deriva 1.7.11__py3-none-any.whl → 1.7.12__py3-none-any.whl

deriva/core/utils/globus_auth_utils.py

@@ -1179,19 +1179,13 @@ class DerivaGlobusAuthUtilCLI(BaseCLI):
                 self.gau = GlobusAuthUtil(**vars(args))
 
             response = args.func(args)
-            if args.pretty:
-                if isinstance(response, dict) or isinstance(response, list):
-                    try:
-                        print(json.dumps(response, indent=2))
-                        return
-                    except:
-                        pprint(response)
-                        return
-                elif not isinstance(response, str):
-                    pprint(response)
-                    return
-            print(response)
-            return
+            if isinstance(response, dict) or isinstance(response, list):
+                print(json.dumps(response, indent=2 if args.pretty else None))
+            elif not isinstance(response, str):
+                pprint(response)
+            else:
+                print(response)
+            return 0
 
         except UsageException as e:
             eprint("{prog} {subcmd}: {msg}".format(prog=self.parser.prog, subcmd=args.subcmd, msg=e))

deriva/transfer/backup/deriva_backup.py

@@ -54,8 +54,8 @@ class DerivaBackup(DerivaDownload):
 
             logging.debug("Inspecting catalog model...")
             model = self.catalog.getCatalogModel()
-            # if we dont have catalog ownership rights, its a hard error for now
-            if not model.acls:
+            ignore_acl = kwargs.get("ignore_acl", False)
+            if not model.acls and not ignore_acl:
                 raise DerivaBackupAuthorizationError("Only catalog owners may perform full catalog dumps.")
 
             if kwargs.get("no_data", False):

deriva/transfer/backup/deriva_backup_cli.py

@@ -25,6 +25,11 @@ class DerivaBackupCLI(DerivaDownloadCLI):
                                           "references to asset files in the bag's \"fetch.txt\" file.")
         self.parser.add_argument("--bag-archiver", choices=['zip', 'tgz', 'bz2'],
                                  help="Format for compressed bag output.")
+        self.parser.add_argument("--ignore-acl", action="store_true",
+                                     help="If no ACL is present in the catalog schema, which may mean the user is not "
+                                          "the catalog owner, proceed anyway. WARNING: this will result in the backup "
+                                          "process running under whatever permissions the user possesses, which may be "
+                                          "limited enough to result in incomplete schema, incomplete data, or both.")
         self.parser.add_argument("--exclude-data", default=list(),
                                  type=lambda s: [item.strip() for item in s.split(',')],
                                  metavar="<schema>, <schema:table>, ...",

deriva/transfer/upload/deriva_upload.py

@@ -695,6 +695,16 @@ class DerivaUpload(object):
         # 6. Perform the Hatrac upload
         self._getFileHatracMetadata(asset_mapping)
         hatrac_options = asset_mapping.get("hatrac_options", {})
+        v = hatrac_options.get("chunk_size")
+        try:
+            chunk_size = int(v) if v not in (None, "") else DEFAULT_CHUNK_SIZE
+        except (TypeError, ValueError):
+            chunk_size = DEFAULT_CHUNK_SIZE
+        if chunk_size <= 0:
+            chunk_size = DEFAULT_CHUNK_SIZE
+            logger.warning(
+                "Specified chunk_size must be a positive integer (> 0) - falling back to default chunk size: %d." %
+                DEFAULT_CHUNK_SIZE)
         file_size = self.metadata["file_size"]
         versioned_uri = \
             self._hatracUpload(self.metadata["URI"],
@@ -704,8 +714,10 @@ class DerivaUpload(object):
                                content_type=self.guessContentType(file_path),
                                content_disposition=self.metadata.get("content-disposition"),
                                chunked=True if (file_size > DEFAULT_CHUNK_SIZE or file_size == 0) else False,
+                               chunk_size=chunk_size,
                                create_parents=stob(hatrac_options.get("create_parents", True)),
                                allow_versioning=stob(hatrac_options.get("allow_versioning", True)),
+                               force=stob(hatrac_options.get("force", False)),
                                callback=callback)
         logger.debug("Hatrac upload successful. Result object URI: %s" % versioned_uri)
         versioned_uris = True
@@ -942,9 +954,11 @@ class DerivaUpload(object):
                       content_type=None,
                       content_disposition=None,
                       chunked=True,
+                      chunk_size=DEFAULT_CHUNK_SIZE,
                       create_parents=True,
                       allow_versioning=True,
-                      callback=None):
+                      callback=None,
+                      force=False):
 
         # 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
@@ -979,10 +993,12 @@ class DerivaUpload(object):
                                       content_type=content_type,
                                       content_disposition=content_disposition,
                                       chunked=chunked,
+                                      chunk_size=chunk_size,
                                       create_parents=create_parents,
                                       allow_versioning=allow_versioning,
                                       callback=callback,
-                                      cancel_job_on_error=False)
+                                      cancel_job_on_error=False,
+                                      force=force)
 
     def _get_catalog_table_columns(self, table):
         table_columns = set()

{deriva-1.7.11.dist-info → deriva-1.7.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva
-Version: 1.7.11
+Version: 1.7.12
 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
@@ -19,6 +19,8 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Python: >=3.8, <4
 Description-Content-Type: text/markdown
 License-File: LICENSE

{deriva-1.7.11.dist-info → deriva-1.7.12.dist-info}/RECORD

@@ -8,17 +8,17 @@ deriva/config/dump_catalog_annotations.py,sha256=QzaWDLfWIAQ0eWVV11zeceWgwDBOYIe
 deriva/config/rollback_annotation.py,sha256=vqrIcen-KZX8LDpu2OVNivzIHpQoQgWkZAChZJctvtk,3015
 deriva/config/examples/group_owner_policy.json,sha256=8v3GWM1F_BWnYD9x_f6Eo4kBDvyy8g7mRqujfoEKLNc,2408
 deriva/config/examples/self_serve_policy.json,sha256=pW-cqWz4rJNNXwY4eVZFkQ8gKCHclC9yDa22ylfcDqY,1676
-deriva/core/__init__.py,sha256=u3pzQuTb0mKvl0GenoQWGuiUMDDdzjVnoPXHmX5pdwY,4976
+deriva/core/__init__.py,sha256=eknMCmzhKiL-URSE8NKY6-D1OLP0oaFZKtiOjEeH3XI,4976
 deriva/core/annotation.py,sha256=PkAkPkxX1brQsb8_drR1Qj5QjQA5mjkpXhkq9NuZ1g8,13432
 deriva/core/base_cli.py,sha256=78Ilf3_f2xREQb3IIj6q0jwWAiXSObZszG0JURs36lA,2902
-deriva/core/catalog_cli.py,sha256=CwfTf7C81SpU1J_aPsWiIbPOBAyekkIh384KUivq5H8,23550
+deriva/core/catalog_cli.py,sha256=2Hq0yVVYtH7wSkGyXTvDjSJ8hwGfAMk7Z6X3JnwcKDA,23390
 deriva/core/datapath.py,sha256=h9WzLipAYctppoiZehyDNJdFpCnbU9-z-AWVD80z2Pk,90525
 deriva/core/deriva_binding.py,sha256=6yGXIbnayDtb9LU-JVK43zk02-aQwshrKiaLi1pru-8,13086
 deriva/core/deriva_server.py,sha256=nsW3gwg1sIaHl3BTf-nL41AkSj3dEpcEBlatvjvN8CQ,200
-deriva/core/ermrest_catalog.py,sha256=2mShQgo35DIQ-0UOEqu2VgCDTE3sUrQSWVDm1jW_tQ8,55547
-deriva/core/ermrest_model.py,sha256=oydtO6IU54ihjWQXcq0nfCyqAFJSW2FI9Z_0FjU7Uk0,124936
-deriva/core/hatrac_cli.py,sha256=l9QmneLRHSMiG_z9S83ea0QGVhTS3Wq1KGPEKEDpecM,14522
-deriva/core/hatrac_store.py,sha256=NcVuO4h4hswbEAct8tTKZ1pNtXBn74Nn9TelKN_jr8Q,22323
+deriva/core/ermrest_catalog.py,sha256=-iCYwuzO55HmDLB-BYGfQWDdqKTS4mYAfUlrBmq0KmY,55557
+deriva/core/ermrest_model.py,sha256=sgg9PF-Y1jg-2KUrM9WgpR3A0O8KcQ_wGs0_KG38ckM,128196
+deriva/core/hatrac_cli.py,sha256=G4iDQe7h45UCmd1uM6c1UpgLSu0lKiqUhm-OFirCFCY,15934
+deriva/core/hatrac_store.py,sha256=k783qeX3Wo1285ncN6Mr_Hbn9cSfmEDhSpQGF3dCm_M,24637
 deriva/core/mmo.py,sha256=dcB8akgsqbYMi22ClbVpOKVL6so8FjSDjSb6gP4_jFo,17852
 deriva/core/polling_ermrest_catalog.py,sha256=KsjiFqPQaHWnJZCVF5i77sdzfubqZHgMBbQ1p8V8D3s,10351
 deriva/core/schemas/app_links.schema.json,sha256=AxrkC2scxomM6N7jyjtdYA73BbZzPrmuqU8PYWe7okI,954
@@ -44,9 +44,9 @@ deriva/core/schemas/visible_columns.schema.json,sha256=-JKqvhfKT-5btKBtzKn3p6EgY
 deriva/core/schemas/visible_foreign_keys.schema.json,sha256=K-oa2qzj5EbmJCEyN6mN3vubblHENFxxbZEeQfFV_QQ,3364
 deriva/core/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva/core/utils/__init__.py,sha256=XSbGaWe44hebxYvoh5huFzZkMY6TSKPOCRSjUOvaY70,124
-deriva/core/utils/core_utils.py,sha256=bMPVBG0W5-OAPcY7rXYlIfPAofmN1We6h1uyzXYnR9s,19821
-deriva/core/utils/credenza_auth_utils.py,sha256=JX-sOwSltfmXbDWdaWJHP5gCMOOBkELKEsnnhqxoRk8,12435
-deriva/core/utils/globus_auth_utils.py,sha256=x5Dh4PlAMIKTm4b8nKUeuCMSFn7NMgj_NqtmnS_FM0I,57366
+deriva/core/utils/core_utils.py,sha256=rSidaI2oY_eAO6MT68QAK9eJTLpibcaPni5Rg5axYuU,29569
+deriva/core/utils/credenza_auth_utils.py,sha256=0LlZeYgivBiWGAnKie7qHtSNdOH13frPyd0DYDDkkBo,25705
+deriva/core/utils/globus_auth_utils.py,sha256=fzMFvNIkaaCHNMB6xXPXWCeo0DblLrVVbek6MzB9EY0,57184
 deriva/core/utils/hash_utils.py,sha256=JqUYVB3jXusCQYX9fkKmweUKBC0WQi8ZI2N8m-uKygQ,2299
 deriva/core/utils/mime_utils.py,sha256=ZT7pMjY2kQWBsgsGC3jY6kjfygdsIyiYW3BKNw_pPyg,1128
 deriva/core/utils/version_utils.py,sha256=HWNUQAZrPXu0oGjhG6gMNm3kWtfa3nR50vfH2uQxBA0,2954
@@ -57,8 +57,8 @@ deriva/seo/sitemap_cli.py,sha256=miCqRfpSj5Dx5BfJGSd8Pi2e4OOQjotDzP_JubukhCM,265
 deriva/transfer/__init__.py,sha256=VRxmElD5SIOGzrB1biUU8bP3_iXPMvJuau-9alU5oy0,1266
 deriva/transfer/backup/__init__.py,sha256=vxsZiDLMTJQPybXT89G-07GsUoLhnItTCbLdXcDSyeA,465
 deriva/transfer/backup/__main__.py,sha256=dT12--8C6sKGEtMhsYuy013ebXKpVnBJfhcQNlVtv6Y,361
-deriva/transfer/backup/deriva_backup.py,sha256=IO9Tmzx6jHfUCkP-41nSsAeOFLn9T-0HwQcpRLpM_zs,5228
-deriva/transfer/backup/deriva_backup_cli.py,sha256=T0tvPKWniRinMQt0qG7FI8AoK3GgtlT6EyBZmZCAjL8,2157
+deriva/transfer/backup/deriva_backup.py,sha256=CgMvi0HwQohf2F7bvPk3LF2sFs3AS8ikvNSStF2VETk,5223
+deriva/transfer/backup/deriva_backup_cli.py,sha256=GcutL_3JjzYMHMQ02pckLby_37b8rR48CXHjeYrPq60,2706
 deriva/transfer/download/__init__.py,sha256=Pr7Zud4AFsIWwopTxeC_pupslgCG_lzycO9w9Xyh88Q,350
 deriva/transfer/download/__main__.py,sha256=YUg7AZ07t_xaOgtfJnU_l1nkEHCCPR8sU5X-l1An6SY,363
 deriva/transfer/download/deriva_download.py,sha256=ulFrHHEDj3oJA2pAo7MGvGyDF9rA3l8yCUoK3FMvHEk,17100
@@ -88,7 +88,7 @@ deriva/transfer/restore/deriva_restore.py,sha256=s0h7cXit2USSdjrIfrj0dr7BJ0rrHHM
 deriva/transfer/restore/deriva_restore_cli.py,sha256=2ViZ1Lyl5ndXPKeJFCHHGnwzkg3DfHhTuRa_bN7eJm8,5603
 deriva/transfer/upload/__init__.py,sha256=4mlc_iUX-v7SpXzlCZmhxQtSiW5JeDGb2FX7bb1E6tY,304
 deriva/transfer/upload/__main__.py,sha256=hqnXtGpRqPthwpO6uvrnf_TQm7McheeyOt960hStSMY,340
-deriva/transfer/upload/deriva_upload.py,sha256=CFWhvsMl9Ndw6QJYvQoOsErwQuF1wOpgqGju8G0QgTQ,61708
+deriva/transfer/upload/deriva_upload.py,sha256=UPwg8qt_JJkCjpgN4JpLED0ITallTsCgcR30rOLbOAM,62514
 deriva/transfer/upload/deriva_upload_cli.py,sha256=-Q6xgiYabQziTQcMQdGNDAv-eLxCCHO-BCSo4umbDE4,5082
 deriva/transfer/upload/processors/__init__.py,sha256=sMM5xdJ82UIRdB1lGMKk7ft0BgtjS2oJ0sI4SQSqiIU,2481
 deriva/transfer/upload/processors/archive_processor.py,sha256=ID0lDwDn4vPe5nbxy6m28Ssj_TsZpK4df2xRrM6nJRQ,2015
@@ -98,9 +98,9 @@ deriva/transfer/upload/processors/metadata_update_processor.py,sha256=Hgu5huZf7Z
 deriva/transfer/upload/processors/rename_processor.py,sha256=UQ-JQuQgyYCGT-fU9kHA53kPdQ20kt-2Bb486od7B14,2423
 deriva/transfer/upload/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva/utils/__init__.py,sha256=jv2YF__bseklT3OWEzlqJ5qE24c4aWd5F4r0TTjOrWQ,65
-deriva-1.7.11.dist-info/licenses/LICENSE,sha256=tAkwu8-AdEyGxGoSvJ2gVmQdcicWw3j1ZZueVV74M-E,11357
-deriva-1.7.11.dist-info/METADATA,sha256=8K51AvD17zR_kZpJf2PDUA8ObbFUbSBSuIADf_9yS_M,1840
-deriva-1.7.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-deriva-1.7.11.dist-info/entry_points.txt,sha256=uS-e7FxTP7lVm-QJdq_ErytmAbXvlRkEvrjab33ctRE,922
-deriva-1.7.11.dist-info/top_level.txt,sha256=OoTnCAuRnf-pPKMre5HA7mgLMIPl_2-lAWoZ63y74-U,7
-deriva-1.7.11.dist-info/RECORD,,
+deriva-1.7.12.dist-info/licenses/LICENSE,sha256=tAkwu8-AdEyGxGoSvJ2gVmQdcicWw3j1ZZueVV74M-E,11357
+deriva-1.7.12.dist-info/METADATA,sha256=OTDbjqhWLZwSiWGwo9aTcV_Alp9vvYqbN4repIpNo9w,1944
+deriva-1.7.12.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+deriva-1.7.12.dist-info/entry_points.txt,sha256=uS-e7FxTP7lVm-QJdq_ErytmAbXvlRkEvrjab33ctRE,922
+deriva-1.7.12.dist-info/top_level.txt,sha256=OoTnCAuRnf-pPKMre5HA7mgLMIPl_2-lAWoZ63y74-U,7
+deriva-1.7.12.dist-info/RECORD,,

{deriva-1.7.11.dist-info → deriva-1.7.12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any