| Previous changeset 63:fb44b003e29b (2024-06-28) |
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Commit message:
planemo upload |
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modified:
snp-cache.py |
| snp-cache.py |
| diff -r fb44b003e29b -r b5cf2ec0c540 snp-cache.py |
| snp-cache.py |
| --- a/snp-cache.py Fri Jun 28 23:03:53 2024 -0400 +++ b/snp-cache.py Sat Jun 29 06:56:11 2024 -0400 @@ -23,22 +23,22 @@ class NoCacheNoCommandException(Exception): pass -@contextlib.contextmanager -def open(filename=None, mode='r'): - "basically a wrapper to make sys.stdout usable where there's a contextmanager" - writer = sys.stdout.buffer - try: - if filename: - writer = io.FileIO(filename, mode) - if 'r' in mode: - writer = io.BufferedReader(writer) - elif 'w' in mode: - writer = io.BufferedWriter(writer) - yield writer - writer.flush() - finally: - if filename: - writer.close() +# @contextlib.contextmanager +# def open(filename=None, mode='r'): +# "basically a wrapper to make sys.stdout usable where there's a contextmanager" +# writer = sys.stdout.buffer +# try: +# if filename: +# writer = io.FileIO(filename, mode) +# if 'r' in mode: +# writer = io.BufferedReader(writer) +# elif 'w' in mode: +# writer = io.BufferedWriter(writer) +# yield writer +# writer.flush() +# finally: +# if filename: +# writer.close() # class stream_over(io.IOBase): # "a file-like object that works as a tee, for API's that accept a file-like" @@ -85,11 +85,11 @@ # multistream.flush() # multistream.close() -def stream_to(input_stream, output_stream): - for i, line in enumerate(input_stream.readlines()): - if i < 8: - logging.getLogger('strm').info(str(line[:70])) - output_stream.write(line) +# def stream_to(input_stream, output_stream): +# for i, line in enumerate(input_stream.readlines()): +# if i < 8: +# logging.getLogger('strm').info(str(line[:70])) +# output_stream.write(line) @@ -98,29 +98,29 @@ table = table.strip() name = "{table}/{id}".format(**locals()) with open(output, 'wb') as output_f: - #lookup ID in table and get a FH to the resource - try: - import boto3 - api_key = os.environ.get('AWS_API_KEY', '') - s3 = boto3.resource('s3').Bucket(CACHE_NAMESPACE) - s3.download_fileobj(name, output_f) - logging.getLogger('snp-cache.cache').info("cache hit on {name}, retrieved.".format(**locals())) - except Exception as e: - if type(e) is not ImportError: - logging.getLogger('snp-cache.cache').info("cache miss on {name}".format(**locals())) - else: - logging.getLogger('snp-cache.cache').error(e) - #if we couldn't find the data, we need to run the command to generate it - if not command: - raise NoCacheNoCommandException("No cached result for this id, and no command given to generate.") - logging.getLogger('snp-cache.cmd').info(command) - # sub = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - # cached, err = sub.communicate() - # cached, err = io.BytesIO(cached), io.BytesIO(err) + # #lookup ID in table and get a FH to the resource + # try: + # import boto3 + # api_key = os.environ.get('AWS_API_KEY', '') + # s3 = boto3.resource('s3').Bucket(CACHE_NAMESPACE) + # s3.download_fileobj(name, output_f) + # logging.getLogger('snp-cache.cache').info("cache hit on {name}, retrieved.".format(**locals())) + # except Exception as e: + # if type(e) is not ImportError: + # logging.getLogger('snp-cache.cache').info("cache miss on {name}".format(**locals())) + # else: + # logging.getLogger('snp-cache.cache').error(e) + # #if we couldn't find the data, we need to run the command to generate it + # if not command: + # raise NoCacheNoCommandException("No cached result for this id, and no command given to generate.") + # logging.getLogger('snp-cache.cmd').info(command) + # # sub = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # # cached, err = sub.communicate() + # # cached, err = io.BytesIO(cached), io.BytesIO(err) try: cached = subprocess.check_output(command, shell=True) try: - s3.upload_fileobj(BytesIO(cached), name) + pass # s3.upload_fileobj(BytesIO(cached), name) except Exception as e: logging.getLogger('snp-cache.cache').error('Error writing to cache:') logging.getLogger('snp-cache.cache').error(e) |