servername = options.server
credentialsfilename = options.credentials
catalog = 1
schema = 'Microscopy'
table = 'Scan'
column = 'Thumbnail'
prefix = '/var/www/html'
output = '%s_add_border.sh' % servername.split('.')[0]
credentials = json.load(open(credentialsfilename))
catalog = ErmrestCatalog('https', servername, catalog, credentials)
url = '/attribute/%s:%s/!%s::null::%s/%s' % (urlquote(schema), urlquote(table), urlquote(column), RMT, urlquote(column))
print ('Query URL: "https://%s/ermrest/catalog/1%s"' % (servername, url))
resp = catalog.get(url)
resp.raise_for_status()
rows = resp.json()
thumbnails = []
for row in rows:
thumbnails.append(row[column])
"""
Generate the shell script.
"""
fp = open(output, 'w')
fp.write('#!/bin/bash\n\n')
for thumbnail in thumbnails:
filename = '%s%s' % (prefix, urlunquote(thumbnail))
original = '%s_original' % (filename)
credentialsfilename = options.credentials
catalog = 1
schema = 'Microscopy'
table = 'Scan'
column = 'Thumbnail'
prefix = '/var/www/html'
output = '%s_add_border.sh' % servername.split('.')[0]
credentials = json.load(open(credentialsfilename))
catalog = ErmrestCatalog('https', servername, catalog, credentials)
url = '/attribute/%s:%s/!%s::null::%s/%s' % (
urlquote(schema), urlquote(table), urlquote(column), RMT, urlquote(column))
print('Query URL: "https://%s/ermrest/catalog/1%s"' % (servername, url))
resp = catalog.get(url)
resp.raise_for_status()
rows = resp.json()
thumbnails = []
for row in rows:
thumbnails.append(row[column])
"""
Generate the shell script.
"""
fp = open(output, 'w')
fp.write('#!/bin/bash\n\n')
for thumbnail in thumbnails:
filename = '%s%s' % (prefix, urlunquote(thumbnail))
original = '%s_original' % (filename)
fp.write('if [ ! -f "%s" ]\n' % (original))
class DerivaUpload(object):
"""
Base class for upload tasks. Encapsulates a catalog instance and a hatrac store instance and provides some common
and reusable functions.
This class is not intended to be instantiated directly, but rather extended by a specific implementation.
"""
DefaultConfigFileName = "config.json"
DefaultServerListFileName = "servers.json"
DefaultTransferStateFileName = "transfers.json"
def __init__(self, config_file=None, credential_file=None, server=None):
self.server_url = None
self.catalog = None
self.store = None
self.config = None
self.credentials = None
self.asset_mappings = None
self.transfer_state = dict()
self.transfer_state_fp = None
self.cancelled = False
self.metadata = dict()
self.file_list = OrderedDict()
self.file_status = OrderedDict()
self.skipped_files = set()
self.override_config_file = config_file
self.override_credential_file = credential_file
self.server = self.getDefaultServer() if not server else server
self.initialize()
def __del__(self):
self.cleanupTransferState()
def initialize(self, cleanup=False):
info = "%s v%s [Python %s, %s]" % (self.__class__.__name__, VERSION,
platform.python_version(),
platform.platform(aliased=True))
logging.info("Initializing uploader: %s" % info)
# cleanup invalidates the current configuration and credentials in addition to clearing internal state
if cleanup:
self.cleanup()
# reset just clears the internal state
else:
self.reset()
if not self.server:
logging.warning(
"A server was not specified and an internal default has not been set."
)
return
# server variable initialization
protocol = self.server.get('protocol', 'https')
host = self.server.get('host', '')
self.server_url = protocol + "://" + host
catalog_id = self.server.get("catalog_id", "1")
session_config = self.server.get('session')
# overriden credential initialization
if self.override_credential_file:
self.credentials = get_credential(host, self.override_config_file)
# catalog and file store initialization
if self.catalog:
del self.catalog
self.catalog = ErmrestCatalog(protocol,
host,
catalog_id,
self.credentials,
session_config=session_config)
if self.store:
del self.store
self.store = HatracStore(protocol,
host,
self.credentials,
session_config=session_config)
# transfer state initialization
self.loadTransferState()
"""
Configuration initialization - this is a bit complex because we allow for:
1. Run-time overriding of the config file location.
2. Sub-classes of this class to bundle their own default configuration files in an arbitrary location.
3. The updating of already deployed configuration files if bundled internal defaults are newer.
"""
config_file = self.override_config_file if self.override_config_file else None
# 1. If we don't already have a valid (i.e., overridden) path to a config file...
if not (config_file and os.path.isfile(config_file)):
# 2. Get the currently deployed config file path, which could possibly be overridden by subclass
config_file = self.getDeployedConfigFilePath()
# 3. If the deployed default path is not valid, OR, it is valid AND is older than the bundled default
if (not (config_file and os.path.isfile(config_file))
or self.isFileNewer(self.getDefaultConfigFilePath(),
self.getDeployedConfigFilePath())):
# 4. If we can locate a bundled default config file,
if os.path.isfile(self.getDefaultConfigFilePath()):
# 4.1 Copy the bundled default config file to the deployment-specific config path
copy_config(self.getDefaultConfigFilePath(), config_file)
else:
# 4.2 Otherwise, fallback to writing a failsafe default based on internal hardcoded settings
write_config(config_file, DefaultConfig)
# 5. Finally, read the resolved configuration file into a config object
self._update_internal_config(read_config(config_file))
def _update_internal_config(self, config):
"""This updates the internal state of the uploader based on the config.
"""
self.config = config
# uploader initialization from configuration
self.asset_mappings = self.config.get('asset_mappings', [])
mu.add_types(self.config.get('mime_overrides'))
def cancel(self):
self.cancelled = True
def reset(self):
self.metadata.clear()
self.file_list.clear()
self.file_status.clear()
self.skipped_files.clear()
self.cancelled = False
def cleanup(self):
self.reset()
self.config = None
self.credentials = None
self.cleanupTransferState()
def setServer(self, server):
cleanup = self.server != server
self.server = server
self.initialize(cleanup)
def setCredentials(self, credentials):
host = self.server['host']
self.credentials = credentials
self.catalog.set_credentials(self.credentials, host)
self.store.set_credentials(self.credentials, host)
@classmethod
def getDefaultServer(cls):
servers = cls.getServers()
for server in servers:
lower = {k.lower(): v for k, v in server.items()}
if lower.get("default", False):
return server
return servers[0] if len(servers) else {}
@classmethod
def getServers(cls):
"""
This method must be implemented by subclasses.
"""
raise NotImplementedError(
"This method must be implemented by a subclass.")
@classmethod
def getVersion(cls):
"""
This method must be implemented by subclasses.
"""
raise NotImplementedError(
"This method must be implemented by a subclass.")
@classmethod
def getConfigPath(cls):
"""
This method must be implemented by subclasses.
"""
raise NotImplementedError(
"This method must be implemented by a subclass.")
@classmethod
def getDeployedConfigPath(cls):
return os.path.expanduser(os.path.normpath(cls.getConfigPath()))
def getVersionCompatibility(self):
return self.config.get("version_compatibility", list())
def isVersionCompatible(self):
compatibility = self.getVersionCompatibility()
if len(compatibility) > 0:
return vu.is_compatible(self.getVersion(), compatibility)
else:
return True
@classmethod
def getFileDisplayName(cls, file_path, asset_mapping=None):
return os.path.basename(file_path)
@staticmethod
def isFileNewer(src, dst):
if not (os.path.isfile(src) and os.path.isfile(dst)):
return False
# This comparison wont work with PyInstaller single-file bundles because the bundle is extracted to a temp dir
# and every timestamp for every file in the bundle is reset to the bundle extraction/creation time.
if getattr(sys, 'frozen', False):
prefix = os.path.sep + "_MEI"
if prefix in src:
return False
src_mtime = os.path.getmtime(os.path.abspath(src))
dst_mtime = os.path.getmtime(os.path.abspath(dst))
return src_mtime > dst_mtime
@staticmethod
def getFileSize(file_path):
return os.path.getsize(file_path)
@staticmethod
def guessContentType(file_path):
return mu.guess_content_type(file_path)
@staticmethod
def getFileHashes(file_path, hashes=frozenset(['md5'])):
return hu.compute_file_hashes(file_path, hashes)
@staticmethod
def getCatalogTable(asset_mapping, metadata_dict=None):
schema_name, table_name = asset_mapping.get('target_table',
[None, None])
if not (schema_name and table_name):
metadata_dict_lower = {
k.lower(): v
for k, v in metadata_dict.items()
}
schema_name = metadata_dict_lower.get("schema")
table_name = metadata_dict_lower.get("table")
if not (schema_name and table_name):
raise ValueError(
"Unable to determine target catalog table for asset type.")
return '%s:%s' % (urlquote(schema_name), urlquote(table_name))
@staticmethod
def interpolateDict(src, dst, allowNone=False):
if not (isinstance(src, dict) and isinstance(dst, dict)):
raise ValueError(
"Invalid input parameter type(s): (src = %s, dst = %s), expected (dict, dict)"
% (type(src).__name__, type(dst).__name__))
dst = dst.copy()
# prune None values from the src, we don't want those to be replaced with the string 'None' in the dest
empty = [k for k, v in src.items() if v is None]
for k in empty:
del src[k]
# perform the string replacement for the values in the destination dict
for k, v in dst.items():
try:
value = v.format(**src)
except KeyError:
value = v
if value:
if value.startswith('{') and value.endswith('}'):
value = None
dst.update({k: value})
# remove all None valued entries in the dest, if disallowed
if not allowNone:
empty = [k for k, v in dst.items() if v is None]
for k in empty:
del dst[k]
return dst
@staticmethod
def pruneDict(src, dst, stringify=True):
dst = dst.copy()
for k in dst.keys():
value = src.get(k)
dst[k] = str(value) if (stringify and value is not None) else value
return dst
def getCurrentConfigFilePath(self):
return self.override_config_file if self.override_config_file else self.getDeployedConfigFilePath(
)
def getDefaultConfigFilePath(self):
return os.path.normpath(
resource_path(os.path.join("conf", self.DefaultConfigFileName)))
def getDeployedConfigFilePath(self):
return os.path.join(self.getDeployedConfigPath(),
self.server.get('host', ''),
self.DefaultConfigFileName)
def getDeployedTransferStateFilePath(self):
return os.path.join(self.getDeployedConfigPath(),
self.server.get('host', ''),
self.DefaultTransferStateFileName)
def getRemoteConfig(self):
catalog_config = CatalogConfig.fromcatalog(self.catalog)
return catalog_config.annotation_obj(
"tag:isrd.isi.edu,2017:bulk-upload")
def getUpdatedConfig(self):
# if we are using an overridden config file, skip the update check
if self.override_config_file:
return
logging.info("Checking for updated configuration...")
remote_config = self.getRemoteConfig()
if not remote_config:
logging.info(
"Remote configuration not present, using default local configuration file."
)
return
deployed_config_file_path = self.getDeployedConfigFilePath()
if os.path.isfile(deployed_config_file_path):
current_md5 = hu.compute_file_hashes(deployed_config_file_path,
hashes=['md5'])['md5'][0]
else:
logging.info("Local config not found.")
current_md5 = None
tempdir = tempfile.mkdtemp(prefix="deriva_upload_")
if os.path.exists(tempdir):
updated_config_path = os.path.abspath(
os.path.join(tempdir, DerivaUpload.DefaultConfigFileName))
with io.open(updated_config_path,
'w',
newline='\n',
encoding='utf-8') as config:
config.write(
json.dumps(remote_config,
ensure_ascii=False,
sort_keys=True,
separators=(',', ': '),
indent=2))
new_md5 = hu.compute_file_hashes(updated_config_path,
hashes=['md5'])['md5'][0]
if current_md5 != new_md5:
logging.info("Updated configuration found.")
config = read_config(updated_config_path)
self._update_internal_config(config)
else:
logging.info("Configuration is up-to-date.")
config = None
shutil.rmtree(tempdir, ignore_errors=True)
return config
def getFileStatusAsArray(self):
result = list()
for key in self.file_status.keys():
item = {"File": key}
item.update(self.file_status[key])
result.append(item)
return result
def validateFile(self, root, path, name):
file_path = os.path.normpath(os.path.join(path, name))
asset_group, asset_mapping, groupdict = self.getAssetMapping(file_path)
if not asset_mapping:
return None
return asset_group, asset_mapping, groupdict, file_path
def scanDirectory(self, root, abort_on_invalid_input=False):
"""
:param root:
:param abort_on_invalid_input:
:return:
"""
root = os.path.abspath(root)
if not os.path.isdir(root):
raise ValueError("Invalid directory specified: [%s]" % root)
logging.info("Scanning files in directory [%s]..." % root)
file_list = OrderedDict()
for path, dirs, files in walk(root):
for file_name in files:
file_path = os.path.normpath(os.path.join(path, file_name))
file_entry = self.validateFile(root, path, file_name)
if not file_entry:
logging.info(
"Skipping file: [%s] -- Invalid file type or directory location."
% file_path)
self.skipped_files.add(file_path)
if abort_on_invalid_input:
raise ValueError("Invalid input detected, aborting.")
else:
asset_group = file_entry[0]
group_list = file_list.get(asset_group, [])
group_list.append(file_entry)
file_list[asset_group] = group_list
# make sure that file entries in both self.file_list and self.file_status are ordered by the declared order of
# the asset_mapping for the file
for group in sorted(file_list.keys()):
self.file_list[group] = file_list[group]
for file_entry in file_list[group]:
file_path = file_entry[3]
logging.info("Including file: [%s]." % file_path)
status = self.getTransferStateStatus(file_path)
if status:
self.file_status[file_path] = FileUploadState(
UploadState.Paused, status)._asdict()
else:
self.file_status[file_path] = FileUploadState(
UploadState.Pending, "Pending")._asdict()
def getAssetMapping(self, file_path):
"""
:param file_path:
:return:
"""
asset_group = -1
for asset_type in self.asset_mappings:
asset_group += 1
groupdict = dict()
dir_pattern = asset_type.get('dir_pattern', '')
ext_pattern = asset_type.get('ext_pattern', '')
file_pattern = asset_type.get('file_pattern', '')
path = file_path.replace("\\", "/")
if dir_pattern:
match = re.search(dir_pattern, path)
if not match:
logging.debug(
"The dir_pattern \"%s\" failed to match the input path [%s]"
% (dir_pattern, path))
continue
groupdict.update(match.groupdict())
if ext_pattern:
match = re.search(ext_pattern, path, re.IGNORECASE)
if not match:
logging.debug(
"The ext_pattern \"%s\" failed to match the input path [%s]"
% (ext_pattern, path))
continue
groupdict.update(match.groupdict())
if file_pattern:
match = re.search(file_pattern, path)
if not match:
logging.debug(
"The file_pattern \"%s\" failed to match the input path [%s]"
% (file_pattern, path))
continue
groupdict.update(match.groupdict())
return asset_group, asset_type, groupdict
return None, None, None
def uploadFiles(self, status_callback=None, file_callback=None):
for group, assets in self.file_list.items():
for asset_group_num, asset_mapping, groupdict, file_path in assets:
if self.cancelled:
self.file_status[file_path] = FileUploadState(
UploadState.Cancelled, "Cancelled by user")._asdict()
continue
try:
self.file_status[file_path] = FileUploadState(
UploadState.Running, "In-progress")._asdict()
if status_callback:
status_callback()
self.uploadFile(file_path, asset_mapping, groupdict,
file_callback)
self.file_status[file_path] = FileUploadState(
UploadState.Success, "Complete")._asdict()
except HatracJobPaused:
status = self.getTransferStateStatus(file_path)
if status:
self.file_status[file_path] = FileUploadState(
UploadState.Paused,
"Paused: %s" % status)._asdict()
continue
except HatracJobTimeout:
status = self.getTransferStateStatus(file_path)
if status:
self.file_status[file_path] = FileUploadState(
UploadState.Timeout, "Timeout")._asdict()
continue
except HatracJobAborted:
self.file_status[file_path] = FileUploadState(
UploadState.Aborted, "Aborted by user")._asdict()
except:
(etype, value, traceback) = sys.exc_info()
self.file_status[file_path] = FileUploadState(
UploadState.Failed, format_exception(value))._asdict()
self.delTransferState(file_path)
if status_callback:
status_callback()
failed_uploads = dict()
for key, value in self.file_status.items():
if (value["State"]
== UploadState.Failed) or (value["State"]
== UploadState.Timeout):
failed_uploads[key] = value["Status"]
if self.skipped_files:
logging.warning(
"The following file(s) were skipped because they did not satisfy the matching criteria "
"of the configuration:\n\n%s\n" %
'\n'.join(sorted(self.skipped_files)))
if failed_uploads:
logging.warning(
"The following file(s) failed to upload due to errors:\n\n%s\n"
% '\n'.join([
"%s -- %s" % (key, failed_uploads[key])
for key in sorted(failed_uploads.keys())
]))
raise RuntimeError(
"One or more file(s) failed to upload due to errors.")
def uploadFile(self,
file_path,
asset_mapping,
match_groupdict,
callback=None):
"""
Primary API subclass function.
:param file_path:
:param asset_mapping:
:param match_groupdict:
:param callback:
:return:
"""
logging.info("Processing file: [%s]" % file_path)
if asset_mapping.get("asset_type", "file") == "table":
self._uploadTable(file_path, asset_mapping, match_groupdict)
else:
self._uploadAsset(file_path, asset_mapping, match_groupdict,
callback)
def _uploadAsset(self,
file_path,
asset_mapping,
match_groupdict,
callback=None):
# 1. Populate metadata by querying the catalog
self._queryFileMetadata(file_path, asset_mapping, match_groupdict)
# 2. If "create_record_before_upload" specified in asset_mapping, check for an existing record, creating a new
# one if necessary. Otherwise delay this logic until after the file upload.
record = None
if stob(asset_mapping.get("create_record_before_upload", False)):
record = self._getFileRecord(asset_mapping)
# 3. Perform the Hatrac upload
self._getFileHatracMetadata(asset_mapping)
hatrac_options = asset_mapping.get("hatrac_options", {})
versioned_uri = \
self._hatracUpload(self.metadata["URI"],
file_path,
md5=self.metadata.get("md5_base64"),
sha256=self.metadata.get("sha256_base64"),
content_type=self.guessContentType(file_path),
content_disposition=self.metadata.get("content-disposition"),
chunked=True,
create_parents=stob(hatrac_options.get("create_parents", True)),
allow_versioning=stob(hatrac_options.get("allow_versioning", True)),
callback=callback)
logging.debug("Hatrac upload successful. Result object URI: %s" %
versioned_uri)
if stob(hatrac_options.get("versioned_uris", True)):
self.metadata["URI"] = versioned_uri
else:
self.metadata["URI"] = versioned_uri.rsplit(":")[0]
self.metadata["URI_urlencoded"] = urlquote(self.metadata["URI"])
# 3. Check for an existing record and create a new one if necessary
if not record:
record = self._getFileRecord(asset_mapping)
# 4. Update an existing record, if necessary
column_map = asset_mapping.get("column_map", {})
updated_record = self.interpolateDict(self.metadata, column_map)
if updated_record != record:
logging.info("Updating catalog for file [%s]" %
self.getFileDisplayName(file_path))
self._catalogRecordUpdate(self.metadata['target_table'], record,
updated_record)
def _uploadTable(self,
file_path,
asset_mapping,
match_groupdict,
callback=None):
if self.cancelled:
return None
self._initFileMetadata(file_path, asset_mapping, match_groupdict)
try:
default_columns = asset_mapping.get("default_columns")
if not default_columns:
default_columns = self.catalog.getDefaultColumns(
{}, self.metadata['target_table'])
default_param = (
'?defaults=%s' %
','.join(default_columns)) if len(default_columns) > 0 else ''
file_ext = self.metadata['file_ext']
if file_ext == 'csv':
headers = {'content-type': 'text/csv'}
elif file_ext == 'json':
headers = {'content-type': 'application/json'}
else:
raise CatalogCreateError(
"Unsupported file type for catalog bulk upload: %s" %
file_ext)
with open(file_path, "rb") as fp:
result = self.catalog.post(
'/entity/%s%s' %
(self.metadata['target_table'], default_param),
fp,
headers=headers)
return result
except:
(etype, value, traceback) = sys.exc_info()
raise CatalogCreateError(format_exception(value))
def _getFileRecord(self, asset_mapping):
"""
Helper function that queries the catalog to get a record linked to the asset, or create it if it doesn't exist.
:return: the file record
"""
column_map = asset_mapping.get("column_map", {})
rqt = asset_mapping['record_query_template']
try:
path = rqt.format(**self.metadata)
except KeyError as e:
raise ConfigurationError(
"Record query template substitution error: %s" %
format_exception(e))
result = self.catalog.get(path).json()
if result:
self._updateFileMetadata(result[0])
return self.pruneDict(result[0], column_map)
else:
row = self.interpolateDict(self.metadata, column_map)
result = self._catalogRecordCreate(self.metadata['target_table'],
row)
if result:
self._updateFileMetadata(result[0])
return self.interpolateDict(self.metadata,
column_map,
allowNone=True)
def _urlEncodeMetadata(self, safe_overrides=None):
urlencoded = dict()
if not safe_overrides:
safe_overrides = dict()
for k, v in self.metadata.items():
if k.endswith("_urlencoded"):
continue
urlencoded[k + "_urlencoded"] = urlquote(str(v),
safe_overrides.get(k, ""))
self._updateFileMetadata(urlencoded)
def _initFileMetadata(self, file_path, asset_mapping, match_groupdict):
self.metadata.clear()
self._updateFileMetadata(match_groupdict)
self.metadata['target_table'] = self.getCatalogTable(
asset_mapping, match_groupdict)
self.metadata["file_name"] = self.getFileDisplayName(file_path)
self.metadata["file_size"] = self.getFileSize(file_path)
self._urlEncodeMetadata(
asset_mapping.get("url_encoding_safe_overrides"))
def _updateFileMetadata(self, src, strict=False):
if not (isinstance(src, dict)):
ValueError(
"Invalid input parameter type(s): (src = %s), expected (dict)"
% type(src).__name__)
if strict:
for k in src.keys():
if k in UploadMetadataReservedKeyNames:
logging.warning(
"Context metadata update specified reserved key name [%s], "
"ignoring value: %s " % (k, src[k]))
del src[k]
self.metadata.update(src)
def _queryFileMetadata(self, file_path, asset_mapping, match_groupdict):
"""
Helper function that queries the catalog to get required metadata for a given file/asset
"""
file_name = self.getFileDisplayName(file_path)
logging.info("Computing metadata for file: [%s]." % file_name)
self._initFileMetadata(file_path, asset_mapping, match_groupdict)
logging.info("Computing checksums for file: [%s]. Please wait..." %
file_name)
hashes = self.getFileHashes(
file_path, asset_mapping.get('checksum_types', ['md5', 'sha256']))
for alg, checksum in hashes.items():
alg = alg.lower()
self.metadata[alg] = checksum[0]
self.metadata[alg + "_base64"] = checksum[1]
for uri in asset_mapping.get("metadata_query_templates", []):
try:
path = uri.format(**self.metadata)
except KeyError as e:
raise RuntimeError(
"Metadata query template substitution error: %s" %
format_exception(e))
result = self.catalog.get(path).json()
if result:
self._updateFileMetadata(result[0], True)
self._urlEncodeMetadata(
asset_mapping.get("url_encoding_safe_overrides"))
else:
raise RuntimeError(
"Metadata query did not return any results: %s" % path)
self._getFileExtensionMetadata(self.metadata.get("file_ext"))
for k, v in asset_mapping.get("column_value_templates", {}).items():
try:
self.metadata[k] = v.format(**self.metadata)
except KeyError as e:
logging.warning(
"Column value template substitution error: %s" %
format_exception(e))
continue
self._urlEncodeMetadata(
asset_mapping.get("url_encoding_safe_overrides"))
def _getFileExtensionMetadata(self, ext):
ext_map = self.config.get("file_ext_mappings", {})
entry = ext_map.get(ext)
if entry:
self._updateFileMetadata(entry)
def _getFileHatracMetadata(self, asset_mapping):
try:
hatrac_templates = asset_mapping["hatrac_templates"]
# URI is required
self.metadata["URI"] = hatrac_templates["hatrac_uri"].format(
**self.metadata)
# overridden content-disposition is optional
content_disposition = hatrac_templates.get("content-disposition")
self.metadata["content-disposition"] = \
None if not content_disposition else content_disposition.format(**self.metadata)
self._urlEncodeMetadata(
asset_mapping.get("url_encoding_safe_overrides"))
except KeyError as e:
raise ConfigurationError("Hatrac template substitution error: %s" %
format_exception(e))
def _hatracUpload(self,
uri,
file_path,
md5=None,
sha256=None,
content_type=None,
content_disposition=None,
chunked=True,
create_parents=True,
allow_versioning=True,
callback=None):
# check if there is already an in-progress transfer for this file,
# and if so, that the local file has not been modified since the original upload job was created
can_resume = False
transfer_state = self.getTransferState(file_path)
if transfer_state:
content_md5 = transfer_state.get("content-md5")
content_sha256 = transfer_state.get("content-sha256")
if content_md5 or content_sha256:
if (md5 == content_md5) or (sha256 == content_sha256):
can_resume = True
if transfer_state and can_resume:
logging.info(
"Resuming upload (%s) of file: [%s] to host %s. Please wait..."
% (self.getTransferStateStatus(file_path), file_path,
transfer_state.get("host")))
path = transfer_state["target"]
job_id = transfer_state['url'].rsplit("/", 1)[1]
if not (transfer_state["total"] == transfer_state["completed"]):
self.store.put_obj_chunked(
path,
file_path,
job_id,
callback=callback,
start_chunk=transfer_state["completed"])
return self.store.finalize_upload_job(path, job_id)
else:
logging.info("Uploading file: [%s] to host %s. Please wait..." %
(self.getFileDisplayName(file_path), self.server_url))
return self.store.put_loc(uri,
file_path,
md5=md5,
sha256=sha256,
content_type=content_type,
content_disposition=content_disposition,
chunked=chunked,
create_parents=create_parents,
allow_versioning=allow_versioning,
callback=callback)
def _catalogRecordCreate(self, catalog_table, row, default_columns=None):
"""
:param catalog_table:
:param row:
:param default_columns:
:return:
"""
if self.cancelled:
return None
try:
missing = self.catalog.validateRowColumns(row, catalog_table)
if missing:
raise CatalogCreateError(
"Unable to update catalog entry because one or more specified columns do not exist in the "
"target table: [%s]" % ','.join(missing))
if not default_columns:
default_columns = self.catalog.getDefaultColumns(
row, catalog_table)
default_param = (
'?defaults=%s' %
','.join(default_columns)) if len(default_columns) > 0 else ''
# for default in default_columns:
# row[default] = None
create_uri = '/entity/%s%s' % (catalog_table, default_param)
logging.debug(
"Attempting catalog record create [%s] with data: %s" %
(create_uri, json.dumps(row)))
return self.catalog.post(create_uri, json=[row]).json()
except:
(etype, value, traceback) = sys.exc_info()
raise CatalogCreateError(format_exception(value))
def _catalogRecordUpdate(self, catalog_table, old_row, new_row):
"""
:param catalog_table:
:param new_row:
:param old_row:
:return:
"""
if self.cancelled:
return None
try:
keys = sorted(list(new_row.keys()))
old_keys = sorted(list(old_row.keys()))
if keys != old_keys:
raise RuntimeError(
"Cannot update catalog - "
"new row column list and old row column list do not match: New: %s != Old: %s"
% (keys, old_keys))
combined_row = {
'o%d' % i: old_row[keys[i]]
for i in range(len(keys))
}
combined_row.update(
{'n%d' % i: new_row[keys[i]]
for i in range(len(keys))})
update_uri = '/attributegroup/%s/%s;%s' % (catalog_table, ','.join(
["o%d:=%s" % (i, urlquote(keys[i]))
for i in range(len(keys))]), ','.join([
"n%d:=%s" % (i, urlquote(keys[i]))
for i in range(len(keys))
]))
logging.debug(
"Attempting catalog record update [%s] with data: %s" %
(update_uri, json.dumps(combined_row)))
return self.catalog.put(update_uri, json=[combined_row]).json()
except:
(etype, value, traceback) = sys.exc_info()
raise CatalogUpdateError(format_exception(value))
def defaultFileCallback(self, **kwargs):
completed = kwargs.get("completed")
total = kwargs.get("total")
file_path = kwargs.get("file_path")
file_name = os.path.basename(file_path) if file_path else ""
job_info = kwargs.get("job_info", {})
job_info.update()
if completed and total:
file_name = " [%s]" % file_name
job_info.update({
"completed": completed,
"total": total,
"host": kwargs.get("host")
})
status = "Uploading file%s: %d%% complete" % (
file_name,
round(((float(completed) / float(total)) % 100) * 100))
self.setTransferState(file_path, job_info)
else:
summary = kwargs.get("summary", "")
file_name = "Uploaded file: [%s] " % file_name
status = file_name # + summary
if status:
# logging.debug(status)
pass
if self.cancelled:
return -1
return True
def loadTransferState(self):
transfer_state_file_path = self.getDeployedTransferStateFilePath()
transfer_state_dir = os.path.dirname(transfer_state_file_path)
try:
if not os.path.isdir(transfer_state_dir):
try:
os.makedirs(transfer_state_dir)
except OSError as error:
if error.errno != errno.EEXIST:
raise
if not os.path.isfile(transfer_state_file_path):
with open(transfer_state_file_path, "w") as tsfp:
json.dump(self.transfer_state, tsfp)
self.transfer_state_fp = \
open(transfer_state_file_path, 'r+')
self.transfer_state = json.load(self.transfer_state_fp,
object_pairs_hook=OrderedDict)
except Exception as e:
logging.warning(
"Unable to read transfer state file, transfer checkpointing will not be available. "
"Error: %s" % format_exception(e))
def getTransferState(self, file_path):
return self.transfer_state.get(file_path)
def setTransferState(self, file_path, transfer_state):
self.transfer_state[file_path] = transfer_state
self.writeTransferState()
def delTransferState(self, file_path):
transfer_state = self.getTransferState(file_path)
if transfer_state:
del self.transfer_state[file_path]
self.writeTransferState()
def writeTransferState(self):
if not self.transfer_state_fp:
return
try:
self.transfer_state_fp.seek(0, 0)
self.transfer_state_fp.truncate()
json.dump(self.transfer_state, self.transfer_state_fp, indent=2)
self.transfer_state_fp.flush()
except Exception as e:
logging.warning("Unable to write transfer state file: %s" %
format_exception(e))
def cleanupTransferState(self):
if self.transfer_state_fp and not self.transfer_state_fp.closed:
try:
self.transfer_state_fp.flush()
self.transfer_state_fp.close()
except Exception as e:
logging.warning(
"Unable to flush/close transfer state file: %s" %
format_exception(e))
def getTransferStateStatus(self, file_path):
transfer_state = self.getTransferState(file_path)
if transfer_state:
return "%d%% complete" % (round(
((float(transfer_state["completed"]) /
float(transfer_state["total"])) % 100) * 100))
return None
