pysodafair 0.1.66__py3-none-any.whl → 0.1.68__py3-none-any.whl

pysoda/schema/subjects.json

@@ -10,7 +10,7 @@
         "subject_id": {
           "type": "string",
           "description": "Unique identifier for the subject. This should be a unique identifier for the subject within the dataset.",
-          "minLength": 1
+          "pattern": "^(pop-)?sub-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
         },
         "pool_id": {
           "type": "string",
@@ -26,11 +26,11 @@
         },
         "sex": {
           "type": "string",
-          "description": "Sex of the subject."
+          "description": "Sex of the subject. Can be represented as freetext or a CURIE or IRI from a standard ontology such as PATO."
         },
         "species": {
           "type": "string",
-          "description": "Species of the subject. This should be the scientific name of the species."
+          "description": "Species of the subject. This should be the scientific name of the species. For example CURIE or IRI from NCBI taxonomy or something free form."
         },
         "strain": {
           "type": "string",
@@ -38,7 +38,8 @@
         },
         "rrid_for_strain": {
           "type": "string",
-          "description": "RRID for strain. This should be a unique identifier for the strain in the Research Resource Identifier (RRID) database."
+          "description": "RRID for strain. This should be a unique identifier for the strain in the Research Resource Identifier (RRID) database.",
+          "pattern": "^$|^RRID:"
         },
         "age_category": {
           "type": "string",
@@ -46,7 +47,7 @@
         },
         "also_in_dataset": {
           "type": "string",
-          "description": "Indicates if the subject is also part of another dataset."
+          "description": "Indicates if the subject is also part of another dataset. Should be a DOI or https link to another dataset or an other identifier."
         },
         "member_of": {
           "type": "string",
@@ -56,6 +57,10 @@
           "type": "string",
           "description": "Indicates if this entry is metadata only."
         },
+        "number_of_directly_derived_samples": {
+          "type": "string",
+          "description": "Number of samples directly derived from this sample."
+        },
         "laboratory_internal_id": {
           "type": "string",
           "description": "Internal identifier used by the laboratory for the subject."
@@ -73,8 +78,24 @@
           "description": "Maximum age range of the subject."
         },
         "body_mass": {
-          "type": "string",
-          "description": "Body mass of the subject."
+          "oneOf": [
+            {
+              "type": "string",
+              "description": "Body mass of the subject."
+            },
+            {
+              "type": "number",
+              "description": "Body mass of the subject."
+            },
+            {
+              "type": "object",
+              "properties": {
+                "type": { "type": "string" },
+                "value": { "type": "number" },
+                "unit": { "type": "string" }
+              }
+            }
+          ]
         },
         "genotype": {
           "type": "string",
@@ -100,7 +121,7 @@
           "type": "string",
           "description": "Date of the experiment involving the subject."
         },
-        "disease_or_disorder": {
+        "disease": {
           "type": "string",
           "description": "Disease or disorder associated with the subject."
         },
@@ -118,10 +139,20 @@
         },
         "protocol_url_or_doi": {
           "type": "string",
-          "description": "URL or DOI of the protocol used for the subject."
+          "description": "URL or DOI of the protocol used for the subject.",
+          "anyOf": [
+            { "pattern": "^$" },
+            {
+              "pattern": "^https://[A-Za-z0-9.-]+[A-Za-z0-9](:[0-9]+)?(/.*)?$"
+            },
+            { "pattern": "^10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$" },
+            {
+              "pattern": "^https://doi\\.org/10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$"
+            }
+          ]
         }
       },
-      "required": ["subject_id"],
+      "required": ["subject_id", "species"],
       "additionalProperties": {
         "type": "string",
         "description": "Additional properties for the subject. This can include any other relevant information about the subject that is not covered by the predefined fields."

pysoda/schema/submission_schema.json

@@ -4,7 +4,8 @@
   "properties": {
     "consortium_data_standard": {
       "type": "string",
-      "description": "The consortium data standard used for the submssion. Examples include SDS, BIDS, etc."
+      "description": "The consortium data standard used for the submssion. At the moment SPARC is the only supported standard in pysoda. Future support for HEAL is planned.",
+      "enum": ["SPARC", "HEAL"]
     },
     "funding_consortium": {
       "type": "string",
@@ -12,7 +13,7 @@
     },
     "award_number": {
       "type": "string",
-      "description": "The award number associated with the funding. This is typically a unique identifier assigned by the funding agency."
+      "description": "The award number associated with the funding. This is typically a unique identifier assigned by the funding agency. TODO: Check regex coverage for RE-JOIN before applying pattern."
     },
     "milestone_achieved": {
       "type": "array",
@@ -21,8 +22,10 @@
     },
     "milestone_completion_date": {
       "type": "string",
-      "description": "The date when the milestone was completed. This should be in ISO 8601 format."
+      "description": "The date when the milestone was completed. This should be in ISO 8601 format.",
+      "pattern": "^([0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[12][0-9]|3[01])T([01][0-9]|2[0-3]):[0-5][0-9](:[0-5][0-9]([.,][0-9]{1,9})?)?(Z|[+-]([01][0-9]|2[0-3]):[0-5][0-9]))?$"
     }
   },
-  "required": []
+  "required": [],
+  "description": "TODO: Add funding_consortium, milestone_completion_date, and consortium_data_standard to required fields list once SODA front end has validation page."
 }

pysoda/utils/exceptions.py

@@ -17,6 +17,14 @@ class PennsieveAgentError(Exception):
     def __str__(self):
         return self.error_message
     
+
+class PennsieveAgentRPCError(Exception):
+    def __init__(self, error_message):
+        self.error_message = error_message
+
+    def __str__(self):
+        return self.error_message
+    
 class FailedToFetchPennsieveDatasets(Exception):
     def __init__(self, error_message):
         self.error_message = error_message
@@ -120,7 +128,7 @@ class PennsieveDatasetNameInvalid(Exception):
 class PennsieveAccountInvalid(Exception):
     def __init__(self, account_name):
         self.account_name = account_name
-        self.error_message = f"The Pennsieve account name {self.account_name} is invalid."
+        self.error_message = f"The Pennsieve account name {self.account_name} is invalid. Please try again. If the issue persists, please contact the SODA team."
 
     def __str__(self):
         return self.error_message
@@ -138,7 +146,7 @@ def validation_error_message(e):
     input: e (ValidationError): The validation error from the validate library.
     output: human readable message for the validation error.
     """
-    msg = "There following error was found in your metadata:"
+    msg = "The following error was found in your metadata:"
     e_type = e.schema_path.pop().strip()
     print(e.schema_path)
     if e_type == "type":

pysoda/utils/pennsieveAgentUtils.py

@@ -1,5 +1,5 @@
 from pennsieve2.pennsieve import Pennsieve
-from .exceptions import PennsieveAgentError
+from .exceptions import PennsieveAgentError, PennsieveAgentRPCError, PennsieveAccountInvalid
 
 def connect_pennsieve_client(account_name):
     """
@@ -8,4 +8,13 @@ def connect_pennsieve_client(account_name):
     try:
         return Pennsieve(profile_name=account_name)
     except Exception as e:
-        raise PennsieveAgentError(f"Could not connect to the Pennsieve agent: {e}")
+        if "End of TCP stream" in str(e):
+            raise PennsieveAgentRPCError(f"Could not connect to the Pennsieve Agent error coming from the Agent. This can likely be resolved by retrying. If the issue persists, please contact the SODA team and they will reach out to Pennsieve to help resolve this.") from e
+        elif isinstance(e, AttributeError):
+            raise Exception("The Pennsieve Agent cannot access datasets but needs to in order to work. Please try again. If the issue persists, please contact the SODA team. The SODA team will contact Pennsieve to help resolve this issue.") from e
+        elif "Profile not found" in str(e):
+            raise PennsieveAccountInvalid(account_name) from e
+        elif "Error connecting to server" in str(e):
+            raise PennsieveAgentError(f"Could not connect to the Pennsieve agent: {e}") from e
+        else:
+            raise PennsieveAgentError("An unknown error occurred when trying to connect to the Pennsieve Agent. If this issue persists, please contact the SODA team.") from e

{pysodafair-0.1.66.dist-info → pysodafair-0.1.68.dist-info}/METADATA

@@ -1,17 +1,14 @@
 Metadata-Version: 2.4
 Name: pysodafair
-Version: 0.1.66
+Version: 0.1.68
 Summary: Pysoda package for Fairdataihub tools
 License: MIT
 License-File: LICENSE
 Author: Christopher Marroquin
 Author-email: cmarroquin@calmi2.org
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11

{pysodafair-0.1.66.dist-info → pysodafair-0.1.68.dist-info}/RECORD

@@ -4,13 +4,13 @@ pysoda/core/__init__.py,sha256=bXnu4fYemJ915xId8nwh-Gy2IUEvVuoS9Hk3CXyJp8U,235
 pysoda/core/dataset_generation/__init__.py,sha256=tisLmJeXLeAINXf7BdNZGi2i9vQwImWGa_S5FNwQFbs,299
 pysoda/core/dataset_generation/manifestSession/__init__.py,sha256=kqkTAFEhluyQJ9mmMhYQTh1tgowBeJdH-Q9s5ifGkSE,51
 pysoda/core/dataset_generation/manifestSession/manifest_session.py,sha256=TML_KOJ-1REohqSaHCZNFJrbDR1UDQ9sFcithJRx9t8,4669
-pysoda/core/dataset_generation/upload.py,sha256=lnU6od0LtJOjuzNj-VX2HzOp66xUBr1V6nXtpJjkdIg,172804
+pysoda/core/dataset_generation/upload.py,sha256=XC1ELfTKEV9T0HY8xxUa3poGTq9H2sL-VT356IDrXH4,172819
 pysoda/core/dataset_importing/__init__.py,sha256=NbWs4HAqqydFLACFoVwl6g457dkYvjiZKx9NzB9wFxE,114
 pysoda/core/dataset_importing/import_dataset.py,sha256=cx8qCQmR_BKdC2G-jzqE4dWg2JhkOS3jM8kpjLIsObk,29487
 pysoda/core/metadata/__init__.py,sha256=Tkx6vdEQEPwAHmVSc9GfdbDZUkvuAqEgHJOxRDeX5vE,821
-pysoda/core/metadata/code_description.py,sha256=sWbRPWPf32txpN048oQ9lT3y7GAoDkrS-GHivwwv55Y,4104
+pysoda/core/metadata/code_description.py,sha256=DlHcbKkegZ_hJ1kYrYX0wUBW0h0P_ew_CCE3Yt0-FiQ,5964
 pysoda/core/metadata/constants.py,sha256=PR78huqBKdBpzDUGxVKy9YW3pUrJ4ftuF4MfqpNb1bU,1052
-pysoda/core/metadata/dataset_description.py,sha256=icIRH2TYXWqrc4gu_RUK0yP_WQmy9BGAkVOEVQ--GfA,10275
+pysoda/core/metadata/dataset_description.py,sha256=KH7koPzGaB7wy3w_jwBfIHior7zZnsn9onsoWpYglq4,10356
 pysoda/core/metadata/excel_utils.py,sha256=FQ8-DBq2lxFdpDUZeABfFKe284JzRTe6AYPxEw7yzsg,1216
 pysoda/core/metadata/helpers.py,sha256=jDf4KPTbx4unHT7pDlFEa0jls1OZY-dpdKf3kUGMtvg,10609
 pysoda/core/metadata/manifest.py,sha256=LO8ZP8oJ0vEjbXU0yPVEYm62MLOZwIYVUaW4VEczO9k,4195
@@ -18,29 +18,30 @@ pysoda/core/metadata/manifest_package/__init__.py,sha256=7qiNT62WsI1LKb-lvnK31lW
 pysoda/core/metadata/manifest_package/manifest.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pysoda/core/metadata/manifest_package/manifest_import.py,sha256=5rKOBf-NMt2dVsPJYotk5V855wnmtiMqrpknSOYOEl0,1347
 pysoda/core/metadata/manifest_package/manifest_writer.py,sha256=AjtKdGYd9e2TS9hpPTPXH0mqer5PH_hLbxvYQPhhFHg,27358
-pysoda/core/metadata/performances.py,sha256=s5nPF9il8m73PADK6YMSfWT0JADn-NDpXzB7K7X3X1o,1851
-pysoda/core/metadata/resources.py,sha256=v0CUl5Lg-_2DkR0h9NJMBQkCkydQL15qzRZvkFDnMdc,1790
-pysoda/core/metadata/samples.py,sha256=sSaHZ0LEYd6oQFKQxoS0xb1m4k1NPNqKxp38CJjzi3U,8389
-pysoda/core/metadata/sites.py,sha256=gpmC7_WIi2wtaCa8BpS0eUYJPeBaOxwXyLIjVEXBhJA,1751
-pysoda/core/metadata/subjects.py,sha256=kaerhYVUsz2BJSGIvETbl1YSliYAGMPg2-ne8AnsXdU,7968
+pysoda/core/metadata/performances.py,sha256=0DZevDiGJ1Zf493Ayc0f8rSS2-5w32nE2RLKq6-XTyA,2527
+pysoda/core/metadata/resources.py,sha256=6EGR6f70pMj2gOxA9ZvJ78yhPPhafw3UM8aRNsTQCyE,2563
+pysoda/core/metadata/samples.py,sha256=IOUPpRkGI47Cv7wJThFlLzocydqTKI0SQ6uy-f6XHQk,6360
+pysoda/core/metadata/sites.py,sha256=Dh0UTesFj_MFNEmNp_0PeRLR4AQ4prEdRxybkyGfiyI,2427
+pysoda/core/metadata/subjects.py,sha256=vIe29xj3HdMFqh8y4H4-zbTY2xm62h4N4Llv0v-7nVM,9046
 pysoda/core/metadata/submission.py,sha256=Ym949kEIzdjjyyNWCvtP8OftFKKUBDQy98HOOTUEej4,3002
 pysoda/core/metadata/text_metadata.py,sha256=GYiRxNiQp5Lw-6na80jcrvQBMF4-KHp3CGK2Mmv6TFI,1846
+pysoda/core/metadata_templates/.dss,sha256=mAgD4xcDXkcAx01ZfZ-vJbD_Klkkgago2s1XyQNNwss,12
 pysoda/core/metadata_templates/CHANGES,sha256=XIdY2AIWPX8aEtMJeXprL1kHXRH173l5ubTxzMDoCH4,78
 pysoda/core/metadata_templates/LICENSE,sha256=XIdY2AIWPX8aEtMJeXprL1kHXRH173l5ubTxzMDoCH4,78
 pysoda/core/metadata_templates/README.md,sha256=rIxGEC2qoPl4YcSj-G64MX5fmM1JdNed1KCDUFVYRnc,129
 pysoda/core/metadata_templates/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pysoda/core/metadata_templates/code_description.xlsx,sha256=hONjq4nmDxtHbMmCTAcrosoIA6rxnlt1fub-EjDFDS0,12007
 pysoda/core/metadata_templates/code_parameters.xlsx,sha256=vhHX99V7Abye8dN3GkjzFuJ8g9MUOSQDfAMRrR8DehQ,6027
-pysoda/core/metadata_templates/dataset_description.xlsx,sha256=qTwz8_J0JeZdm_wGzq6-tMnZbKWJlmYdBSR4JN88Saw,16138
+pysoda/core/metadata_templates/dataset_description.xlsx,sha256=G79X1UKI5LEu30asVWKAQF_9lxXOlX9rOZjDhuln7NA,18417
 pysoda/core/metadata_templates/manifest.xlsx,sha256=uHUVfmy_jcNeW5qctDLyymOdhyVOwRJCQavungPBR0o,5273
 pysoda/core/metadata_templates/performances.xlsx,sha256=jjiPBb669FHjC7W8hTo3gChTspX5DluBdrvO6UZhFOk,5184
 pysoda/core/metadata_templates/resources.xlsx,sha256=mT-KbF1KzZjV3AifENZHkY2nX6AHB6sLO34pX_6xcAI,5155
-pysoda/core/metadata_templates/samples.xlsx,sha256=5ramdIEUjk0d5rB6RvE_3aiE4vaKz_cKX7KBI_TE7sc,8448
+pysoda/core/metadata_templates/samples.xlsx,sha256=AQtHRIssRrrPjBSHPX5-bNE0b2rWL3OafaHZhiyp0cY,8462
 pysoda/core/metadata_templates/sites.xlsx,sha256=C_XehlNXZSUUxjayZr0XW6OvuGRxoFzA8xM6OklXszM,8081
-pysoda/core/metadata_templates/subjects.xlsx,sha256=_lFYP2WkTz-n_IfocaBgZWYwFtNdaDIFtYoXAQ4AcQE,8621
+pysoda/core/metadata_templates/subjects.xlsx,sha256=CqhZvmHhwN_JPtr4bFlm9tFkUlOoji959jLl5KaOGOg,8626
 pysoda/core/metadata_templates/subjects_pools_samples_structure.xlsx,sha256=AXUBNtYBIAN9C3l7-clGFTCnyLkSFhuoFca227jbxgc,12154
 pysoda/core/metadata_templates/subjects_pools_samples_structure_example.xlsx,sha256=69DcsxOR6H8oTZZq43vOuoyud1D_BOXdzLxJlotdQVk,12154
-pysoda/core/metadata_templates/submission.xlsx,sha256=DIVcio7QyR-6-o1esDn1Gl7vu19xSCyGHhwGkW3RaBI,6002
+pysoda/core/metadata_templates/submission.xlsx,sha256=gWQy0_ZnluGcSOwLO8P2jFJLVWSKtXn2DTJx150ZV9w,5039
 pysoda/core/permissions/__init__.py,sha256=YUoJACCe8SO7_TXrn27jzz5gWx1xvCMPy37cNPmV2Mw,85
 pysoda/core/permissions/permissions.py,sha256=l8OTNhzjidF7PrL74PYjcpxVYd1YQpgcs202yh4CJyg,1076
 pysoda/core/pysoda/__init__.py,sha256=gNQ5O-A6wqTc88OGGfLy0UoeFxgPi0T5NMtF7YdUY_U,58
@@ -49,29 +50,29 @@ pysoda/core/pysoda/soda_object.py,sha256=ISkV2uRREp-ScHt5_ZH_4K20O3veVxYGnP-9Avv
 pysoda/core/upload_manifests/__init__.py,sha256=SOiyflYmZDtkLwWpeu7flyn3J2SAj9WL4y82O6cEpzg,74
 pysoda/core/upload_manifests/upload_manifests.py,sha256=Hd2XSXYieG-EMcPTLSYXvdtraipp1XBSo5cGpZR-vbA,1223
 pysoda/schema/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pysoda/schema/code_description.json,sha256=FJOyJBC2TKjTTdtew3B4wdq_WIrti-r2F-M6t5OVNB0,17854
-pysoda/schema/dataset_description.json,sha256=U725xGDmy4oeJe0IOFcJc7a0oA5pAbpsRVQsjhPEj1k,10069
-pysoda/schema/manifest.json,sha256=dClcVIR3IlesjWC9peLAnyuIECwNDHfbIFmCsj9l2Wk,3006
-pysoda/schema/performances.json,sha256=TJw7ERC6eMR-9cImOg7xoEVRyOR4xViJqZO8U2X2OXo,1254
-pysoda/schema/resources.json,sha256=9-rwCTX523V5XaKmXLTUGzackOl7tk-qijbbBDoeuhY,1232
-pysoda/schema/samples.json,sha256=NvuYhskV9QFrkSX4ant9G4KFCe9JLnVG98vDv2Puuvk,3340
-pysoda/schema/sites.json,sha256=lMkglgi4R7_qqUHh6uwbZ38TjkUzRKGY9pdF1CpZh4E,1133
+pysoda/schema/code_description.json,sha256=UhZjGNp1LLA035FhBm0ThmKWoQzlYc6R51TTGtba6qM,20607
+pysoda/schema/dataset_description.json,sha256=hhVLzKm4B-WCROkxbV8THsHPjP_1pIJLynBdEH-0uaA,10298
+pysoda/schema/manifest.json,sha256=u78jhXWEmp_fR_2TLyvorWP3fUNTATFj6AgmeYwKwwo,3043
+pysoda/schema/performances.json,sha256=2d8l9SrNVpHlrbHqw6qEwMG0i7DMvFybm5IqcOcg6LA,1927
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+pysoda/schema/samples.json,sha256=sXMxp_8LvvrWTQKm_qraLZPNIb0WO7ZpPaA6fXRIcgk,4255
+pysoda/schema/sites.json,sha256=wmpjuPpwdmqUvh094NUgjhia0aNzKxTgM8MpnIVzecU,1288
 pysoda/schema/soda_schema.json,sha256=QSe8G39wOMO5wS_MUU0mW6yeM4etufACE6iuAzZMBoA,19290
-pysoda/schema/subjects.json,sha256=j5au8ak0Q_Nxs6EDoJ7FJDr0SeS0Y-X40X-XQwSnRts,4799
-pysoda/schema/submission_schema.json,sha256=b0FfBP_fDFxU8vT1mDAThbUyYMJA7PJ1S6lOpdPpSkY,1103
+pysoda/schema/subjects.json,sha256=Dmst7DFzrmuZGW6rkBlwR6MWFAAucgGkZrs6EAHYcTA,6062
+pysoda/schema/submission_schema.json,sha256=-ASgTEHjGtBQhrEN5P78DFAEIo8VGstftfcb0sk2F7U,1609
 pysoda/utils/__init__.py,sha256=cdrc-Ueb7djdA9rPl5FR3nsinCxfOB9lbOhicNCbeCY,1243
 pysoda/utils/authentication.py,sha256=Ed6xXaCSyi23qGz_LkdDB-Cjum5G5az_tMhSWKBGVSY,11943
 pysoda/utils/config.py,sha256=8UC0j89ihuMnPCwl9bTVUupC9Kg_39ly9Hju5W4OmWo,2471
-pysoda/utils/exceptions.py,sha256=H4_bvp-Zq4e-_GHQ5n3wxg4cH12iVgJZEw8tz8jRGfw,4812
+pysoda/utils/exceptions.py,sha256=mvGgfag0KN7GvSqb75RkY3eZsGSlfCnjxgSNERxsAmc,5068
 pysoda/utils/logger.py,sha256=fxqJoqxe_wdVTq7IXN5QsWSC-z7mSfsLaJsKU9-UhqA,211
 pysoda/utils/metadata_utils.py,sha256=nCQc24biSsrpnXbjXiZEtISWkfBS-CV00sv5MMydoww,1804
-pysoda/utils/pennsieveAgentUtils.py,sha256=Un0qnVQm1DNg3u5l7PZI-X61sNaJtSmDlcXP_lRbv8Q,422
+pysoda/utils/pennsieveAgentUtils.py,sha256=yoHYBl2EXmLA0Ty-zrYG8LYhofnR8II9OkcE2c6EGqE,1439
 pysoda/utils/pennsieveUtils.py,sha256=B_L2NicOR3eQin0sd7TsRLWNDSxhSxyGgUJCGoWBVkM,4622
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 pysoda/utils/schema_validation.py,sha256=3w3FRPyn4P3xMhITzItk-jYte8TTlNrgCWmY-s05x9Y,4438
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