uc-cdis · paulineribeyre · Apr 23, 2024 · Apr 12, 2024 · Apr 16, 2024 · Apr 22, 2024
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,6 +11,6 @@ repos:
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 24.4.0
     hooks:
     -   id: black
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -75,6 +75,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -123,7 +127,7 @@
         "filename": "README.md",
         "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3",
         "is_verified": false,
-        "line_number": 72
+        "line_number": 74
       }
     ],
     "bin/settings.py": [
@@ -350,5 +354,5 @@
       }
     ]
   },
-  "generated_at": "2024-02-08T23:30:59Z"
+  "generated_at": "2024-04-22T20:07:28Z"
 }
diff --git a/README.md b/README.md
@@ -68,7 +68,7 @@ Ensure you've run `poetry install`.
 
 Ensure you have Postgresql 13 set up and running.
 
-Ensure there is a postgres user `postgres` *and* `test` setup with password `test`:
+Ensure there are 2 postgres users `postgres` and `test`, both set up with password `test`:
 
 ```
 CREATE USER postgres WITH PASSWORD 'test';

diff --git a/poetry.lock b/poetry.lock
diff --git a/sheepdog/blueprint/routes/views/__init__.py b/sheepdog/blueprint/routes/views/__init__.py
@@ -237,9 +237,9 @@ def get_templates():
         )
     )
     suffix = "json" if file_format == "json" else "tar.gz"
-    response.headers[
-        "Content-Disposition"
-    ] = "attachment; filename=submission_templates.{}".format(suffix)
+    response.headers["Content-Disposition"] = (
+        "attachment; filename=submission_templates.{}".format(suffix)
+    )
     return response
 
 

diff --git a/sheepdog/blueprint/routes/views/program/project.py b/sheepdog/blueprint/routes/views/program/project.py
@@ -823,9 +823,9 @@ def get_project_templates(program, project):
     )
     response = flask.make_response(template)
     suffix = "json" if file_format == "json" else "tar.gz"
-    response.headers[
-        "Content-Disposition"
-    ] = "attachment; filename=submission_templates.{}".format(suffix)
+    response.headers["Content-Disposition"] = (
+        "attachment; filename=submission_templates.{}".format(suffix)
+    )
     return response
 
 
@@ -1144,8 +1144,8 @@ def delete_project(program, project):
         transaction_args = dict(
             program=program, project=project, flask_config=flask.current_app.config
         )
-        with (
-            transactions.deletion.transaction.DeletionTransaction(**transaction_args)
+        with transactions.deletion.transaction.DeletionTransaction(
+            **transaction_args
         ) as trans:
             session.delete(node)
             trans.claim_transaction_log()

diff --git a/sheepdog/transactions/submission/entity.py b/sheepdog/transactions/submission/entity.py
@@ -13,7 +13,6 @@
 
 
 class SubmissionEntity(EntityBase):
-
     """Models an entity to be marked submitted."""
 
     def __init__(self, transaction, node):

diff --git a/sheepdog/transactions/submission/transaction.py b/sheepdog/transactions/submission/transaction.py
@@ -19,7 +19,6 @@
 
 
 class SubmissionTransaction(TransactionBase):
-
     """Models a transaction to mark all nodes in a project submitted."""
 
     REQUIRED_PROJECT_STATES = ["review"]

diff --git a/sheepdog/transactions/upload/entity_factory.py b/sheepdog/transactions/upload/entity_factory.py
@@ -1,6 +1,7 @@
 """
 Class Factory for creating new upload entities
 """
+
 import psqlgraph
 
 from sheepdog.transactions.upload.entity import UploadEntity

diff --git a/sheepdog/transactions/upload/sub_entities.py b/sheepdog/transactions/upload/sub_entities.py
@@ -2,6 +2,7 @@
 Subclasses for UploadEntity that handle different types of
 uploaded entites.
 """
+
 import uuid
 import requests
 import json

diff --git a/sheepdog/utils/transforms/__init__.py b/sheepdog/utils/transforms/__init__.py
@@ -8,6 +8,7 @@
 from flask import current_app
 from psqlgraph import Node
 
+from sheepdog import dictionary
 from sheepdog.errors import UserError
 from sheepdog.utils.transforms.bcr_xml_to_json import (
     BcrXmlToJsonParser,
@@ -30,7 +31,7 @@ def parse_bool_from_string(value):
     return mapping.get(strip(value).lower(), value)
 
 
-def parse_list_from_string(value, list_type=None):
+def parse_list_from_string(value, list_item_type=None):
     """
     Handle array fields by converting them to a list.
     Try to cast to float to handle arrays of numbers.
@@ -40,37 +41,29 @@ def parse_list_from_string(value, list_type=None):
     """
     items = [x.strip() for x in value.split(",")]
 
-    all_ints = True
-    try:
-        # TODO: Actually pass in and use list_type as the expected type
-        #       and don't try to infer it this way.
-        for item in items:
-            if not float(item).is_integer():
-                all_ints = False
-                break
-    except ValueError as exc:
-        current_app.logger.warning(
-            f"list of values {items} are likely NOT ints or floats so we're leaving "
-            f"them as-is. Exception: {exc}"
-        )
-        return items
-
-    if all_ints:
-        current_app.logger.warning(
-            f"list of values {items} could all be integers, so we are ASSUMING they "
-            "are instead of defaulting to float."
-        )
-        # all can be ints, infer `int` as correct type
-        new_items = [int(float(item)) for item in items]
+    if list_item_type == int:
+        items = [int(float(item)) for item in items]
+    elif list_item_type == float:
+        items = [list_item_type(item) for item in items]
+    elif list_item_type == bool:
+        items = [e.lower() in ["true", "t", "yes", "y"] for e in items]
     else:
         current_app.logger.warning(
-            f"list of values {items} are NOT all integers, so we are ASSUMING they "
-            "they are all float by default."
+            f"'parse_list_from_string' does not know how to handle type '{list_item_type}' so assuming string is fine... Value is '{value}'"
         )
-        # default to float for backwards compatibility
-        new_items = [float(item) for item in items]
 
-    return new_items
+    return items
+
+
+def jsonschema_to_python_type(str_type):
+    return {
+        "string": str,
+        "integer": int,
+        "number": float,
+        "float": float,
+        "boolean": bool,
+        "array": list,
+    }.get(str_type)
 
 
 def set_row_type(row):
@@ -234,29 +227,29 @@ def value_to_list_value(self, cls, link_name, prop, value):
 
     @staticmethod
     def get_converted_type_from_list(cls, prop_name, value):
-        current_app.logger.debug(f"cls.__pg_properties__:{cls.__pg_properties__}")
         types = cls.__pg_properties__.get(prop_name, (str,))
-        current_app.logger.debug(f"types:{types}")
         value_type = types[0]
-
-        property_list = cls.get_property_list()
-        current_app.logger.debug(f"property_list:{property_list}")
-
-        # TODO: list_type is not used b/c for some reason it's always
-        #       str even if the dictionary says it's an array of ints
-        list_type = None
-        if len(types) > 1:
-            list_type = types[1]
-
-        current_app.logger.debug(f"prop_name:{prop_name}")
-        current_app.logger.debug(f"value:{value}")
-        current_app.logger.debug(f"value_type:{value_type}")
-
         try:
             if value_type == bool:
                 return parse_bool_from_string(value)
             elif value_type == list:
-                return parse_list_from_string(value, list_type=list_type)
+                # Parse the item type from the dictionary schema.
+                # NOTE: `cls.__pg_properties__.get(prop_name)` would be easier but the value is
+                # only `list` and does not include the item type.
+                # https://github.com/uc-cdis/gdcdatamodel/blob/190f998/gdcdatamodel/models/__init__.py#L120
+                # Setting this ^ to `list[<item type>]` may work but it breaks other code.
+                list_item_type = (
+                    dictionary.schema.get(cls.label, {})
+                    .get("properties", {})
+                    .get(prop_name, {})
+                    .get("items", {})
+                    .get("type")
+                )
+                list_item_type = jsonschema_to_python_type(list_item_type)
+                current_app.logger.debug(
+                    f"get_converted_type_from_list: {cls.label}.{prop_name} items type is {list_item_type}"
+                )
+                return parse_list_from_string(value, list_item_type=list_item_type)
             elif value_type == float:
                 if float(value).is_integer():
                     return int(float(value))

diff --git a/sheepdog/utils/transforms/graph_to_doc.py b/sheepdog/utils/transforms/graph_to_doc.py
@@ -902,7 +902,7 @@ def dict_props_to_list(obj, props, titles_linked, file_format):
 
     l_prop_values = [str(obj.get(k)) for k in props]
     link_fields = []
-    for (link_name, link_prop) in link_props_split:
+    for link_name, link_prop in link_props_split:
         s = sub_splitter.join(
             list(
                 filter(

diff --git a/tests/ci_setup.sh b/tests/ci_setup.sh
@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+set -e
 poetry run python bin/setup_test_database.py
 mkdir -p tests/integration/resources/keys
 cd tests/integration/resources/keys

diff --git a/tests/integration/datadict/conftest.py b/tests/integration/datadict/conftest.py
@@ -36,6 +36,7 @@
     + "/datadict/schemas"
 )
 
+
 # update these settings if you want to point to another db
 def pg_config(use_ssl=False, isolation_level=None):
     test_host = (

diff --git a/tests/integration/datadict/submission/test_admin_endpoints.py b/tests/integration/datadict/submission/test_admin_endpoints.py
@@ -1,6 +1,7 @@
 """
 Tests for admin endpoint functionality.
 """
+
 # pylint: disable=unused-argument, no-member
 
 import json

diff --git a/tests/integration/datadict/submission/test_upload.py b/tests/integration/datadict/submission/test_upload.py
@@ -2,6 +2,7 @@
 Test upload entities (mostly data file handling and communication with
 index service).
 """
+
 import csv
 import json
 import copy

diff --git a/tests/integration/datadictwithobjid/schemas/dictionary.json b/tests/integration/datadictwithobjid/schemas/dictionary.json
diff --git a/tests/integration/datadictwithobjid/submission/test_endpoints.py b/tests/integration/datadictwithobjid/submission/test_endpoints.py
@@ -3,6 +3,7 @@
 # pylint: disable=superfluous-parens
 # pylint: disable=no-member
 import contextlib
+import csv
 import json
 import os
 import uuid
@@ -682,6 +683,71 @@ def test_export_node_with_array_json(
     assert len(js_data["data"][0]["consent_codes"]) == len(consent_codes)
 
 
+@pytest.mark.parametrize(
+    "property_name,tsv_value,expected_value",
+    [
+        ("consent_codes", "1.1,70", ["1.1", "70"]),
+        ("consent_codes_ints", "1,70", [1, 70]),
+        ("consent_codes_floats", "1.1,70.0", [1.1, 70.0]),
+        ("consent_codes_bools", "true,false", [True, False]),
+    ],
+)
+def test_submit_tsv_array_type(
+    client,
+    pg_driver,
+    cgci_blgsp,
+    require_index_exists_off,
+    submitter,
+    property_name,
+    tsv_value,
+    expected_value,
+):
+    """
+    Ensure arrays of strings with values that look like numbers can be submitted via TSV. Also
+    test arrays of other types.
+    Test arrays of strings, ints and flots using the `case` node's `consent_codes`,
+    `consent_codes_ints`, `consent_codes_floats` and `consent_codes_bools` properties.
+
+    This is a regression test for this error:
+        Validation error while validating entity '{'type': 'case', 'consent_codes': [4], ...'
+        against subschema '{'type': 'string'}': 4 is not of type 'string'
+    """
+    # submit records for parent nodes
+    resp = post_example_entities_together(client, submitter, extended_data_fnames)
+    assert resp.status_code == 201, resp.data
+
+    with pg_driver.session_scope() as s:
+        case = pg_driver.nodes(md.Case).first()
+        assert (
+            case
+        ), "`post_example_entities_together` should have submitted a case record"
+        case_submitter_id = case.props["submitter_id"]
+        experiment = pg_driver.nodes(md.Experiment).first()
+        assert (
+            experiment
+        ), "`post_example_entities_together` should have submitted an experiment record"
+        experiment_submitter_id = experiment.props["submitter_id"]
+
+    # generate and submit the TSV data
+    data = f"{property_name}	submitter_id	experiments.submitter_id	type\n{tsv_value}	{case_submitter_id}	{experiment_submitter_id}	case"
+    print(f"Submitting TSV data:\n{data}")
+    r = client.put(
+        BLGSP_PATH, headers={**submitter, "Content-Type": "text/tsv"}, data=data
+    )
+    assert r.status_code == 200, r.data
+
+    # query the data and check that the values are of the expected type even when they look
+    # like ints/floats
+    path = "/v0/submission/CGCI/BLGSP/export/?node_label=case&format=json"
+    r = client.get(path, headers=submitter)
+    assert r.status_code == 200, r.data
+    assert r.json, "Expected to receive a json body"
+    assert (
+        len(r.json.get("data", [])) == 1
+    ), f"Expected exactly 1 case but got: {r.json}"
+    assert r.json["data"][0][property_name] == expected_value
+
+
 def test_export_all_node_types_json(
     client, pg_driver, cgci_blgsp, require_index_exists_off, submitter
 ):

diff --git a/tests/integration/datadictwithobjid/submission/test_upload.py b/tests/integration/datadictwithobjid/submission/test_upload.py
@@ -2,6 +2,7 @@
 Test upload entities (mostly data file handling and communication with
 index service).
 """
+
 import json
 import copy
Original file line number	Diff line number	Diff line change
Expand Up		@@ -13,7 +13,6 @@


		class SubmissionEntity(EntityBase):

		"""Models an entity to be marked submitted."""

		def __init__(self, transaction, node):
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -19,7 +19,6 @@


		class SubmissionTransaction(TransactionBase):

		"""Models a transaction to mark all nodes in a project submitted."""

		REQUIRED_PROJECT_STATES = ["review"]
Expand Down