pysodafair 0.1.62__py3-none-any.whl

pysoda/core/permissions/__init__.py

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+from .permissions import pennsieve_get_current_user_permissions, has_edit_permissions

pysoda/core/permissions/permissions.py

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+import requests
+from ...constants import PENNSIEVE_URL
+from ...utils import PennsieveActionNoPermission
+
+def pennsieve_get_current_user_permissions(dataset_id, ps_or_token):
+
+    if type(ps_or_token) is str:
+        access_token = ps_or_token
+    else:
+        access_token = ps_or_token.get_user().session_token
+
+    r = requests.get(f"{PENNSIEVE_URL}/datasets/{dataset_id}/role", headers={"Authorization": f"Bearer {access_token}"})
+    r.raise_for_status()
+
+    return r.json()
+
+
+def has_edit_permissions(ps_or_token, selected_dataset_id):
+    """
+        Checks if the current user has permission to edit the given dataset.
+
+        Input:
+            selected_dataset_id: Pennsieve dataset ID to check permissions for
+            ps: Pennsieve client object of a user that has been authenticated
+    """
+    try:
+        role = pennsieve_get_current_user_permissions(selected_dataset_id, ps_or_token)["role"]
+    except Exception as e:
+        raise PennsieveActionNoPermission("edit on " + selected_dataset_id) from e
+
+    return role in ["owner", "manager", "editor"]  

pysoda/core/pysoda/__init__.py

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+from .soda_object import soda
+from soda import soda_create

pysoda/core/pysoda/soda.py

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+from soda_object import soda as soda_object
+
+class Soda:
+    def __init__(self, standard=""):
+        self.soda_object = soda_object
+        self.soda_object["standard"] = standard
+
+    def set_standard(self, standard):
+        self.soda_object["standard"] = standard
+
+    def get_soda_object(self):
+        return self.soda_object
+
+    # Add more methods to alter the soda_object as needed
+    def update_metadata(self, key, value):
+        if key in self.soda_object["dataset-metadata"]:
+            self.soda_object["dataset-metadata"][key] = value
+        else:
+            raise KeyError(f"{key} not found in dataset-metadata")
+
+    def add_performance(self, performance):
+        self.soda_object["performances"].append(performance)
+
+    def add_subject_metadata(self, metadata):
+        self.soda_object["subject-metadata"].append(metadata)
+
+    def set_dataset_name(self, name):
+        self.soda_object["dataset-metadata"]["name"] = name
+
+    def get_dataset_name(self):
+        return self.soda_object["dataset-metadata"]["name"]
+
+    def get_submission(self):
+        return self.soda_object["dataset-metadata"]["submission-metadata"]

pysoda/core/pysoda/soda_object.py

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+soda = {
+  "starting-point": {
+
+  },
+  "ps-dataset-selected": {
+
+  },
+  "ps-accoint-selected": {
+
+  },
+  "guided-manifest-file-data": {
+    "headers": [
+      "filename",
+      "timestamp",
+      "description",
+      "file type",
+      "entity",
+      "data modality",
+      "also in dataset",
+      "also in dataset path",
+      "data dictionary path",
+      "entity is transitive",
+      "Additional Metadata"
+    ],
+    "data": []
+  },
+  "dataset-validated": False, 
+  "dataset-validation-errors": {},
+  "dataset-structure": {
+    "folders": {
+      "data": {}
+    }, 
+    "files": {},
+    "relativePath": "/"
+  },
+  "dataset-metadata": {
+    "description-metadata": {},
+    "shared-metadata": {},
+    "protocol-data": {},
+    "subject-metadata": {},
+    "sample-metadata": {},
+    "submission-metadata": {},
+    "code-metadata": {},
+    "README.md": "",
+    "CHANGES": "",
+    "performances": {},
+    "sites": {},
+    "resources": {}
+  },
+  "digital-metadata": {},
+  "generate-dataset": {},
+  "dataset-entity-structure": {},
+  "dataset-entity-obj": {},
+  "standard": ""
+}

pysoda/core/upload_manifests/__init__.py

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+from .upload_manifests import get_upload_manifests, get_files_for_manifest

pysoda/core/upload_manifests/upload_manifests.py

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+import requests
+from .. import logger
+from ...constants import PENNSIEVE_2_URL
+from ...utils import get_access_token, create_request_headers
+
+
+
+
+def get_files_for_manifest(manifest_id, limit, continuation_token=None):
+    """
+    Get the number of verified files in an upload manifest. For a file to be verified its status must be 
+    one of the following: VERIFIED | FAILED | FINALIZED.
+    """
+
+    global logger
+
+
+    if continuation_token is None or continuation_token == "":
+        r = requests.get(f"{PENNSIEVE_2_URL}/manifest/files?manifest_id={manifest_id}&limit={limit}", headers=create_request_headers(get_access_token()))
+    else:
+        r = requests.get(f"{PENNSIEVE_2_URL}/manifest/files?manifest_id={manifest_id}&limit={limit}&continuation_token={continuation_token}", headers=create_request_headers(get_access_token()))
+    r.raise_for_status()
+    return r.json()
+
+
+
+def get_upload_manifests(dataset_id):
+    """
+    Get the ids of all upload manifests that have been initiated by the Pennsieve Agent.
+    """
+
+    global logger
+
+    r = requests.get(f"{PENNSIEVE_2_URL}/manifest?dataset_id={dataset_id}", headers=create_request_headers(get_access_token()))
+    r.raise_for_status()
+
+    return r.json()