deriva 1.7.6__tar.gz → 1.7.7__tar.gz

{deriva-1.7.6/deriva.egg-info → deriva-1.7.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deriva
-Version: 1.7.6
+Version: 1.7.7
 Summary: Python APIs and CLIs (Command-Line Interfaces) for the DERIVA platform.
 Home-page: https://github.com/informatics-isi-edu/deriva-py
 Author: USC Information Sciences Institute, Informatics Systems Research Division

{deriva-1.7.6 → deriva-1.7.7}/deriva/core/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.7.6"
+__version__ = "1.7.7"
 
 from deriva.core.utils.core_utils import *
 from deriva.core.base_cli import BaseCLI, KeyValuePairArgs

{deriva-1.7.6 → deriva-1.7.7}/deriva/core/base_cli.py

@@ -53,6 +53,11 @@ class BaseCLI(object):
 
         return args
 
+    # Function to convert comma-separated CLI input into a tuple
+    @staticmethod
+    def parse_tuple(value):
+        # Split the input by commas and convert to a tuple
+        return tuple(map(float, value.split(',')))
 
 class KeyValuePairArgs(argparse.Action):
     def __init__(self, option_strings, dest, nargs=None, **kwargs):

{deriva-1.7.6 → deriva-1.7.7}/deriva/core/hatrac_store.py

@@ -184,6 +184,7 @@ class HatracStore(DerivaBinding):
 
         headers = headers.copy()
 
+        file_opened = False
         if hasattr(data, 'read') and hasattr(data, 'seek'):
             data.seek(0, os.SEEK_END)
             file_size = data.tell()
@@ -192,6 +193,7 @@ class HatracStore(DerivaBinding):
         else:
             file_size = os.path.getsize(data)
             f = open(data, 'rb')
+            file_opened = True
 
         if not (md5 or sha256):
             md5 = hu.compute_hashes(f, hashes=['md5'])['md5'][1]
@@ -208,7 +210,8 @@ class HatracStore(DerivaBinding):
                 if (md5 and r.headers.get('Content-MD5') == md5 or
                         sha256 and r.headers.get('Content-SHA256') == sha256):
                     # object already has same content so skip upload
-                    f.close()
+                    if file_opened:
+                        f.close()
                     return r.headers.get('Content-Location')
                 elif not allow_versioning:
                     raise NotModified("The data cannot be uploaded because content already exists for this object "
@@ -232,6 +235,8 @@ class HatracStore(DerivaBinding):
         url = '%s%s' % (url.rstrip("/") if url.endswith("/") else url,
                         "" if not parents else "?parents=%s" % str(parents).lower())
         r = self._session.put(url, data=f, headers=headers)
+        if file_opened:
+            f.close()
         self._response_raise_for_status(r)
         loc = r.text.strip() or r.url
         if loc.startswith(self._server_uri):

{deriva-1.7.6 → deriva-1.7.7}/deriva/transfer/download/deriva_download.py

@@ -8,8 +8,8 @@ import requests
 from requests.exceptions import HTTPError
 from bdbag import bdbag_api as bdb, bdbag_ro as ro, BAG_PROFILE_TAG, BDBAG_RO_PROFILE_ID
 from bdbag.bdbagit import BagValidationError
-from deriva.core import ErmrestCatalog, HatracStore, format_exception, get_credential, format_credential, read_config, \
-    stob, Megabyte, __version__ as VERSION
+from deriva.core import DerivaServer, ErmrestCatalog, HatracStore, format_exception, get_credential, \
+                         format_credential, read_config, stob, Megabyte, __version__ as VERSION
 from deriva.core.utils.version_utils import get_installed_version
 from deriva.transfer.download.processors import find_query_processor, find_transform_processor, find_post_processor
 from deriva.transfer.download.processors.base_processor import LOCAL_PATH_KEY, REMOTE_PATHS_KEY, SERVICE_URL_KEY, \
@@ -76,14 +76,9 @@ class DerivaDownload(object):
                                                  password=password)
 
         # catalog and file store initialization
-        if self.catalog:
-            del self.catalog
-        self.catalog = ErmrestCatalog(
-            protocol, self.hostname, catalog_id, self.credentials, session_config=session_config)
-        if self.store:
-            del self.store
-        self.store = HatracStore(
-            protocol, self.hostname, self.credentials, session_config=session_config)
+        server = DerivaServer(protocol, self.hostname, credentials=self.credentials, session_config=session_config)
+        self.catalog = server.connect_ermrest(catalog_id)
+        self.store = HatracStore(protocol, self.hostname, self.credentials, session_config=session_config)
 
         # init dcctx cid
         self.set_dcctx_cid(kwargs.get("dcctx_cid", "api/" + self.__class__.__name__))

{deriva-1.7.6 → deriva-1.7.7}/deriva/transfer/download/deriva_export.py

@@ -29,7 +29,8 @@ Client tool for interacting with DERIVA Export service.
 :param envars (dict): A dictionary of variables used for template substitution. Optional.
 :param output_dir (str): The directory where exported data will be stored (default: "."). Optional.
 :param defer_download (bool): Whether to defer the actual data download. Optional.
-:param timeout (int): Timeout value for export operations. Optional.
+:param timeout (tuple) OR (float): Timeout value as a tuple of floats in seconds for (connect,read) export operations. 
+        If a single float value is passed, it will apply to both connect and read operations. Optional.
 :param export_type (str): The type of export to perform (default: "bdbag"). Optional.
 
 :return: The full path to the downloaded file. If "defer_download" is True, the URL(s) where the export can be downloaded.
@@ -47,10 +48,20 @@ class DerivaExport:
         self.base_server_uri = "https://" + self.host
         self.service_url = self.base_server_uri + EXPORT_SERVICE_PATH % self.export_type
         self.session_config = DEFAULT_SESSION_CONFIG.copy()
-        if self.timeout is not None:
-            self.session_config["timeout"] = self.timeout
+        if isinstance(self.timeout, tuple):
+            if len(self.timeout) == 2:
+                self.session_config["timeout"] = self.timeout
+            else:
+                self.session_config["timeout"] = float(self.timeout[0])
+        elif self.timeout is not None:
+            try:
+                self.session_config["timeout"] = float(self.timeout)
+            except ValueError:
+                logger.warning("Unparseable timeout value: %r. Defaults will be used: %r." %
+                               (self.timeout, self.session_config["timeout"]))
         self.session = get_new_requests_session(self.service_url, self.session_config)
         self.dcctx = DerivaClientContext()
+        self.dcctx['cid'] = kwargs.get("dcctx_cid", "api/" + self.__class__.__name__)
         self.session.headers.update({'deriva-client-context': self.dcctx.encoded()})
 
         # credential initialization
@@ -190,8 +201,10 @@ class DerivaExportCLI(BaseCLI):
         BaseCLI.__init__(self, description, epilog, **kwargs)
         self.parser.add_argument("--defer-download", action="store_true",
                                  help="Do not download exported file(s). Default: False")
-        self.parser.add_argument("--timeout", metavar="<seconds>",
-                                 help="Total number of seconds elapsed before the download is aborted.")
+        self.parser.add_argument("--timeout", metavar="<connect,read>", type=BaseCLI.parse_tuple,
+                                 help="Timeout value(s) in seconds (int or float) for connect and read operations. "
+                                      "Separate using commas. If a single value is provided it will be used for both "
+                                      "connect and read timeouts.")
         self.parser.add_argument("--export-type", choices=["bdbag", "file"], default="bdbag",
                                  help="Export type: {bdbag|file}. Default is bdbag.",)
         self.parser.add_argument("--output-dir", metavar="<output dir>", default=".",
@@ -212,7 +225,7 @@ class DerivaExportCLI(BaseCLI):
             sys.stderr.write("\n")
 
         try:
-            exporter = DerivaExport(**vars(args))
+            exporter = DerivaExport(**vars(args), dcctx_cid="cli/" + self.__class__.__name__)
             exporter.export()
         except (DerivaDownloadError, DerivaDownloadConfigurationError, DerivaDownloadAuthenticationError,
                 DerivaDownloadAuthorizationError, DerivaDownloadTimeoutError) as e:

{deriva-1.7.6 → deriva-1.7.7}/deriva/transfer/download/processors/query/base_query_processor.py

@@ -2,7 +2,7 @@ import os
 import errno
 import certifi
 import requests
-from deriva.core import urlsplit, get_new_requests_session, stob, make_dirs, DEFAULT_SESSION_CONFIG
+from deriva.core import urlsplit, get_new_requests_session, stob, make_dirs, format_exception, DEFAULT_SESSION_CONFIG
 from deriva.transfer.download import DerivaDownloadError, DerivaDownloadConfigurationError, \
     DerivaDownloadAuthenticationError, DerivaDownloadAuthorizationError
 from deriva.transfer.download.processors.base_processor import BaseProcessor, \
@@ -83,12 +83,12 @@ class BaseQueryProcessor(BaseProcessor):
                 return self.catalog.get(self.query, headers=headers).json()
         except requests.HTTPError as e:
             if e.response.status_code == 401:
-                raise DerivaDownloadAuthenticationError(e)
+                raise DerivaDownloadAuthenticationError(format_exception(e))
             if e.response.status_code == 403:
-                raise DerivaDownloadAuthorizationError(e)
+                raise DerivaDownloadAuthorizationError(format_exception(e))
             if as_file:
                 os.remove(self.output_abspath)
-            raise DerivaDownloadError("Error executing catalog query: %s" % e)
+            raise DerivaDownloadError("Error executing catalog query: %s" % format_exception(e))
         except Exception:
             if as_file:
                 os.remove(self.output_abspath)

{deriva-1.7.6 → deriva-1.7.7/deriva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deriva
-Version: 1.7.6
+Version: 1.7.7
 Summary: Python APIs and CLIs (Command-Line Interfaces) for the DERIVA platform.
 Home-page: https://github.com/informatics-isi-edu/deriva-py
 Author: USC Information Sciences Institute, Informatics Systems Research Division