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remove unneeded funtions from publish.sh
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healthedata1 committed Apr 14, 2024
1 parent 1815e69 commit 3808035
Showing 1 changed file with 76 additions and 44 deletions.
120 changes: 76 additions & 44 deletions publish.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ trap "echo '=================================================================';
NA='http://tx.fhir.org'
GEN_OFF=''
VAL_OFF=''
while getopts abcdefghikmnopqrstvxyz option;
while getopts abcdefghiknopqrstuvxy option;
do
case "${option}"
in
Expand All @@ -23,20 +23,20 @@ do
i) IG_PUBLISH=1;;
k) NO_PROFILE=1;;
# l) LOAD_TEMPLATE=1;;
m) MERGE_CSV=1;;
# m) MERGE_CSV=1;;
n) NO_META=1;;
o) PUB=1;;
p) UPDATE=1;;
q) VIEW_QA=1;;
r) CLEAR_JSON=1;;
s) SUSHI=1;;
t) NA='N/A';;
# u) TEST_TEMPLATE=$OPTARG;;
u) UPDATE_IGJSON=1;;
v) VIEW_OUTPUT=1;;
# w) WATCH=1;;
x) RECENT_YAML=1;;
y) YAML_JSON=1;;
z) ZIP_SCH=1;;
# z) ZIP_SCH=1;;
esac

done
Expand All @@ -48,14 +48,14 @@ else
outpath=output
fi

if [[ $RECENT_YAML ]]; then
YAML_JSON=1
All_YAML=0
days=1
elif [[ $YAML_JSON ]]; then
All_YAML=1
days=400 # 400 days is about 1 year
fi
# if [[ $RECENT_YAML ]]; then
# YAML_JSON=1
# All_YAML=0
# days=1
# elif [[ $YAML_JSON ]]; then
# All_YAML=1
# days=400 # 400 days is about 1 year
# fi


echo "================================================================="
Expand All @@ -80,18 +80,19 @@ echo "-g flag to turn off narrative generation to speed up build times = $GEN_OF
echo "-h flag to turn off validation to speed up build times = $VAL_OFF"
echo "-i parameter for running only ig-publisher = $IG_PUBLISH"
echo "-k remove the meta.profile elements from all the examples = $NO_PROFILE"
echo "-m merge all StructureDefinition csv files with single header = $MERGE_CSV"
# echo "-m merge all StructureDefinition csv files with single header = $MERGE_CSV" # no longer this needed?
echo "-n remove the meta.extension elements from all the examples = $NO_META"
echo "-o parameter for running previous version of the igpublisher= $PUB"
echo "-p parameter for downloading latest version of the igpublisher from source = $UPDATE"
echo "-q view qa output in current browser = ./$outpath/qa.html = $VIEW_QA"
echo "-r remove all generated json files = $CLEAR_JSON"
echo "-s parameter for running only sushi = $SUSHI"
echo "-t parameter for no terminology server (run faster and offline)= $NA"
echo "-u parameter for updating ig.json file (until SUSHI catches up)= $UPDATE_IGJSON"
echo "-v view ig home page in current browser = ./$outpath/index.html = $VIEW_OUTPUT"
echo "-x tranform all yaml that changed in the last day to json files = $RECENT_YAML"
echo "-y tranform all yaml that changed in the last year to json files = $All_YAML"
echo "-z zip up all schematrons = $ZIP_SCH"
# echo "-x tranform all yaml that changed in the last day to json files = $RECENT_YAML"
echo "-y delete all json files and tranform all yaml files to json files = $All_YAML"
# echo "-z zip up all schematrons = $ZIP_SCH" # no longer needed?
#echo "-w parameter for using watch on igpublisher from source default is off = $WATCH"
#echo '-l parameter for downloading HL7 ig template from source = ' $LOAD_TEMPLATE
#echo '-u parameter for downloading test ig template from source or file= ' $TEST_TEMPLATE
Expand Down Expand Up @@ -162,9 +163,20 @@ fi

if [[ $YAML_JSON ]] && ls -U $inpath/resources-yaml/*.yml; then
echo "========================================================================"
echo "delete all yaml created json files is resources directory and"
echo "convert all yml files in resources-yaml directory to json files"
echo "outgoingPython 3.7 and PyYAML, json and sys modules are required"
for yaml_file in $(find $inpath/resources-yaml/*.yml -type f -mtime -$days)
rm -f $inpath/resources/StructureDefinition*.json
sleep 3
rm -f $inpath/resources/OperationDefinition*.json
sleep 3
rm -f $inpath/resources/SearchParameter*.json
sleep 3
rm -f $inpath/resources/CodeSystem*.json
sleep 3
rm -f $inpath/resources/ValueSet*.json
sleep 3
for yaml_file in $(find $inpath/resources-yaml/*.yml -type f) # -mtime -$days)
do
echo convert $yaml_file to ...
json_file=$inpath/resources/$(basename $yaml_file)
Expand All @@ -174,11 +186,14 @@ echo $json_file
done
fi


if [[ $YAML_JSON ]] && ls -U $inpath/examples-yaml/*.yml; then
echo "========================================================================"
echo "delete all json files is examples directory and"
echo "convert all yml files in examples-yaml directory to examples/json files"
echo "outgoingPython 3.7 and PyYAML, json and sys modules are required"
for yaml_file in $(find $inpath/examples-yaml/*.yml -type f -mtime -$days)
rm -f $inpath/examples/*.json
for yaml_file in $(find $inpath/examples-yaml/*.yml -type f) # -mtime -$days)
do
echo convert $yaml_file to ...
json_file=$inpath/examples/$(basename $yaml_file)
Expand All @@ -190,9 +205,11 @@ fi

if [[ $YAML_JSON ]] && ls -U $inpath/includes-yaml/*.yml; then
echo "======================================================================="
echo "delete all json files is includes directory and"
echo "convert all yml files in includes-yaml directory to json files"
echo "outgoingPython 3.7 and PyYAML, json and sys modules are required"
for yaml_file in $(find $inpath/includes-yaml/*.yml -type f -mtime -$days)
rm -f $inpath/includes/*.json
for yaml_file in $(find $inpath/includes-yaml/*.yml -type f) # -mtime -$days)
do
echo convert $yaml_file to ...
json_file=$inpath/includes/$(basename $yaml_file)
Expand Down Expand Up @@ -262,11 +279,12 @@ if [[ $SUSHI ]]; then
python3.7 -c 'import sys, yaml, json; yaml.dump(json.load(sys.stdin), sys.stdout, sort_keys=False, indent=2,)' < $ig_json > $ig_yaml
echo "========== ig_yaml = $ig_yaml =========="
done

echo "================================================================="

fi




if [[ $NO_META ]]; then
echo "================================================================="
echo "===remove the meta extension element from all the examples==="
Expand Down Expand Up @@ -328,11 +346,24 @@ if [[ $APP_VERSION ]]; then
done
mv -f $tmp/*.json $examples
# update ig json file
jq --arg ver "$ver" --arg canon "$canon" '.definition.resource = [.definition.resource[] | if .exampleCanonical then if .exampleCanonical | contains($canon) then .exampleCanonical += "|" + $ver else . end else . end]' $IGJSON > $tmp/ig.json
jq --arg ver "$ver" --arg canon "$canon" '.definition.resource = [.definition.resource[] | if .exampleCanonical then if .exampleCanonical | contains($canon) then .exampleCanonical += "|" + $ver else . end else . end]' $IGJSON > $tmp/ig.json
mv $tmp/ig.json $IGJSON
rm -rf $tmp
fi

if [[ $UPDATE_IGJSON ]]; then
echo "==============================================================================="
echo "================ move the ig-link-dependency extensions from =================="
echo "============ImplementationGuide to ImplementationGuide.definition ============="
echo "==============================================================================="
IGJSON=$(echo fsh-generated/resources/ImplementationGuide*.json)
echo "========= IGJSON is $IGJSON ==========="
tmp=$(mktemp -d -d $inpath/_examples)
jq --arg url "http://hl7.org/fhir/tools/StructureDefinition/ig-link-dependency" '.definition += { "extension": [.extension[] | select(.url == $url)] } | del(.extension[] | select(.url == $url))' $IGJSON > $tmp/ig.json
mv $tmp/ig.json $IGJSON
rm -rf $tmp
fi


if [[ $IG_PUBLISH ]]; then
echo "================================================================="
Expand Down Expand Up @@ -398,29 +429,29 @@ if [[ $TERMINOLOGY_TABLES ]]; then
cp $outpath/codesystem-ref-all-list.csv $inpath/data
fi

if [[ $ZIP_SCH ]]; then
echo "================================================================="
echo "===zip up schematrons and put in==="
echo "===$outpath/input/images/schematrons.zip file for downloads==="
echo "===zip -j input/images/schematrons.zip $outpath/*.sch==="
echo "================================================================="
zip -j input/images/schematrons.zip $outpath/*.sch
fi
# if [[ $ZIP_SCH ]]; then
# echo "================================================================="
# echo "===zip up schematrons and put in==="
# echo "===$outpath/input/images/schematrons.zip file for downloads==="
# echo "===zip -j input/images/schematrons.zip $outpath/*.sch==="
# echo "================================================================="
# zip -j input/images/schematrons.zip $outpath/*.sch
# fi

if [[ $MERGE_CSV ]]; then
echo "================================================================="
echo "===merge all StructureDefinition CSV and output as Excel too ==="
echo "Python 3.7 and pyexcel-cli, pyexcel, and pyexcel-xlsx are required"
echo "===require header file in $outpath/input/images-source/all_profiles.csv file ==="
echo "===creates $outpath/input/images/all_profiles.csv file ==="
echo "===creates $outpath/input/images/all_profiles.xlsx file ==="
echo "================================================================="
cp input/images-source/all_profiles.csv input/images/all_profiles.csv
echo "===find $outpath -name StructureDefinition-*.csv -exec tail -qn +2 {} + >> input/images/all_profiles.csv==="
find $outpath -name StructureDefinition-*.csv -exec tail -qn +2 {} + >> input/images/all_profiles.csv
echo "===pyexcel merge input/images/all_profiles.csv input/images all_profiles.xlsx==="
pyexcel merge input/images/all_profiles.csv input/images/all_profiles.xlsx
fi
# if [[ $MERGE_CSV ]]; then
# echo "================================================================="
# echo "===merge all StructureDefinition CSV and output as Excel too ==="
# echo "Python 3.7 and pyexcel-cli, pyexcel, and pyexcel-xlsx are required"
# echo "===require header file in $outpath/input/images-source/all_profiles.csv file ==="
# echo "===creates $outpath/input/images/all_profiles.csv file ==="
# echo "===creates $outpath/input/images/all_profiles.xlsx file ==="
# echo "================================================================="
# cp input/images-source/all_profiles.csv input/images/all_profiles.csv
# echo "===find $outpath -name StructureDefinition-*.csv -exec tail -qn +2 {} + >> input/images/all_profiles.csv==="
# find $outpath -name StructureDefinition-*.csv -exec tail -qn +2 {} + >> input/images/all_profiles.csv
# echo "===pyexcel merge input/images/all_profiles.csv input/images all_profiles.xlsx==="
# pyexcel merge input/images/all_profiles.csv input/images/all_profiles.xlsx
# fi

if [[ $VIEW_OUTPUT ]]; then
echo "=============== open $PWD/$outpath/index.html ================"
Expand All @@ -431,3 +462,4 @@ if [[ $VIEW_QA ]]; then
echo "============ open $PWD/$outpath/qa.html ============"
open ./$outpath/qa.html
fi

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