galaxy_codex/sources/bin/get_community_workflows.sh at fd5e067b69ad76023bf1839cdaa071c4924cb5dc · galaxyproject/galaxy_codex · GitHub

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#!/usr/bin/env bash

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

                if [[ ! -z $1  && $1 == "test" && "$community" != "microgalaxy" ]]; then
                        continue
                fi;


                if [[ "$community" != "all" &&  -f "communities/$community/metadata/workflow_tags" ]]; then
                        echo "$community";
                        python sources/bin/extract_galaxy_workflows.py \
                                filter \
                                --all "communities/all/resources/workflows.json" \
                                --filtered "communities/$community/resources/tag_filtered_workflows.json" \
                                --tsv-filtered "communities/$community/resources/tag_filtered_workflows.tsv" \
                                --tags "communities/$community/metadata/workflow_tags" \
                                --status "communities/$community/metadata/workflow_status.tsv"

                        if [[ -f "communities/$community/metadata/workflow_status.tsv" ]]; then
                                python sources/bin/extract_galaxy_workflows.py \
                                        curate \
                                        --filtered "communities/$community/resources/tag_filtered_workflows.json" \
                                        --status "communities/$community/metadata/workflow_status.tsv" \
                                        --curated "communities/$community/resources/curated_workflows.json" \
                                        --tsv-curated "communities/$community/resources/curated_workflows.tsv" \
                                        --yml "communities/$community/resources/curated_workflows.yml"

                                if [[ -f "communities/$community/metadata/curated_workflows.yml" ]]; then
                                        mkdir -p _data/communities/$community/
                                        ln -sf ../../../communities/$community/resources/curated_workflows.yml _data/communities/$community/curated_workflows.yml
                                        #For pages - Can't copy from template, need to copy from existing md file
                                        cp pages/microgalaxy_workflows.md pages/${community}_workflows.md
                                        sed -i -e "s/microgalaxy/${community}/g" pages/${community}_workflows.md
                                        #For _includes - To keep same process as above, copying from existing file
                                        mkdir -p _includes/communities/$community/
                                        cp _includes/communities/microgalaxy/workflows.html _includes/communities/$community/workflows.html
                                        sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/workflows.html
                                fi;

                                if [[ -e "communities/$community/resources/curated_workflows.tsv" ]]; then
                                        python sources/bin/create_interactive_table.py \
                                                --input "communities/$community/resources/curated_workflows.tsv" \
                                                --template "sources/data/interactive_table_template.html" \
                                                --output "communities/$community/resources/workflows.html"
                                fi;
                        fi;
                fi;
        fi;
done