fix_repos.sh

#!/bin/bash
# 1 - options: software, data-experiment, workflows
# 2 - options: replace, reset, diff, push, status
# 3 - (optional) package name(s)
# 4 - (optional) commit message

## replace - Run replacement script and bump package 'z' version
## reset - revert the package changes to most recent commit
## diff - see changes with git diff
## push - push changes to git.bioc

pkg_type=$1
CMD=$2
PKGS=$3
CMT_MSG=$4

if [ -z "${CMT_MSG// }" ]; then
    CMT_MSG="additional updates from BiocInstaller to BiocManager"
fi

. ./utils/setBIOC.sh

LIST_FILE="${pkg_type}_BiocInstaller_biocLite_PKGS.txt"
EXCLUDE=( BiocInstaller AnnotationHub AnnotationHubData BiocCheck )

cd $BIOC

# GIST_FOLDER clone
# git clone git@gist.github.com:$GIST_FOLDER.git

if [ -z "${PKGS// }" ]; then
    readarray -t PKGS < $BIOC/$GIST_FOLDER/$LIST_FILE
fi

for dex in ${EXCLUDE[@]}
do
    PKGS=("${PKGS[@]/$dex}")
done

for i in ${PKGS[@]}
do
    cd $BIOC/git.bioconductor.org/$pkg_type/$i
    echo "Working on package: $i..."

    if [ "$CMD" == "replace" ]; then
        $BIOC/utils/replace_alt_keywords.sh
        retVal=$?
        if [ $retVal -ne 0 ]; then
            $BIOC/utils/version_bump.sh
        fi
    elif [ "$CMD" == "reset" ]; then
        echo "  Resetting changes to $i"
        git checkout -- .
    elif [ "$CMD" == "push" ]; then
        git remote set-url origin git@git.bioconductor.org:packages/$i.git
        git remote -v
        git commit -am "$CMT_MSG"
        git push origin master
    elif [ "$CMD" == "diff" ]; then
        git diff
    elif [ "$CMD" == "status" ]; then
        git status
    else
        echo "$CMD is not a valid option"
    fi
done

cd $BIOC