NGPIris 5.2.0.dev1__tar.gz → 5.2.1.dev1__tar.gz

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/NGPIris/cli/__init__.py

@@ -94,11 +94,13 @@ def upload(context : Context, bucket : str, source : str, destination : str):
     """
     hcph : HCPHandler = get_HCPHandler(context)
     hcph.mount_bucket(bucket)
-    source = add_trailing_slash(source)
     destination = add_trailing_slash(destination)
     if Path(source).is_dir():
+        source = add_trailing_slash(source)
         hcph.upload_folder(source, destination)
     else:
+        file_name = Path(source).name
+        destination += file_name
         hcph.upload_file(source, destination)
 
 @cli.command()

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/NGPIris/hcp/hcp.py

@@ -67,13 +67,30 @@ class HCPHandler:
         self.hcp = credentials_handler.hcp
         self.endpoint = "https://" + self.hcp["endpoint"]
 
+        gmc_tenant_map = {
+            "gmc-joint" : "vgtn0008",
+            "gmc-west" : "vgtn0012",
+            "gmc-southeast" : "vgtn0014",
+            "gmc-south" : "vgtn0015",
+            "gmc-orebro" : "vgtn0016",
+            "gmc-karolinska" : "vgtn0017",
+            "gmc-north" : "vgtn0018",
+            "gmc-uppsala" : "vgtn0019"
+        }
+
         self.tenant = None
         for endpoint_format_string in ["https://{}.ngp-fs1000.vgregion.se", "https://{}.ngp-fs2000.vgregion.se", "https://{}.ngp-fs3000.vgregion.se", "https://{}.vgregion.sjunet.org"]:
             tenant_parse = parse(endpoint_format_string, self.endpoint) 
             if type(tenant_parse) is Result:
-                self.tenant = str(tenant_parse[0])
+                tenant = str(tenant_parse[0])
+                if endpoint_format_string == "https://{}.vgregion.sjunet.org": # Check if endpoint is Sjunet
+                    self.tenant = gmc_tenant_map[tenant]
+                else:
+                    self.tenant = tenant
+                
                 break
         
+
         if not self.tenant:
             raise RuntimeError("Unable to parse endpoint. Make sure that you have entered the correct endpoint in your credentials JSON file. Hint: The endpoint should *not* contain \"https://\" or port numbers")
         self.base_request_url = self.endpoint + ":9090/mapi/tenants/" + self.tenant
@@ -403,6 +420,9 @@ class HCPHandler:
             file_name = Path(local_file_path).name
             key = file_name
 
+        if "\\" in local_file_path:
+            raise RuntimeError("The \"\\\" character is not allowed in the file path")
+
         if self.object_exists(key):
             raise ObjectAlreadyExist("The object \"" + key + "\" already exist in the mounted bucket")
         else:

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/NGPIris.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: NGPIris
-Version: 5.2.0.dev1
+Version: 5.2.1.dev1
 Author-email: Erik Brink <erik.brink@gu.se>, Isak Sylvin <isak.sylvin@gu.se>
 Description-Content-Type: text/markdown
 License-File: LICENSE

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/NGPIris.egg-info/SOURCES.txt

@@ -114,6 +114,7 @@ docs/_build/html/_static/styles/furo.css.map
 tests/test_hci.py
 tests/test_hcp.py
 tests/test_parse_credentials.py
+tests/data/.DS_Store
 tests/data/80MB_test_file
 tests/data/complete_creds_0.json
 tests/data/complete_creds_1.json

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: NGPIris
-Version: 5.2.0.dev1
+Version: 5.2.1.dev1
 Author-email: Erik Brink <erik.brink@gu.se>, Isak Sylvin <isak.sylvin@gu.se>
 Description-Content-Type: text/markdown
 License-File: LICENSE

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "NGPIris"
-version = "5.2.0.dev1"
+version = "5.2.1.dev1"
 readme = "README.md"
 dependencies = [
     "requests >= 2.31.0",
@@ -32,6 +32,10 @@ inputs = ["NGPIris"]
 pythonpath = [
   "."
 ]
+testpaths = [
+  "tests"
+]
+addopts = "--strict-markers"  # Adds command-line options
 filterwarnings = "ignore::urllib3.connectionpool.InsecureRequestWarning"
 
 [project.scripts]

{ngpiris-5.2.0.dev1 → ngpiris-5.2.1.dev1}/tests/test_hci.py

@@ -1,10 +1,14 @@
 
+from configparser import ConfigParser
 from NGPIris.hci import HCIHandler
 from random import randint
 from json import dump
 from os import remove
 
-hci_h = HCIHandler("credentials/testCredentials.json")
+ini_config = ConfigParser()
+ini_config.read("tests/test_conf.ini")
+
+hci_h = HCIHandler(ini_config.get("General", "credentials_path"))
 hci_h.request_token()
 
 def test_list_index_names_type() -> None:

ngpiris-5.2.1.dev1/tests/test_hcp.py

@@ -0,0 +1,213 @@
+
+
+from pathlib import Path
+from filecmp import cmp
+from typing import Any, Callable
+
+from conftest import CustomConfig
+
+from NGPIris.hcp import HCPHandler
+
+# --------------------------- Helper fucntions ---------------------------------
+
+def _without_mounting(hcp_h : HCPHandler, hcp_h_method : Callable[..., Any]) -> None:
+    hcp_h.bucket_name = None
+    try:
+        hcp_h_method(hcp_h)
+    except:
+        assert True
+    else: # pragma: no cover
+        assert False
+
+# --------------------------- Test suite ---------------------------------------
+
+def test_list_buckets(custom_config : CustomConfig) -> None:
+    assert custom_config.hcp_h.list_buckets() 
+
+def test_mount_bucket(custom_config : CustomConfig) -> None:
+    custom_config.hcp_h.mount_bucket(custom_config.test_bucket) 
+
+def test_mount_nonexisting_bucket(custom_config : CustomConfig) -> None:
+    try:
+        custom_config.hcp_h.mount_bucket("aBucketThatDoesNotExist") 
+    except:
+        assert True
+    else: # pragma: no cover
+        assert False
+
+def test_test_connection(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.test_connection() 
+
+def test_test_connection_with_bucket_name(custom_config : CustomConfig) -> None:
+    custom_config.hcp_h.test_connection(bucket_name = custom_config.test_bucket) 
+
+def test_test_connection_without_mounting_bucket(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.test_connection)
+
+def test_list_objects(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    assert type(list(custom_config.hcp_h.list_objects())) == list 
+
+def test_list_objects_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.list_objects)
+
+def test_upload_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.upload_file(custom_config.test_file_path) 
+
+def test_upload_file_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.upload_file)
+
+def test_upload_file_in_sub_directory(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.upload_file(custom_config.test_file_path, "a_sub_directory/a_file") 
+
+def test_upload_nonexistent_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    try: 
+        custom_config.hcp_h.upload_file("tests/data/aTestFileThatDoesNotExist") 
+    except:
+        assert True
+    else: # pragma: no cover
+        assert False
+
+def test_upload_folder(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.upload_folder("tests/data/a folder of data/", "a folder of data/") 
+
+def test_upload_folder_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.upload_folder)
+
+def test_upload_nonexisting_folder(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    try: 
+        custom_config.hcp_h.upload_folder("tests/data/aFolderOfFilesThatDoesNotExist") 
+    except:
+        assert True
+    else: # pragma: no cover
+        assert False
+
+def test_get_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    assert custom_config.hcp_h.object_exists("a_sub_directory/a_file") 
+    assert custom_config.hcp_h.get_object("a_sub_directory/a_file") 
+
+def test_get_folder_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.object_exists)
+    _without_mounting(_hcp_h, HCPHandler.get_object)
+
+def test_get_file_in_sub_directory(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    test_file = Path(custom_config.test_file_path).name 
+    assert custom_config.hcp_h.object_exists(test_file) 
+    assert custom_config.hcp_h.get_object(test_file) 
+
+def test_download_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    Path(custom_config.result_path).mkdir() 
+    test_file = Path(custom_config.test_file_path).name 
+    custom_config.hcp_h.download_file(test_file, custom_config.result_path + test_file) 
+    assert cmp(custom_config.result_path + test_file, custom_config.test_file_path) 
+
+def test_download_file_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.download_file)
+
+def test_download_nonexistent_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    try:
+        custom_config.hcp_h.download_file("aFileThatDoesNotExist", custom_config.result_path + "aFileThatDoesNotExist") 
+    except:
+        assert True
+    else: # pragma: no cover
+        assert False
+
+def test_download_folder(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.download_folder("a folder of data/", custom_config.result_path) 
+
+def test_search_objects_in_bucket(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    test_file = Path(custom_config.test_file_path).name 
+    custom_config.hcp_h.search_objects_in_bucket(test_file) 
+
+def test_search_objects_in_bucket_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.search_objects_in_bucket)
+
+def test_get_object_acl(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    test_file = Path(custom_config.test_file_path).name 
+    custom_config.hcp_h.get_object_acl(test_file) 
+
+def test_get_object_acl_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.get_object_acl)
+
+def test_get_bucket_acl(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.get_bucket_acl() 
+
+def test_get_bucket_acl_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.get_bucket_acl)
+
+# ------------------ Possibly future ACL tests ---------------------------------
+
+#def test_modify_single_object_acl(custom_config : CustomConfig) -> None:
+#    test_mount_bucket(custom_config)
+#    custom_config.hcp_h.modify_single_object_acl()
+#
+#def test_modify_single_bucket_acl(custom_config : CustomConfig) -> None:
+#    test_mount_bucket(custom_config)
+#    custom_config.hcp_h.modify_single_bucket_acl()
+#
+#def test_modify_object_acl(custom_config : CustomConfig) -> None:
+#    test_mount_bucket(custom_config)
+#    custom_config.hcp_h.modify_object_acl()
+#
+#def test_modify_bucket_acl(custom_config : CustomConfig) -> None:
+#    test_mount_bucket(custom_config)
+#    custom_config.hcp_h.modify_bucket_acl()
+
+# ------------------------------------------------------------------------------
+
+def test_delete_file(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    test_file = Path(custom_config.test_file_path).name 
+    custom_config.hcp_h.delete_object(test_file) 
+    custom_config.hcp_h.delete_object("a_sub_directory/a_file") 
+    custom_config.hcp_h.delete_object("a_sub_directory") 
+
+def test_delete_file_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.delete_object)
+
+def test_delete_folder_with_sub_directory(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.upload_file(custom_config.test_file_path, "a folder of data/a sub dir/a file") 
+    try:
+        custom_config.hcp_h.delete_folder("a folder of data/") 
+    except: 
+        assert True
+    else: # pragma: no cover 
+        assert False
+    custom_config.hcp_h.delete_folder("a folder of data/a sub dir/") 
+
+def test_delete_folder(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.delete_folder("a folder of data/") 
+
+def test_delete_folder_without_mounting(custom_config : CustomConfig) -> None:
+    _hcp_h = custom_config.hcp_h 
+    _without_mounting(_hcp_h, HCPHandler.delete_folder)
+
+def test_delete_nonexistent_files(custom_config : CustomConfig) -> None:
+    test_mount_bucket(custom_config)
+    custom_config.hcp_h.delete_objects(["some", "files", "that", "does", "not", "exist"]) 

ngpiris-5.2.0.dev1/tests/test_hcp.py

@@ -1,216 +0,0 @@
-
-from typing import Callable
-from NGPIris.hcp import HCPHandler
-from configparser import ConfigParser
-from pathlib import Path
-from shutil import rmtree
-from filecmp import cmp
-
-hcp_h = HCPHandler("credentials/testCredentials.json")
-
-ini_config = ConfigParser()
-ini_config.read("tests/test_conf.ini")
-
-test_bucket = ini_config.get("hcp_tests", "bucket")
-
-test_file = ini_config.get("hcp_tests","data_test_file")
-test_file_path = "tests/data/" + test_file
-
-result_path = "tests/data/results/"
-
-def _without_mounting(test : Callable) -> None:
-    try:
-        test()
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_list_buckets() -> None:
-    assert hcp_h.list_buckets()
-
-def test_mount_bucket() -> None:
-    hcp_h.mount_bucket(test_bucket)
-
-def test_mount_nonexisting_bucket() -> None:
-    try:
-        hcp_h.mount_bucket("aBucketThatDoesNotExist")
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_test_connection() -> None:
-    test_mount_bucket()
-    hcp_h.test_connection()
-
-def test_test_connection_with_bucket_name() -> None:
-    hcp_h.test_connection(bucket_name = test_bucket)
-
-def test_test_connection_without_mounting_bucket() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    try:
-        _hcp_h.test_connection()
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_list_objects() -> None:
-    test_mount_bucket()
-    assert type(list(hcp_h.list_objects())) == list
-
-def test_list_objects_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.list_objects)
-
-def test_upload_file() -> None:
-    test_mount_bucket()
-    hcp_h.upload_file(test_file_path)
-
-def test_upload_file_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.upload_file)
-
-def test_upload_file_in_sub_directory() -> None:
-    test_mount_bucket()
-    hcp_h.upload_file(test_file_path, "a_sub_directory/a_file")
-
-def test_upload_nonexistent_file() -> None:
-    test_mount_bucket()
-    try: 
-        hcp_h.upload_file("tests/data/aTestFileThatDoesNotExist")
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_upload_folder() -> None:
-    test_mount_bucket()
-    hcp_h.upload_folder("tests/data/a folder of data/", "a folder of data/")
-
-def test_upload_folder_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.upload_folder)
-
-def test_upload_nonexisting_folder() -> None:
-    test_mount_bucket()
-    try: 
-        hcp_h.upload_folder("tests/data/aFolderOfFilesThatDoesNotExist")
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_get_file() -> None:
-    test_mount_bucket()
-    assert hcp_h.object_exists("a_sub_directory/a_file")
-    assert hcp_h.get_object("a_sub_directory/a_file")
-
-def test_get_folder_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.object_exists)
-    _without_mounting(_hcp_h.get_object)
-
-def test_get_file_in_sub_directory() -> None:
-    test_mount_bucket()
-    assert hcp_h.object_exists(test_file)
-    assert hcp_h.get_object(test_file)
-
-def test_download_file() -> None:
-    test_mount_bucket()
-    Path(result_path).mkdir()
-    hcp_h.download_file(test_file, result_path + test_file)
-    assert cmp(result_path + test_file, test_file_path)
-
-def test_download_file_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.download_file)
-
-def test_download_nonexistent_file() -> None:
-    test_mount_bucket()
-    try:
-        hcp_h.download_file("aFileThatDoesNotExist", result_path + "aFileThatDoesNotExist")
-    except:
-        assert True
-    else: # pragma: no cover
-        assert False
-
-def test_download_folder() -> None:
-    test_mount_bucket()
-    hcp_h.download_folder("a folder of data/", result_path)
-
-def test_search_objects_in_bucket() -> None:
-    test_mount_bucket()
-    hcp_h.search_objects_in_bucket(test_file)
-
-def test_search_objects_in_bucket_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.search_objects_in_bucket)
-
-def test_get_object_acl() -> None:
-    test_mount_bucket()
-    hcp_h.get_object_acl(test_file)
-
-def test_get_object_acl_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.get_object_acl)
-
-def test_get_bucket_acl() -> None:
-    test_mount_bucket()
-    hcp_h.get_bucket_acl()
-
-def test_get_bucket_acl_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.get_bucket_acl)
-
-#def test_modify_single_object_acl() -> None:
-#    test_mount_bucket()
-#    hcp_h.modify_single_object_acl()
-#
-#def test_modify_single_bucket_acl() -> None:
-#    test_mount_bucket()
-#    hcp_h.modify_single_bucket_acl()
-#
-#def test_modify_object_acl() -> None:
-#    test_mount_bucket()
-#    hcp_h.modify_object_acl()
-#
-#def test_modify_bucket_acl() -> None:
-#    test_mount_bucket()
-#    hcp_h.modify_bucket_acl()
-
-def test_delete_file() -> None:
-    test_mount_bucket()
-    hcp_h.delete_object(test_file)
-    hcp_h.delete_object("a_sub_directory/a_file")
-    hcp_h.delete_object("a_sub_directory")
-
-def test_delete_file_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.delete_object)
-
-def test_delete_folder_with_sub_directory() -> None:
-    test_mount_bucket()
-    hcp_h.upload_file(test_file_path, "a folder of data/a sub dir/a file")
-    try:
-        hcp_h.delete_folder("a folder of data/")
-    except: 
-        assert True
-    else: # pragma: no cover 
-        assert False
-    hcp_h.delete_folder("a folder of data/a sub dir/")
-
-def test_delete_folder() -> None:
-    test_mount_bucket()
-    hcp_h.delete_folder("a folder of data/")
-
-def test_delete_folder_without_mounting() -> None:
-    _hcp_h = HCPHandler("credentials/testCredentials.json")
-    _without_mounting(_hcp_h.delete_folder)
-
-def test_delete_nonexistent_files() -> None:
-    hcp_h.delete_objects(["some", "files", "that", "does", "not", "exist"])
-
-def test_clean_up() -> None:
-    rmtree(result_path)