Protein function prediction with GO - Part 3 #59
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| name: Check consistency of tokens.txt file | |
| # Define the file paths under `paths` to trigger this check only when specific files are modified. | |
| # This script will then execute checks only on files that have changed, rather than all files listed in `paths`. | |
| # **Note** : To add a new token file for checks, include its path in: | |
| # - `on` -> `push` and `pull_request` sections | |
| # - `jobs` -> `check_tokens` -> `steps` -> Set global variable for multiple tokens.txt paths -> `TOKENS_FILES` | |
| on: | |
| push: | |
| paths: | |
| - "chebai/preprocessing/bin/smiles_token/tokens.txt" | |
| - "chebai/preprocessing/bin/smiles_token_unlabeled/tokens.txt" | |
| - "chebai/preprocessing/bin/selfies/tokens.txt" | |
| - "chebai/preprocessing/bin/protein_token/tokens.txt" | |
| - "chebai/preprocessing/bin/graph_properties/tokens.txt" | |
| - "chebai/preprocessing/bin/graph/tokens.txt" | |
| - "chebai/preprocessing/bin/deepsmiles_token/tokens.txt" | |
| - "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt" | |
| pull_request: | |
| paths: | |
| - "chebai/preprocessing/bin/smiles_token/tokens.txt" | |
| - "chebai/preprocessing/bin/smiles_token_unlabeled/tokens.txt" | |
| - "chebai/preprocessing/bin/selfies/tokens.txt" | |
| - "chebai/preprocessing/bin/protein_token/tokens.txt" | |
| - "chebai/preprocessing/bin/graph_properties/tokens.txt" | |
| - "chebai/preprocessing/bin/graph/tokens.txt" | |
| - "chebai/preprocessing/bin/deepsmiles_token/tokens.txt" | |
| - "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt" | |
| jobs: | |
| check_tokens: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Get list of changed files | |
| id: changed_files | |
| run: | | |
| git fetch origin dev | |
| # Get the list of changed files compared to origin/dev and save them to a file | |
| git diff --name-only origin/dev > changed_files.txt | |
| # Print the names of changed files on separate lines | |
| echo "Changed files:" | |
| while read -r line; do | |
| echo "Changed File name : $line" | |
| done < changed_files.txt | |
| - name: Set global variable for multiple tokens.txt paths | |
| run: | | |
| # All token files that needs to checked must be included here too, same as in `paths`. | |
| TOKENS_FILES=( | |
| "chebai/preprocessing/bin/smiles_token/tokens.txt" | |
| "chebai/preprocessing/bin/smiles_token_unlabeled/tokens.txt" | |
| "chebai/preprocessing/bin/selfies/tokens.txt" | |
| "chebai/preprocessing/bin/protein_token/tokens.txt" | |
| "chebai/preprocessing/bin/graph_properties/tokens.txt" | |
| "chebai/preprocessing/bin/graph/tokens.txt" | |
| "chebai/preprocessing/bin/deepsmiles_token/tokens.txt" | |
| "chebai/preprocessing/bin/protein_token_3_gram/tokens.txt" | |
| ) | |
| echo "TOKENS_FILES=${TOKENS_FILES[*]}" >> $GITHUB_ENV | |
| - name: Process only changed tokens.txt files | |
| run: | | |
| # Convert the TOKENS_FILES environment variable into an array | |
| TOKENS_FILES=(${TOKENS_FILES}) | |
| # Iterate over each token file path | |
| for TOKENS_FILE_PATH in "${TOKENS_FILES[@]}"; do | |
| # Check if the current token file path is in the list of changed files | |
| if grep -q "$TOKENS_FILE_PATH" changed_files.txt; then | |
| echo "----------------------- Processing $TOKENS_FILE_PATH -----------------------" | |
| # Get previous tokens.txt version | |
| git fetch origin dev | |
| git diff origin/dev -- $TOKENS_FILE_PATH > tokens_diff.txt || echo "No previous tokens.txt found for $TOKENS_FILE_PATH" | |
| # Check for deleted or added lines in tokens.txt | |
| if [ -f tokens_diff.txt ]; then | |
| # Check for deleted lines (lines starting with '-') | |
| deleted_lines=$(grep '^-' tokens_diff.txt | grep -v '^---' | sed 's/^-//' || true) | |
| if [ -n "$deleted_lines" ]; then | |
| echo "Error: Lines have been deleted from $TOKENS_FILE_PATH." | |
| echo -e "Deleted Lines: \n$deleted_lines" | |
| exit 1 | |
| fi | |
| # Check for added lines (lines starting with '+') | |
| added_lines=$(grep '^+' tokens_diff.txt | grep -v '^+++' | sed 's/^+//' || true) | |
| if [ -n "$added_lines" ]; then | |
| # Count how many lines have been added | |
| num_added_lines=$(echo "$added_lines" | wc -l) | |
| # Get last `n` lines (equal to num_added_lines) of tokens.txt | |
| last_lines=$(tail -n "$num_added_lines" $TOKENS_FILE_PATH) | |
| # Check if the added lines are at the end of the file | |
| if [ "$added_lines" != "$last_lines" ]; then | |
| # Find lines that were added but not appended at the end of the file | |
| non_appended_lines=$(diff <(echo "$added_lines") <(echo "$last_lines") | grep '^<' | sed 's/^< //') | |
| echo "Error: New lines have been added to $TOKENS_FILE_PATH, but they are not at the end of the file." | |
| echo -e "Added lines that are not at the end of the file: \n$non_appended_lines" | |
| exit 1 | |
| fi | |
| fi | |
| if [ "$added_lines" == "" ]; then | |
| echo "$TOKENS_FILE_PATH validation successful: No lines were deleted, and no new lines were added." | |
| else | |
| echo "$TOKENS_FILE_PATH validation successful: No lines were deleted, and new lines were correctly appended at the end." | |
| fi | |
| else | |
| echo "No previous version of $TOKENS_FILE_PATH found." | |
| fi | |
| else | |
| echo "$TOKENS_FILE_PATH was not changed, skipping." | |
| fi | |
| done |