Refactor interface

[yashpatel6]

Description

Refactoring interface from separate validate and generate-checksum commands into a single pipeval command with validate and generate-checksum subcommands

---

Test Results

#!/bin/bash
echo "empty BAM"
pipeval validate  test_files/empty_bam.bam

printf "\n"

echo "invalid BAM"
pipeval validate  test_files/invalid.bam

printf "\n"

echo "pass BAM"
pipeval validate  test_files/pass.bam

printf "\n"

echo "BAM with no index"
pipeval validate  test_files/noindex.bam

printf "\n"

echo "Just text file"
pipeval validate  test_files/hello.txt

printf "\n"

echo "Failing checksum MD5"
pipeval validate  test_files/hello_bad_md5.txt

echo "Failing checksum SHA512"
pipeval validate  test_files/hello_bad_sha512.txt

printf "\n"

echo "Generate md5 checksum"
pipeval generate-checksum -t md5 test_files/togen.txt

echo "Generate sha512 checksum"
pipeval generate-checksum -t sha512 test_files/togen.txt

echo "Validate generated checksums"
pipeval validate test_files/togen.txt

rm test_files/togen.txt.md5
rm test_files/togen.txt.sha512

printf "\n"

echo "Valid VCF"
pipeval validate  test_files/test_vcf.vcf.gz

printf "\n"

echo "Valid CRAM"
pipeval validate test_files/valid.cram -r /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta

printf "\n"

echo "CRAM with no index"
pipeval validate test_files/noindex.cram -r /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta

printf "\n"

echo "CRAM with default reference"
pipeval validate test_files/default_ref.cram

printf "\n"

echo "Invalid CRAM"
pipeval validate test_files/invalid.cram -r /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta

printf "\n"

echo "Valid SAM"
pipeval validate test_files/valid.sam

---

Checklist

File Commits

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

Code Review Best Practices

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Testing

• I have added unit tests for the new feature(s).

• I modified the integration test(s) to include the new feature.

• All new and previously existing tests passed locally and/or on the cluster.

• The docker image built successfully on the cluster.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[nwiltsie]

It's not a critical point, but for input paths I generally use something like this extant_file type rather than str.

def extant_file(x):
    """
    'Type' for argparse - checks that file exists but does not open.
    """
    if not os.path.exists(x):
        # Argparse uses the ArgumentTypeError to give a rejection message like:
        # error: argument input: x does not exist
        raise argparse.ArgumentTypeError("{0} does not exist".format(x))
    return x

[yashpatel6]

That's a good point; since the tool is intended to validate files, the existence check so far has been put into the actual validation rather than letting it happen through argparse. I'll add an issue for moving the existence validation to happen through the argument though!