mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
Wolfgang Maier
bd0f257452
Allows moving all data source tools using the script to profile 20.09. For more recent profiles data_source.py would have to work outside of Galaxy's Python environment.
93 lines
3.5 KiB
Python
93 lines
3.5 KiB
Python
#!/usr/bin/env python
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# Retrieves data from external data source applications and stores in a dataset file.
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# Data source application parameters are temporarily stored in the dataset file.
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import json
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import os
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import sys
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from urllib.parse import (
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urlencode,
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urlparse,
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)
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from urllib.request import urlopen
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from galaxy.datatypes import sniff
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from galaxy.datatypes.registry import Registry
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from galaxy.util import (
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DEFAULT_SOCKET_TIMEOUT,
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get_charset_from_http_headers,
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stream_to_open_named_file,
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)
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GALAXY_PARAM_PREFIX = "GALAXY"
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GALAXY_ROOT_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
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GALAXY_DATATYPES_CONF_FILE = os.path.join(GALAXY_ROOT_DIR, "datatypes_conf.xml")
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def __main__():
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if len(sys.argv) >= 3:
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max_file_size = int(sys.argv[2])
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else:
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max_file_size = 0
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with open(sys.argv[1]) as fh:
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params = json.load(fh)
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out_data_name = params['output_data'][0]["out_data_name"]
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URL = params['param_dict'].get("URL", None) # using exactly URL indicates that only one dataset is being downloaded
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URL_method = params['param_dict'].get("URL_method", "get")
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datatypes_registry = Registry()
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datatypes_registry.load_datatypes(
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root_dir=params["job_config"]["GALAXY_ROOT_DIR"],
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config=params["job_config"]["GALAXY_DATATYPES_CONF_FILE"],
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)
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for data_dict in params["output_data"]:
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cur_filename = data_dict["file_name"]
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cur_URL = params['param_dict'].get("%s|%s|URL" % (GALAXY_PARAM_PREFIX, data_dict["out_data_name"]), URL)
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if not cur_URL or urlparse(cur_URL).scheme not in ("http", "https", "ftp"):
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open(cur_filename, "w").write("")
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sys.exit("The remote data source application has not sent back a URL parameter in the request.")
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# The following calls to urlopen() will use the above default timeout
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try:
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if URL_method == "get":
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page = urlopen(cur_URL, timeout=DEFAULT_SOCKET_TIMEOUT)
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elif URL_method == "post":
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page = urlopen(cur_URL, urlencode(params["param_dict"]).encode("utf-8"), timeout=DEFAULT_SOCKET_TIMEOUT)
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except Exception as e:
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sys.exit("The remote data source application may be off line, please try again later. Error: %s" % str(e))
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if max_file_size:
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file_size = int(page.info().get("Content-Length", 0))
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if file_size > max_file_size:
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sys.exit(
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"The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server."
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% (file_size, max_file_size)
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)
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try:
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cur_filename = stream_to_open_named_file(
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page,
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os.open(cur_filename, os.O_WRONLY | os.O_TRUNC | os.O_CREAT),
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cur_filename,
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source_encoding=get_charset_from_http_headers(page.headers),
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)
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except Exception as e:
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sys.exit("Unable to fetch %s:\n%s" % (cur_URL, e))
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# here import checks that upload tool performs
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try:
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ext = sniff.handle_uploaded_dataset_file(cur_filename, datatypes_registry, ext=data_dict["ext"])
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except Exception as e:
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sys.exit(str(e))
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tool_provided_metadata = {out_data_name: {"ext": ext}}
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with open(params["job_config"]["TOOL_PROVIDED_JOB_METADATA_FILE"], "w") as json_file:
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json.dump(tool_provided_metadata, json_file)
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if __name__ == "__main__":
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__main__()
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