Python write_gemini_config Examples

Example #1

File: install-data.py Project: jsh58/gemini

def install_annotation_files(anno_root_dir, dl_files=False, extra=None):
    """Download required annotation files.
    """
    # create the full gemini data path based on
    # the root dir the user provided
    if anno_root_dir.endswith(("gemini/data", "gemini/data/", "gemini_data")):
        anno_dir = anno_root_dir
    elif anno_root_dir.endswith(("gemini", "gemini/")):
        anno_dir = os.path.join(anno_root_dir, "data")
    else:
        anno_dir = os.path.join(anno_root_dir, "gemini", "data")

    cur_config = read_gemini_config(allow_missing=True)
    cur_config["annotation_dir"] = os.path.abspath(anno_dir)
    cur_config["versions"] = anno_versions
    write_gemini_config(cur_config)

    if dl_files:
        if not os.path.exists(anno_dir):
            os.makedirs(anno_dir)
        if not os.path.isdir(anno_dir):
            sys.exit(anno_dir + " is not a valid directory.")
        _check_dependencies()
        to_dl = anno_files[:]
        if extra:
            to_dl += [extra_anno_files[x] for x in extra]
        _download_anno_files("https://s3.amazonaws.com/gemini-annotations",
                             to_dl, anno_dir, cur_config)

Example #2

File: install-data.py Project: ctb/gemini

def install_annotation_files(anno_root_dir, dl_files=False, extra=None):
    """Download required annotation files.
    """
    # create the full gemini data path based on
    # the root dir the user provided
    if anno_root_dir.endswith(("gemini/data", "gemini/data/", "gemini_data")):
        anno_dir = anno_root_dir
    elif anno_root_dir.endswith(("gemini", "gemini/")):
        anno_dir = os.path.join(anno_root_dir, "data")
    else:
        anno_dir = os.path.join(anno_root_dir, "gemini", "data")

    cur_config = read_gemini_config(allow_missing=True)
    cur_config["annotation_dir"] = os.path.abspath(anno_dir)
    cur_config["versions"] = anno_versions
    write_gemini_config(cur_config)

    if dl_files:
        if not os.path.exists(anno_dir):
            os.makedirs(anno_dir)
        if not os.path.isdir(anno_dir):
            sys.exit(anno_dir + " is not a valid directory.")
        _check_dependencies()
        to_dl = anno_files[:]
        if extra:
            to_dl += [extra_anno_files[x] for x in extra]
        _download_anno_files("https://s3.amazonaws.com/gemini-annotations",
                             to_dl, anno_dir, cur_config)

Example #3

File: install-data.py Project: angelinasusan/gemini

def install_annotation_files(anno_root_dir):
    """Download required annotation files.
    """
    # create the full gemini data path based on
    # the root dir the user provided
    if anno_root_dir.endswith(("gemini", "gemini/")):
        anno_dir = os.path.join(anno_root_dir, "data")
    else:
        anno_dir = os.path.join(anno_root_dir, "gemini", "data")
    if not os.path.exists(anno_dir):
        os.makedirs(anno_dir)

    cur_config = read_gemini_config(allow_missing=True)

    # download and install each of the annotation files
    for orig in anno_files:
        if orig.endswith(".gz"):
            dls = [orig, "%s.tbi" % orig]
        else:
            dls = [orig]
        for dl in dls:
            url = "http://people.virginia.edu/~arq5x/files/gemini/annotations/{fname}".format(fname=dl)
            _download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
                             cur_config.get("versions", {}).get(orig, 1))

    cur_config["annotation_dir"] = anno_dir
    cur_config["versions"] = anno_versions
    write_gemini_config(cur_config)

Example #4

File: install-data.py Project: kunalbhutani/gemini

def _download_anno_files(base_url, file_names, anno_dir, cur_config):
    """Download and install each of the annotation files
    """
    for orig in file_names:
        if orig.endswith(".gz"):
            dls = [orig, "%s.tbi" % orig]
        else:
            dls = [orig]
        for dl in dls:
            url = "{base_url}/{fname}".format(fname=dl, base_url=base_url)
            _download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
                             cur_config.get("versions", {}).get(orig, 1))

    cur_config["annotation_dir"] = anno_dir
    cur_config["versions"] = anno_versions
    write_gemini_config(cur_config)

Example #5

File: install-data.py Project: chapmanb/gemini

def _download_anno_files(base_url, file_names, anno_dir, cur_config):
    """Download and install each of the annotation files
    """
    cur_config["annotation_dir"] = os.path.abspath(anno_dir)
    cur_config["versions"] = anno_versions
    write_gemini_config(cur_config)

    for orig in file_names:
        if orig.endswith(".gz"):
            dls = [orig, "%s.tbi" % orig]
        else:
            dls = [orig]
        for dl in dls:
            url = "{base_url}/{fname}".format(fname=dl, base_url=base_url)
            _download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
                             cur_config.get("versions", {}).get(orig, 1))

Example #6

File: install-data.py Project: hjanime/gemini

def install_annotation_files(anno_root_dir):
    """Download required annotation files.
    """
    # create the full gemini data path based on
    # the root dir the user provided
    if anno_root_dir.endswith(("gemini", "gemini/")):
        anno_dir = os.path.join(anno_root_dir, "data")
    else:
        anno_dir = os.path.join(anno_root_dir, "gemini", "data")
    if not os.path.exists(anno_dir):
        os.makedirs(anno_dir)

    cur_config = read_gemini_config(allow_missing=True)
    cur_config["annotation_dir"] = anno_dir
    write_gemini_config(cur_config)

    # download and install each of the annotation files
    for dl in anno_files:
        url = "http://people.virginia.edu/~arq5x/files/gemini/annotations/{fname}".format(
            fname=dl)
        _download_to_dir(url, anno_dir)