Merge pull request #41 from dnwillia23/master

Initial commit of Seven Bridges file manifest generator

generate_manifest_sevenbridges/v1/Dockerfile

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+FROM rocker/r-ubuntu:22.04
+
+LABEL maintainer="David Williams <dnwilliams@rti.org>"
+LABEL description="This Docker image contains an in-house script written to generate a file manifest of projects in Seven Bridges."
+LABEL base-image="rocker/r-ubuntu:22.04"
+LABEL software-version="1.0"
+
+# Install vim and required packages for R libraries
+RUN apt update && apt install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \ 
+    vim
+
+# Install R libraries
+RUN Rscript -e 'install.packages(c("dplyr","stringr", "lubridate", "openxlsx", "sevenbridges2", "getopt"))'
+
+# Add scripts to make it run
+ADD generate_manifest_sevenbridges.R /
+
+# Add to /opt folder
+RUN mv generate_manifest_sevenbridges.R /opt/
+
+# Change permissions to make things exectuable
+RUN chmod u+x /opt/generate_manifest_sevenbridges.R
+
+# Set wrkdir
+RUN mkdir /data
+WORKDIR /data
+
+# Add to environment
+ENV PATH=$PATH:/opt/
+
+# Set default command to display help message
+CMD ["Rscript", "/opt/generate_manifest_sevenbridges.R", "-h"]

generate_manifest_sevenbridges/v1/README.md

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+# Description
+
+This Docker image contains an in-house script written to create an Excel workbook of a file and folder manifest of a Seven Bridges project.  Its purpose is to get a sense of how folders are structured, how much space is used, and how many files exits.  The Input to this should be a Seven Bridges developer's token and a string indicating which project to get a manifest of, and the output is an Excel file with a manifest of files and folders of the specified Seven Bridges project.  The following information is provided about the project and its files and folders:
+
+Summary metrics:
+- Report Date - date manifest was generated
+- Project ID - supplied project ID in format "\<username\>/\<project-name\>"
+- Project URL - Seven Bridges platform URL in format "https://platform.sb.bioodatacatalyst.nhlbi.nih.gov/u/\<username\>/\<project-name\>"
+- Total number of files uploaded
+- Total size of uploaded files
+- Most recent upload - date and time of most recently uploaded file
+
+Folders:
+- Hierarchy of folders in project
+- Number of files in each folder
+
+Files:
+- File name
+- File Size
+- Upload Date
+- Path - path to folder where file is located
+- SB URI - URI of file in Seven Bridges in format "https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/files/\<file-id\>"
+
+## Sample usage
+
+Build
+```
+docker build -t generate_manifest_sevenbridges:v1 .
+```
+
+Run
+```
+docker run -it -v $PWD:/data generate_manifest_sevenbridges:v1 Rscript generate_manifest_sevenbridges.R
+```
+
+Usage info:
+```
+Usage: convert_ab1_to_fasta.r [OPTIONS]
+             -- Required Parameters --
+              [-t | --token         ]    <Seven Bridges Developer token> (REQUIRED)
+              [-p | --project_id    ]    <Project ID, e.g. "username/test-project"> (REQUIRED)
+             -- Optional Parameters -- 
+              [-v | --verbose       ]    <Activates verbose mode>
+             -- Help Flag --  
+              [-h | --help          ]    <Displays this help message>
+             Example:
+             convert_ab1_to_fasta.r -v -t <token-here> -p <project_id-here>
+```
+
+## Files included
+
+- `Dockerfile`: the Docker file used to build this image
+- `generate_manifest_sevenbridges.R`: R script that serves as the main executable when the Docker container is run.  Expected behavior is to call the Seven Bridges API recursively on a project and generate an Excel report containing the project's summary metrics, a directory manifest, and a file manifest.  In the end, this writes the extracted results to an output Excel sheet (.xlsx) named after the project's name.
+
+## Contact
+
+If you have any questions or feedback, please feel free to contact the maintainers of this project:
+
+- David Williams, email: dnwilliams@rti.org