NGPIris 5.1.1.dev3__tar.gz → 5.2.0__tar.gz

{ngpiris-5.1.1.dev3 → ngpiris-5.2.0}/NGPIris/cli/__init__.py

@@ -19,14 +19,14 @@ def format_list(list_of_things : list) -> str:
     list_of_buckets = list(map(lambda s : s + "\n", list_of_things))
     return "".join(list_of_buckets).strip("\n")
 
-def _list_objects_generator(hcph : HCPHandler, name_only : bool) -> Generator[str, Any, None]:
+def _list_objects_generator(hcph : HCPHandler, path : str, name_only : bool, files_only : bool) -> Generator[str, Any, None]:
     """
     Handle object list as a paginator that `click` can handle. It works slightly 
     different from `list_objects` in `hcp.py` in order to make the output 
     printable in a terminal
     """
     paginator : Paginator = hcph.s3_client.get_paginator("list_objects_v2")
-    pages : PageIterator = paginator.paginate(Bucket = hcph.bucket_name)
+    pages : PageIterator = paginator.paginate(Bucket = hcph.bucket_name, Prefix = path)
     (nb_of_cols, _) = get_terminal_size()
     max_width = floor(nb_of_cols / 5)
     if (not name_only):
@@ -36,7 +36,11 @@ def _list_objects_generator(hcph : HCPHandler, name_only : bool) -> Generator[st
             tablefmt = "plain",
             stralign = "center"
         ) + "\n" + "-"*nb_of_cols + "\n"
-    for object in pages.search("Contents[?!ends_with(Key, '/')][]"): # filter objects that does not end with "/"
+    if files_only:
+        filter_string = "Contents[?!ends_with(Key, '/')][]" # filter objects that does not end with "/"
+    else:
+        filter_string = "Contents[*][]"
+    for object in pages.search(filter_string): 
         if name_only:
             yield str(object["Key"]) + "\n"
         else:
@@ -55,6 +59,11 @@ def _list_objects_generator(hcph : HCPHandler, name_only : bool) -> Generator[st
 def object_is_folder(object_path : str, hcph : HCPHandler) -> bool:
     return (object_path[-1] == "/") and (hcph.get_object(object_path)["ContentLength"] == 0)
 
+def add_trailing_slash(path : str) -> str:
+    if not path[-1] == "/":
+        path += "/"
+    return path
+
 @click.group()
 @click.argument("credentials")
 @click.version_option(package_name = "NGPIris")
@@ -85,9 +94,13 @@ def upload(context : Context, bucket : str, source : str, destination : str):
     """
     hcph : HCPHandler = get_HCPHandler(context)
     hcph.mount_bucket(bucket)
+    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()
@@ -198,22 +211,52 @@ def list_buckets(context : Context):
 
 @cli.command()
 @click.argument("bucket")
+@click.argument("path", required = False)
 @click.option(
     "-no", 
     "--name-only", 
     help = "Output only the name of the objects instead of all the associated metadata", 
-    default = False
+    default = False,
+    is_flag = True
+)
+@click.option(
+    "-p",
+    "--pagination",
+    help = "Output as a paginator",
+    default = False,
+    is_flag = True
+)
+@click.option(
+    "-fo", 
+    "--files-only", 
+    help = "Output only file objects", 
+    default = False,
+    is_flag = True
 )
 @click.pass_context
-def list_objects(context : Context, bucket : str, name_only : bool):
+def list_objects(context : Context, bucket : str, path : str, name_only : bool, pagination : bool, files_only : bool):
     """
     List the objects in a certain bucket/namespace on the HCP.
 
     BUCKET is the name of the bucket in which to list its objects.
+
+    PATH is an optional argument for where to list the objects
     """
     hcph : HCPHandler = get_HCPHandler(context)
     hcph.mount_bucket(bucket)
-    click.echo_via_pager(_list_objects_generator(hcph, name_only))
+    if path:
+        path_with_slash = add_trailing_slash(path)
+
+        if not hcph.object_exists(path_with_slash):
+            raise RuntimeError("Path does not exist")
+    else:
+        path_with_slash = ""
+
+    if pagination:
+        click.echo_via_pager(_list_objects_generator(hcph, path_with_slash, name_only, files_only))
+    else:
+        for obj in hcph.list_objects(path_with_slash, name_only, files_only):
+            click.echo(obj)
 
 @cli.command()
 @click.argument("bucket")

{ngpiris-5.1.1.dev3 → ngpiris-5.2.0}/NGPIris/hcp/hcp.py

@@ -178,6 +178,8 @@ class HCPHandler:
             pass
         else:
             raise RuntimeError("No bucket selected. Either use `mount_bucket` first or supply the optional `bucket_name` parameter for `test_connection`")
+        
+        response = {}
         try:
             response = dict(self.s3_client.head_bucket(Bucket = bucket_name))
         except EndpointConnectionError as e: # pragma: no cover
@@ -234,7 +236,7 @@ class HCPHandler:
         return list_of_buckets
     
     @check_mounted
-    def list_objects(self, path_key : str = "", name_only : bool = False) -> Generator:
+    def list_objects(self, path_key : str = "", name_only : bool = False, files_only : bool = False) -> Generator:
         """
         List all objects in the mounted bucket as a generator. If one wishes to 
         get the result as a list, use :py:function:`list` to type cast the generator
@@ -243,16 +245,35 @@ class HCPHandler:
         :type path_key: str, optional
         :param name_only: If True, yield only a the object names. If False, yield the full metadata about each object. Defaults to False.
         :type name_only: bool, optional
+        :param files_only: If true, only yield file objects. Defaults to False
+        :type files_only: bool, optional
         :yield: A generator of all objects in a bucket
         :rtype: Generator
         """
         paginator : Paginator = self.s3_client.get_paginator("list_objects_v2")
-        pages : PageIterator = paginator.paginate(Bucket = self.bucket_name)
-        for object in pages.search("Contents[?starts_with(Key, '" + path_key + "')][]"):
-            if name_only:
-                yield str(object["Key"])
-            else:
-                yield object
+        pages : PageIterator = paginator.paginate(Bucket = self.bucket_name, Prefix = path_key)
+
+        if files_only:
+            filter_string = "Contents[?!ends_with(Key, '/')][]"
+        else:
+            filter_string = "Contents[*][]"
+
+        split_path_key = len(path_key.split("/")) + 1
+
+        pages_filtered = pages.search(filter_string)
+        for object in pages_filtered:
+            # Split the object key by "/"
+            split_object = object["Key"].split("/")
+            # Check if the object is within the specified path_key depth
+            if len(split_object) <= split_path_key:
+                # Skip objects that are not at the desired depth
+                if (len(split_object) == split_path_key) and split_object[-1]:
+                    continue
+                
+                if name_only:
+                    yield str(object["Key"])
+                else:
+                    yield object
                     
     @check_mounted
     def get_object(self, key : str) -> dict:
@@ -382,6 +403,9 @@ 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:
@@ -510,7 +534,6 @@ class HCPHandler:
         """
         return self.fuzzy_search_in_bucket(search_string, name_only, case_sensitive, 100)
         
-
     @check_mounted
     def fuzzy_search_in_bucket(
         self, 
@@ -556,7 +579,7 @@ class HCPHandler:
                 if name_only:
                     yield item
                 else:
-                    yield full_list[index]
+                    yield full_list[index] # type: ignore
 
     @check_mounted
     def get_object_acl(self, key : str) -> dict:

{ngpiris-5.1.1.dev3 → ngpiris-5.2.0}/NGPIris.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: NGPIris
-Version: 5.1.1.dev3
+Version: 5.2.0
 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/NGPIris.egg-info/SOURCES.txt

@@ -0,0 +1,52 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+NGPIris/__init__.py
+NGPIris.egg-info/PKG-INFO
+NGPIris.egg-info/SOURCES.txt
+NGPIris.egg-info/dependency_links.txt
+NGPIris.egg-info/entry_points.txt
+NGPIris.egg-info/requires.txt
+NGPIris.egg-info/top_level.txt
+NGPIris/cli/__init__.py
+NGPIris/hci/__init__.py
+NGPIris/hci/exceptions.py
+NGPIris/hci/hci.py
+NGPIris/hci/helpers.py
+NGPIris/hcp/__init__.py
+NGPIris/hcp/exceptions.py
+NGPIris/hcp/hcp.py
+NGPIris/hcp/helpers.py
+NGPIris/hcp/statistics.py
+NGPIris/parse_credentials/__init__.py
+NGPIris/parse_credentials/parse_credentials.py
+NGPIris/utils/__init__.py
+NGPIris/utils/utils.py
+docs/IRIS_5_changelog.md
+docs/Makefile
+docs/NGPIris.cli.rst
+docs/NGPIris.hci.rst
+docs/NGPIris.hcp.rst
+docs/NGPIris.parse_credentials.rst
+docs/NGPIris.rst
+docs/NGPIris.utils.rst
+docs/Tutorial.md
+docs/conf.py
+docs/index.rst
+docs/make.bat
+docs/modules.rst
+tests/test_hci.py
+tests/test_hcp.py
+tests/test_parse_credentials.py
+tests/data/80MB_test_file
+tests/data/complete_creds_0.json
+tests/data/complete_creds_1.json
+tests/data/complete_creds_2.json
+tests/data/incomplete_creds_0.json
+tests/data/incomplete_creds_1.json
+tests/data/incomplete_creds_2.json
+tests/data/incomplete_creds_3.json
+tests/data/incomplete_creds_4.json
+tests/data/a folder of data/80MB_test_file_0
+tests/data/a folder of data/80MB_test_file_1

{ngpiris-5.1.1.dev3 → ngpiris-5.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: NGPIris
-Version: 5.1.1.dev3
+Version: 5.2.0
 Author-email: Erik Brink <erik.brink@gu.se>, Isak Sylvin <isak.sylvin@gu.se>
 Description-Content-Type: text/markdown
 License-File: LICENSE

{ngpiris-5.1.1.dev3 → ngpiris-5.2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "NGPIris"
-version = "5.1.1.dev3"
+version = "5.2.0"
 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-5.1.1.dev3 → ngpiris-5.2.0}/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-5.2.0/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-5.1.1.dev3/NGPIris.egg-info/SOURCES.txt

@@ -1,127 +0,0 @@
-LICENSE
-MANIFEST.in
-README.md
-pyproject.toml
-NGPIris/__init__.py
-NGPIris.egg-info/PKG-INFO
-NGPIris.egg-info/SOURCES.txt
-NGPIris.egg-info/dependency_links.txt
-NGPIris.egg-info/entry_points.txt
-NGPIris.egg-info/requires.txt
-NGPIris.egg-info/top_level.txt
-NGPIris/cli/__init__.py
-NGPIris/hci/__init__.py
-NGPIris/hci/exceptions.py
-NGPIris/hci/hci.py
-NGPIris/hci/helpers.py
-NGPIris/hcp/__init__.py
-NGPIris/hcp/exceptions.py
-NGPIris/hcp/hcp.py
-NGPIris/hcp/helpers.py
-NGPIris/hcp/statistics.py
-NGPIris/parse_credentials/__init__.py
-NGPIris/parse_credentials/parse_credentials.py
-NGPIris/utils/__init__.py
-NGPIris/utils/utils.py
-docs/IRIS_5_changelog.md
-docs/Makefile
-docs/NGPIris.cli.rst
-docs/NGPIris.hci.rst
-docs/NGPIris.hcp.rst
-docs/NGPIris.parse_credentials.rst
-docs/NGPIris.rst
-docs/NGPIris.utils.rst
-docs/Tutorial.md
-docs/conf.py
-docs/index.rst
-docs/make.bat
-docs/modules.rst
-docs/_build/.DS_Store
-docs/_build/doctrees/IRIS_5_changelog.doctree
-docs/_build/doctrees/NGPIris.cli.doctree
-docs/_build/doctrees/NGPIris.doctree
-docs/_build/doctrees/NGPIris.hci.doctree
-docs/_build/doctrees/NGPIris.hcp.doctree
-docs/_build/doctrees/NGPIris.parse_credentials.doctree
-docs/_build/doctrees/NGPIris.utils.doctree
-docs/_build/doctrees/README.doctree
-docs/_build/doctrees/Tutorial.doctree
-docs/_build/doctrees/environment.pickle
-docs/_build/doctrees/index.doctree
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