libudunits2-dev \
+  libxml2-dev \
+  libxt-dev \
+  libxt6 \
+  lsb-release \
+  odbc-postgresql \
+  openjdk-8-jdk \
+  openssh-client \
+  pandoc \
+  pandoc-citeproc \
+  postgresql \
+  procps \
+  psmisc \
+  r-cran-cairo \
+  swaks \
+  tcl-dev \
+  tk-dev \
+  unixodbc \
+  zlib1g-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+# get from https://packagemanager.rstudio.com/client/#/repos/1/overview
+# Freezing packages to April 22, 2021:
+RUN echo "options(repos = c(REPO_NAME = 'https://packagemanager.rstudio.com/all/__linux__/focal/2511902'))" >> $R_HOME/etc/Rprofile.site
+
+RUN R -e "install.packages(c('assertthat', \
+  'data.table', \
+  'dplyr', \
+  'DT', \
+  'elastic', \
+  'future', \
+  'future.callr', \
+  'ggplot2', \
+  'ggthemes', \
+  'httr', \
+  'jsonlite', \
+  'leaflet', \
+  'lubridate', \
+  'memoise', \
+  'plotly', \
+  'promises', \
+  'rmarkdown', \
+  'rgdal', \
+  'shiny', \
+  'shinycssloaders', \
+  'shinydashboard', \
+  'shinyjs', \
+  'shinyWidgets', \
+  'sf', \
+  'stringr', \
+  'timetk', \
+  'htmltools'))"
+
+# Add certs for accessing elastic search servers that require them
+COPY elasticsearch/certificates/*.crt /usr/local/share/ca-certificates/
+RUN update-ca-certificates
+
+RUN mkdir /shinyapp
+WORKDIR /shinyapp/
+ADD ./ ./
+
+RUN useradd shiny -u 5000 -m -b /home
+RUN chown -R shiny:shiny /shinyapp
+USER shiny
+
+EXPOSE 3838
+
+CMD ["R", "-e", "shiny::runApp('/shinyapp', host = '0.0.0.0', port = 3838)"]

README.md

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+<img src="www/text_depot_icon/TextDepotIcon_TextImage_S.jpg" width="25%">
+
+Text Depot is a tool to search and analyze topics of interest within a large database of text data. The Text Depot dashboard (this repo) provides a front-end to a set of indexes in ElasticSearch. To use this repository, you must provide one or more [Elastic Search](www.elastic.co) indexes in a particular format.
+
+## Local Machine Setup
+
+1. Clone this repo.
+2. Run `cp .configs_sample .configs` and fill in the relevant values.
+
+### Running Locally
+
+1. Install any missing libraries with `install.packages("DT")` (for example). A list of required libraries can be found in the included `Dockerfile`
+2. Run `Rscript run_text_depot_dashboard.R`
+
+### Running via Docker
+
+1. Optionally, create a `.dockerignore` file to exclude any local files.
+2. Use the provided `Dockerfile` to build and run the app:
+
+```
+$ DOCKER_BUILDKIT=1 docker build -t text_depot_dashboard .
+$ docker run -it -p 8080:3838 text_depot_dashboard
+```
+
+3. Open the dashboard on your browser: [http://localhost:8080](http://localhost:8080)
+
+## ElasticSearch
+
+Each data source should be stored in its own Elastic Search index. For more information, see [elasticsearch/](elasticsearch/)
+
+## Notes
+
+Our workflow contained the following components:
+
+![Overall Workflow](workflow.png)
+
+This repository contains the dashboard code (Blue above) for Text Depot. The green components were scheduled with cron jobs, and keep the indexes up-to-date in the ElasticSearch Database. We wrote a custom Parser for each data source, and a single Annotator class that adds the fields below to each document before insertion. The orange components were added for authentication and embeddings-based search (add to `embedding_api_host` in `.configs`) for your dashboard.
+