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Fix community filtering scripts #182

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merged 1 commit into from
Oct 2, 2024
Merged

Fix community filtering scripts #182

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10 changes: 6 additions & 4 deletions .github/workflows/fetch_filter_resources.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,9 @@ jobs:
- name: Merge all tools
run: | #merge files with only one header -> https://stackoverflow.com/questions/16890582/unixmerge-multiple-csv-files-with-same-header-by-keeping-the-header-of-the-firs; map(.[]) -> https://stackoverflow.com/questions/42011086/merge-arrays-of-json (get flat array, one tool per entry)
awk 'FNR==1 && NR!=1{next;}{print}' communities/all/resources/repositories*.list_tools.tsv > communities/all/resources/tools.tsv
jq -s 'map(.[])' communities/all/resources/repositories*.list_tools.json > communities/all/resources/all_tools.json
jq -s 'map(.[])' communities/all/resources/repositories*.list_tools.json > communities/all/resources/tools.json
rm communities/all/resources/repositories*.list_tools.json
rm communities/all/resources/repositories*.list_tools.tsv
- name: Generate wordcloud and interactive table
run: |
bash sources/bin/format_tools.sh
Expand All @@ -107,9 +109,9 @@ jobs:
- name: Filter tutorials for communities
run: |
bash sources/bin/get_community_tutorials.sh
- name: Update tool to keep and exclude for communities
run: |
bash sources/bin/update_tools_to_keep_exclude.sh
#- name: Update tool to keep and exclude for communities
# run: |
# bash sources/bin/update_tools_to_keep_exclude.sh
- name: Filter tools for communities
run: |
bash sources/bin/get_community_tools.sh
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46 changes: 24 additions & 22 deletions sources/bin/get_community_tools.sh
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Expand Up @@ -32,33 +32,35 @@ else
if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
community=`basename "$com_data_fp"`

echo "$community";
if [ "$community" != "all" ]; then

mkdir -p "communities/$community/resources"
echo "$community";

python sources/bin/extract_galaxy_tools.py \
filter \
--all "communities/all/resources/tools.json" \
--ts-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \
--filtered "communities/$community/resources/tools.tsv" \
--categories "communities/$community/metadata/categories" \
--status "communities/$community/metadata/tool_status.tsv"
mkdir -p "communities/$community/resources"

python sources/bin/create_interactive_table.py \
--input "communities/$community/resources/tools.tsv" \
--remove-col "Reviewed" \
--remove-col "To keep" \
--filter-col "To keep" \
--template "sources/data/interactive_table_template.html" \
--output "communities/$community/resources/tools.html"
python sources/bin/extract_galaxy_tools.py \
filter \
--all "communities/all/resources/tools.json" \
--ts-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \
--filtered "communities/$community/resources/tools.tsv" \
--categories "communities/$community/metadata/categories" \
--status "communities/$community/metadata/tool_status.tsv"

python sources/bin/create_wordcloud.py \
--input "communities/$community/resources/tools.tsv" \
--name-col "Galaxy wrapper id" \
--stat-col "No. of tool users (2022-2023) (usegalaxy.eu)" \
--wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \
--output "communities/$community/resources/tools_wordcloud.png"
python sources/bin/create_interactive_table.py \
--input "communities/$community/resources/tools.tsv" \
--remove-col "Reviewed" \
--remove-col "To keep" \
--filter-col "To keep" \
--template "sources/data/interactive_table_template.html" \
--output "communities/$community/resources/tools.html"

python sources/bin/create_wordcloud.py \
--input "communities/$community/resources/tools.tsv" \
--name-col "Galaxy wrapper id" \
--stat-col "No. of tool users (2022-2023) (usegalaxy.eu)" \
--wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \
--output "communities/$community/resources/tools_wordcloud.png"
fi;
fi;
done
fi
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30 changes: 17 additions & 13 deletions sources/bin/get_community_tutorials.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -14,24 +14,28 @@ then
--output "communities/microgalaxy/resources/tutorials.html"

else
for com_data_fp in data/communities/* ; do
for com_data_fp in communities/* ; do
if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
community=`basename "$com_data_fp"`
if [ "$community" != "all" ]; then
echo "$community"

echo "$community";
if [[ -f "communities/$community/metadata/tutorial_tags" && -f "communities/$community/resources/tutorials.tsv" ]]; then
echo "Filter tutorials"

if [[ -f "data/communities/$community/tutorial_tags" && -f "results/$community/tutorials.tsv" ]]; then
python sources/bin/extract_gtn_tutorials.py \
filter \
--all "communities/all/resources/tutorials.json" \
--filtered "communities/$community/resources/tutorials.tsv" \
--tags "communities/$community/metadata/tutorial_tags"

python sources/bin/extract_gtn_tutorials.py \
filter \
--all "communities/all/resources/tutorials.json" \
--filtered "communities/$community/resources/tutorials.tsv" \
--tags "communities/$community/metadata/tutorial_tags"

python sources/bin/create_interactive_table.py \
--input "communities/$community/resources/tutorials.tsv" \
--template "sources/data/interactive_table_template.html" \
--output "communities/$community/resources/tutorials.html"
python sources/bin/create_interactive_table.py \
--input "communities/$community/resources/tutorials.tsv" \
--template "sources/data/interactive_table_template.html" \
--output "communities/$community/resources/tutorials.html"
fi;

echo ""
fi;
fi;
done
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