deriva 1.7.7__tar.gz → 1.7.8__tar.gz

{deriva-1.7.7/deriva.egg-info → deriva-1.7.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deriva
-Version: 1.7.7
+Version: 1.7.8
 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
@@ -25,7 +25,6 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: packaging
 Requires-Dist: requests
-Requires-Dist: certifi
 Requires-Dist: pika
 Requires-Dist: urllib3<3,>=1.26
 Requires-Dist: portalocker>=1.2.1

{deriva-1.7.7 → deriva-1.7.8}/deriva/core/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.7.7"
+__version__ = "1.7.8"
 
 from deriva.core.utils.core_utils import *
 from deriva.core.base_cli import BaseCLI, KeyValuePairArgs

{deriva-1.7.7 → deriva-1.7.8}/deriva/transfer/__init__.py

@@ -4,8 +4,8 @@ from deriva.transfer.download.deriva_download import DerivaDownload, GenericDown
 from deriva.transfer.download.deriva_download_cli import DerivaDownloadCLI
 from deriva.transfer.download.deriva_export import DerivaExport, DerivaExportCLI
 
-from deriva.transfer.upload.deriva_upload import DerivaUpload, GenericUploader, DerivaUploadError, DerivaUploadError, \
-    DerivaUploadConfigurationError, DerivaUploadCatalogCreateError, DerivaUploadCatalogUpdateError, \
+from deriva.transfer.upload.deriva_upload import DerivaUpload, GenericUploader, UploadState, DerivaUploadError, \
+    DerivaUploadError, DerivaUploadConfigurationError, DerivaUploadCatalogCreateError, DerivaUploadCatalogUpdateError, \
     DerivaUploadAuthenticationError
 from deriva.transfer.upload.deriva_upload_cli import DerivaUploadCLI
 

{deriva-1.7.7 → deriva-1.7.8}/deriva/transfer/download/deriva_export.py

@@ -5,7 +5,6 @@ import traceback
 import requests
 import argparse
 import logging
-import certifi
 import datetime
 from collections.abc import Mapping, Iterable
 from requests.exceptions import HTTPError, ConnectionError, Timeout
@@ -125,7 +124,7 @@ class DerivaExport:
 
         filename = parse_content_disposition(content_disposition)
         output_path = os.path.abspath(os.path.join(self.output_dir, filename))
-        with self.session.get(url, stream=True, verify=certifi.where()) as r:
+        with self.session.get(url, stream=True) as r:
             if r.status_code != 200:
                 file_error = "File [%s] transfer failed." % output_path
                 url_error = 'HTTP GET Failed for url: %s' % url

{deriva-1.7.7 → deriva-1.7.8}/deriva/transfer/download/processors/query/base_query_processor.py

@@ -1,6 +1,5 @@
 import os
 import errno
-import certifi
 import requests
 from deriva.core import urlsplit, get_new_requests_session, stob, make_dirs, format_exception, DEFAULT_SESSION_CONFIG
 from deriva.transfer.download import DerivaDownloadError, DerivaDownloadConfigurationError, \
@@ -162,7 +161,7 @@ class BaseQueryProcessor(BaseProcessor):
         if cookies:
             session.cookies.update(cookies)
         if login_params and auth_url:
-            r = session.post(auth_url, data=login_params, verify=certifi.where())
+            r = session.post(auth_url, data=login_params)
             if r.status_code > 203:
                 raise DerivaDownloadError(
                     'GetExternalSession Failed with Status Code: %s\n%s\n' % (r.status_code, r.text))

{deriva-1.7.7 → deriva-1.7.8}/deriva/transfer/download/processors/query/file_download_query_processor.py

@@ -4,7 +4,6 @@ import uuid
 import datetime
 import logging
 import requests
-import certifi
 from bdbag import bdbag_ro as ro
 from deriva.core import urlsplit, format_exception, get_transfer_summary, make_dirs, DEFAULT_CHUNK_SIZE
 from deriva.core.utils.mime_utils import parse_content_disposition
@@ -39,7 +38,7 @@ class FileDownloadQueryProcessor(BaseQueryProcessor):
             else:
                 headers.update(self.HEADERS)
             session = self.getExternalSession(host)
-            with session.get(url, headers=headers, stream=True, verify=certifi.where()) as r:
+            with session.get(url, headers=headers, stream=True) as r:
                 if r.status_code != 200:
                     file_error = "File [%s] transfer failed." % output_path
                     url_error = 'HTTP GET Failed for url: %s' % url

{deriva-1.7.7 → deriva-1.7.8}/deriva/transfer/upload/deriva_upload.py

@@ -157,8 +157,12 @@ class DerivaUpload(object):
 
         # determine identity
         if self.credentials:
-            attributes = self.catalog.get_authn_session().json()
-            self.identity = attributes.get("client", self.identity)
+            try:
+                attributes = self.catalog.get_authn_session().json()
+                self.identity = attributes.get("client", self.identity)
+            except Exception as e:
+                # not a big deal since the credential token being used could be expired
+                logger.debug("Unable to determine user identity from existing credential (may be expired): %s" % e)
 
         # init dcctx cid to a default
         self.set_dcctx_cid(self.dcctx_cid)
@@ -342,7 +346,7 @@ class DerivaUpload(object):
         return '%s:%s' % (urlquote(schema_name), urlquote(table_name))
 
     @staticmethod
-    def interpolateDict(src, dst, allowNone=False):
+    def interpolateDict(src, dst, allow_none=False, allow_none_column_list=[]):
         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__))
@@ -362,10 +366,10 @@ class DerivaUpload(object):
                     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:
+        # remove all None valued entries in the dest, if globally disallowed or the column is not explicitly allowed
+        empty = [k for k, v in dst.items() if v is None]
+        for k in empty:
+            if not allow_none or (allow_none and k not in allow_none_column_list):
                 del dst[k]
 
         return dst
@@ -720,7 +724,9 @@ class DerivaUpload(object):
 
         # 8. Update an existing record, if necessary
         column_map = asset_mapping.get("column_map", {})
-        updated_record = self.interpolateDict(self.metadata, column_map)
+        allow_none_col_list = asset_mapping.get("allow_empty_columns_on_update", [])
+        allow_none = True if allow_none_col_list else False
+        updated_record = self.interpolateDict(self.metadata, column_map, allow_none, allow_none_col_list)
         if updated_record != record:
             record_update_template = asset_mapping.get("record_update_template")
             require_record_update_template = stob(asset_mapping.get("require_record_update_template", False))
@@ -794,7 +800,7 @@ class DerivaUpload(object):
             if result:
                 record = result[0]
                 self._updateFileMetadata(record)
-            return self.interpolateDict(self.metadata, column_map, allowNone=True), record
+            return self.interpolateDict(self.metadata, column_map, allow_none=True), record
 
     def _urlEncodeMetadata(self, safe_overrides=None):
         urlencoded = dict()

{deriva-1.7.7 → deriva-1.7.8/deriva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deriva
-Version: 1.7.7
+Version: 1.7.8
 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
@@ -25,7 +25,6 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: packaging
 Requires-Dist: requests
-Requires-Dist: certifi
 Requires-Dist: pika
 Requires-Dist: urllib3<3,>=1.26
 Requires-Dist: portalocker>=1.2.1

{deriva-1.7.7 → deriva-1.7.8}/deriva.egg-info/requires.txt

@@ -1,6 +1,5 @@
 packaging
 requests
-certifi
 pika
 urllib3<3,>=1.26
 portalocker>=1.2.1

{deriva-1.7.7 → deriva-1.7.8}/setup.py

@@ -64,7 +64,6 @@ setup(
     install_requires=[
         'packaging',
         'requests',
-        'certifi',
         'pika',
         'urllib3>=1.26,<3',
         'portalocker>=1.2.1',