def _galaxy_library_upload(finfo, sample_info, config):
"""Upload results to galaxy library.
"""
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo,
storage_dir,
pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo,
storage_dir,
pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError(
"Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config"
)
if storage_file and sample_info and not finfo.get(
"index", False) and not finfo.get("plus", False):
_to_datalibrary_safe(storage_file, gi, folder_name, sample_info,
config)
def update_file(finfo, sample_info, config):
"""Update file in Galaxy data libraries.
"""
if GalaxyInstance is None:
raise ImportError("Could not import bioblend.galaxy")
if "dir" not in config:
raise ValueError("Galaxy upload requires `dir` parameter in config specifying the "
"shared filesystem path to move files to.")
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError("Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config")
if storage_file and sample_info and not finfo.get("index", False):
_to_datalibrary(storage_file, gi, folder_name, sample_info, config)
def update_file(finfo, sample_info, config):
"""Update file in Galaxy data libraries.
"""
if GalaxyInstance is None:
raise ImportError("Could not import bioblend.galaxy")
if "dir" not in config:
raise ValueError("Galaxy upload requires `dir` parameter in config specifying the "
"shared filesystem path to move files to.")
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError("Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config")
if storage_file and sample_info and not finfo.get("index", False):
_to_datalibrary_safe(storage_file, gi, folder_name, sample_info, config)
def _galaxy_library_upload(finfo, sample_info, config):
"""Upload results to galaxy library.
"""
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError("Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config")
if storage_file and sample_info and not finfo.get("index", False) and not finfo.get("plus", False):
_to_datalibrary_safe(storage_file, gi, folder_name, sample_info, config)
