comparison chasm_webservice/chasm_webservice.py @ 7:af0c2fa5bc76 draft

Uploaded

6:d88b17f16b14

import os
sheet_map = {0: 'Variant_Analysis.csv',
             1: 'Amino_Acid_Level_Analysis.csv', 2: 'Gene_Level_Analysis.csv'}


def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
    '''Retry calling the decorated function using an exponential backoff.

    http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
    original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry

            request = requests.post(
                __URL__, data=stripped_data, files=file_payload)
        else:
            request = requests.post(
                __URL__, data=stripped_data, files=dict(foo='bar'))
        job_id = json.loads(request.text)['jobid']
        return job_id

    @retry(requests.exceptions.HTTPError)
    def zip_exists(self, job_id):
        url = 'http://www.cravat.us/results/%s/%s.zip' % (job_id, job_id)
        zip_download_request = requests.request('GET', url)
        if zip_download_request.status_code == 404:
            raise requests.HTTPError()
        else:

                        dest='variant_analysis_out',
                        type=str, required=True)
    parser.add_argument('--amino_acid_level_analysis_out',
                        dest='amino_acid_level_analysis_out',
                        type=str, required=True,)
    parser.add_argument('--error_file', dest='error_file_out',
                        type=str, required=True)
    parser.add_argument('--snv_box_out', dest='snv_box_out',
                        type=str, required=False)
    parser.add_argument('--snv_features', dest='snv_features_out',

    file_map = {'Amino_Acid_Level_Analysis.Result.tsv': args.amino_acid_level_analysis_out,
                'SNVBox.tsv': args.snv_box_out,
                'Variant_Analysis.Result.tsv': args.variant_analysis_out,
                'Gene_Level_Analysis.Result.tsv': args.gene_analysis_out,
                'SnvGet Feature Description.xls': args.snv_features_out,
                'error.txt': args.error_file_out
                }
    url = chasm_web.zip_exists(job_id)
    download = chasm_web.download_zip(url, job_id)
    if download:
        chasm_web.move_files(file_map=file_map)

7:af0c2fa5bc76

import os
sheet_map = {0: 'Variant_Analysis.csv',
             1: 'Amino_Acid_Level_Analysis.csv', 2: 'Gene_Level_Analysis.csv'}


def retry(ExceptionToCheck, tries=40000, delay=3, backoff=2, logger=None):
    '''Retry calling the decorated function using an exponential backoff.

    http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
    original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry

            request = requests.post(
                __URL__, data=stripped_data, files=file_payload)
        else:
            request = requests.post(
                __URL__, data=stripped_data, files=dict(foo='bar'))
        print request.text
        job_id = json.loads(request.text)['jobid']
        return job_id

    @retry(requests.exceptions.HTTPError)
    def zip_exists(self, job_id):
        print job_id
        url = 'http://www.cravat.us/results/%s/%s.zip' % (job_id, job_id)
        zip_download_request = requests.request('GET', url)
        if zip_download_request.status_code == 404:
            raise requests.HTTPError()
        else:

                        dest='variant_analysis_out',
                        type=str, required=True)
    parser.add_argument('--amino_acid_level_analysis_out',
                        dest='amino_acid_level_analysis_out',
                        type=str, required=True,)
    parser.add_argument('--codon_level_analysis_out',
                        dest='codon_level_analysis_out',
                        type=str, required=True,)
    parser.add_argument('--error_file', dest='error_file_out',
                        type=str, required=True)
    parser.add_argument('--snv_box_out', dest='snv_box_out',
                        type=str, required=False)
    parser.add_argument('--snv_features', dest='snv_features_out',

    file_map = {'Amino_Acid_Level_Analysis.Result.tsv': args.amino_acid_level_analysis_out,
                'SNVBox.tsv': args.snv_box_out,
                'Variant_Analysis.Result.tsv': args.variant_analysis_out,
                'Gene_Level_Analysis.Result.tsv': args.gene_analysis_out,
                'SnvGet Feature Description.xls': args.snv_features_out,
                'error.txt': args.error_file_out,
                'Codon_Level_Analysis.Result.tsv': args.codon_level_analysis_out,
                }
    url = chasm_web.zip_exists(job_id)
    download = chasm_web.download_zip(url, job_id)
    if download:
        chasm_web.move_files(file_map=file_map)