annotate data_source.py @ 0:fe2937ae3ee2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ commit 13791ad3a67f107e7c5cfd925a2cbc0fb5656ab3

#!/usr/bin/env python
# Retrieves data from external data source applications and stores in a dataset file.
# Data source application parameters are temporarily stored in the dataset file.
import os
import sys
from json import (
    dumps,
    loads,
)
from urllib.parse import (
    urlencode,
    urlparse,
)
from urllib.request import urlopen

from galaxy.datatypes import sniff
from galaxy.datatypes.registry import Registry
from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
from galaxy.util import (
    DEFAULT_SOCKET_TIMEOUT,
    get_charset_from_http_headers,
    stream_to_open_named_file,
)

GALAXY_PARAM_PREFIX = "GALAXY"
GALAXY_ROOT_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
GALAXY_DATATYPES_CONF_FILE = os.path.join(GALAXY_ROOT_DIR, "datatypes_conf.xml")


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def load_input_parameters(filename, erase_file=True):
    datasource_params = {}
    try:
        json_params = loads(open(filename).read())
        datasource_params = json_params.get("param_dict")
    except Exception:
        json_params = None
        for line in open(filename):
            try:
                line = line.strip()
                fields = line.split("\t")
                datasource_params[fields[0]] = fields[1]
            except Exception:
                continue
    if erase_file:
        open(filename, "w").close()  # open file for writing, then close, removes params from file
    return json_params, datasource_params


def __main__():
    filename = sys.argv[1]
    try:
        max_file_size = int(sys.argv[2])
    except Exception:
        max_file_size = 0

    job_params, params = load_input_parameters(filename)
    if job_params is None:  # using an older tabular file
        enhanced_handling = False
        job_params = dict(param_dict=params)
        job_params["output_data"] = [
            dict(out_data_name="output", ext="data", file_name=filename, extra_files_path=None)
        ]
        job_params["job_config"] = dict(
            GALAXY_ROOT_DIR=GALAXY_ROOT_DIR,
            GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE,
            TOOL_PROVIDED_JOB_METADATA_FILE=TOOL_PROVIDED_JOB_METADATA_FILE,
        )
    else:
        enhanced_handling = True
        json_file = open(
            job_params["job_config"]["TOOL_PROVIDED_JOB_METADATA_FILE"], "w"
        )  # specially named file for output junk to pass onto set metadata

    datatypes_registry = Registry()
    datatypes_registry.load_datatypes(
        root_dir=job_params["job_config"]["GALAXY_ROOT_DIR"],
        config=job_params["job_config"]["GALAXY_DATATYPES_CONF_FILE"],
    )

    URL = params.get("URL", None)  # using exactly URL indicates that only one dataset is being downloaded
    URL_method = params.get("URL_method", None)

    for data_dict in job_params["output_data"]:
        cur_filename = data_dict.get("file_name", filename)
        cur_URL = params.get("%s|%s|URL" % (GALAXY_PARAM_PREFIX, data_dict["out_data_name"]), URL)
        if not cur_URL or urlparse(cur_URL).scheme not in ("http", "https", "ftp"):
            open(cur_filename, "w").write("")
            stop_err("The remote data source application has not sent back a URL parameter in the request.")

        # The following calls to urlopen() will use the above default timeout
        try:
            if not URL_method or URL_method == "get":
                page = urlopen(cur_URL, timeout=DEFAULT_SOCKET_TIMEOUT)
            elif URL_method == "post":
                page = urlopen(cur_URL, urlencode(params).encode("utf-8"), timeout=DEFAULT_SOCKET_TIMEOUT)
        except Exception as e:
            stop_err("The remote data source application may be off line, please try again later. Error: %s" % str(e))
        if max_file_size:
            file_size = int(page.info().get("Content-Length", 0))
            if file_size > max_file_size:
                stop_err(
                    "The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server."
                    % (file_size, max_file_size)
                )
        try:
            cur_filename = stream_to_open_named_file(
                page,
                os.open(cur_filename, os.O_WRONLY | os.O_CREAT),
                cur_filename,
                source_encoding=get_charset_from_http_headers(page.headers),
            )
        except Exception as e:
            stop_err("Unable to fetch %s:\n%s" % (cur_URL, e))

        # here import checks that upload tool performs
        if enhanced_handling:
            try:
                ext = sniff.handle_uploaded_dataset_file(filename, datatypes_registry, ext=data_dict["ext"])
            except Exception as e:
                stop_err(str(e))
            info = dict(type="dataset", dataset_id=data_dict["dataset_id"], ext=ext)

            json_file.write("%s\n" % dumps(info))


if __name__ == "__main__":
    __main__()