Repository: Sage-Bionetworks/schematic (language: python)

Issue:
Update synapse client minimum version to `3.2.0`
Update `synapseclient` dependency specification to [`^3.2.0`](https://python-docs.synapse.org/news/#320-2023-11-27)

Resolves [FDS-1569](https://sagebionetworks.jira.com/browse/FDS-1569) and implements [FDS-1570](https://sagebionetworks.jira.com/browse/FDS-1570)

[FDS-1569]: https://sagebionetworks.jira.com/browse/FDS-1569?atlOrigin=eyJpIjoiNWRkNTljNzYxNjVmNDY3MDlhMDU5Y2ZhYzA5YTRkZjUiLCJwIjoiZ2l0aHViLWNvbS1KU1cifQ
[FDS-1570]: https://sagebionetworks.jira.com/browse/FDS-1570?atlOrigin=eyJpIjoiNWRkNTljNzYxNjVmNDY3MDlhMDU5Y2ZhYzA5YTRkZjUiLCJwIjoiZ2l0aHViLWNvbS1KU1cifQ


Discussion / hints:

Fix patch:
diff --git a/poetry.lock b/poetry.lock
index e48b01605..e1457f930 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -607,63 +607,63 @@ tests = ["MarkupSafe (>=0.23)", "aiohttp (>=2.3.10,<4)", "aiohttp-jinja2 (>=0.14
 
 [[package]]
 name = "coverage"
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+version = "7.4.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -1025,13 +1025,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.114.0"
+version = "2.115.0"
 description = "Google API Client Library for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -1043,13 +1043,13 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.26.2"
+version = "2.27.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1613,13 +1613,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.21.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1775,13 +1775,13 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc
 
 [[package]]
 name = "jupyter-server-terminals"
-version = "0.5.1"
+version = "0.5.2"
 description = "A Jupyter Server Extension Providing Terminals."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1794,13 +1794,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.0.10"
+version = "4.0.11"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -2214,13 +2214,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
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-version = "1.5.9"
+version = "1.6.0"
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 python-versions = ">=3.5"
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 [[package]]
@@ -2243,13 +2243,13 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "notebook"
-version = "7.0.6"
+version = "7.0.7"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
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 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -2471,13 +2471,13 @@ files = [
 
 [[package]]
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+version = "7.6.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
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 python-versions = ">=3.6"
 files = [
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 [[package]]
@@ -2644,13 +2644,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
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 [package.extras]
@@ -2707,27 +2707,27 @@ files = [
 
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 [package.dependencies]
@@ -3758,45 +3758,45 @@ synapse = ["synapseclient (>=3.0.0,<4.0.0)"]
 
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+    {file = "scipy-1.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:b360f1b6b2f742781299514e99ff560d1fe9bd1bff2712894b52abe528d1fd1e"},
+    {file = "scipy-1.12.0.tar.gz", hash = "sha256:4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3"},
 ]
 
 [package.dependencies]
-numpy = ">=1.21.6,<1.28.0"
+numpy = ">=1.22.4,<1.29.0"
 
 [package.extras]
 dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
 doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
-test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "secretstorage"
@@ -4313,13 +4313,13 @@ files = [
 
 [[package]]
 name = "toolz"
-version = "0.12.0"
+version = "0.12.1"
 description = "List processing tools and functional utilities"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
 files = [
-    {file = "toolz-0.12.0-py3-none-any.whl", hash = "sha256:2059bd4148deb1884bb0eb770a3cde70e7f954cfbbdc2285f1f2de01fd21eb6f"},
-    {file = "toolz-0.12.0.tar.gz", hash = "sha256:88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194"},
+    {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
+    {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
 ]
 
 [[package]]
diff --git a/schematic/utils/df_utils.py b/schematic/utils/df_utils.py
index 14c8d6b2b..bb3c63073 100644
--- a/schematic/utils/df_utils.py
+++ b/schematic/utils/df_utils.py
@@ -10,7 +10,12 @@
 logger = logging.getLogger(__name__)
 
 
-def load_df(file_path, preserve_raw_input=True, data_model=False, **load_args):
+def load_df(
+    file_path: str,
+    preserve_raw_input: bool = True,
+    data_model: bool = False,
+    **load_args,
+) -> pd.DataFrame:
     """
     Universal function to load CSVs and return DataFrames
     Parses string entries to convert as appropriate to type int, float, and pandas timestamp
@@ -31,14 +36,14 @@ def load_df(file_path, preserve_raw_input=True, data_model=False, **load_args):
     # Read CSV to df as type specified in kwargs
     org_df = pd.read_csv(file_path, keep_default_na=True, encoding="utf8", **load_args)
 
+    # only trim if not data model csv
+    if not data_model:
+        org_df = trim_commas_df(org_df)
+
     # If type inference not allowed: trim and return
     if preserve_raw_input:
-        # only trim if not data model csv
-        if not data_model:
-            org_df = trim_commas_df(org_df)
-
-            # log manifest load and processing time
-            logger.debug(f"Load Elapsed time {perf_counter()-t_load_df}")
+        # log manifest load and processing time
+        logger.debug(f"Load Elapsed time {perf_counter()-t_load_df}")
         return org_df
 
     # If type inferences is allowed: infer types, trim, and return
@@ -75,11 +80,8 @@ def load_df(file_path, preserve_raw_input=True, data_model=False, **load_args):
             # replace values that couldn't be converted to float with the original str values
             float_df[col].fillna(org_df[col][float_df[col].isna()], inplace=True)
 
-        # Trim nans and empty rows and columns
-        processed_df = trim_commas_df(float_df)
-
         # Store values that were converted to type int in the final dataframe
-        processed_df = processed_df.mask(ints_tf_df, other=ints)
+        processed_df = float_df.mask(ints_tf_df, other=ints)
 
         # log manifest load and processing time
         logger.debug(f"Load Elapsed time {perf_counter()-t_load_df}")


Test patch:
diff --git a/tests/data/mock_manifests/Invalid_Test_Manifest.csv b/tests/data/mock_manifests/Invalid_Test_Manifest.csv
index ea0e7685c..1cc8995ef 100644
--- a/tests/data/mock_manifests/Invalid_Test_Manifest.csv
+++ b/tests/data/mock_manifests/Invalid_Test_Manifest.csv
@@ -1,4 +1,5 @@
 Component,Check List,Check Regex List,Check Regex Single,Check Regex Format,Check Regex Integer,Check Num,Check Float,Check Int,Check String,Check URL,Check Match at Least,Check Match at Least values,Check Match Exactly,Check Match Exactly values,Check Recommended,Check Ages,Check Unique,Check Range,Check Date,Check NA
 MockComponent,"ab,cd","ab,cd,ef",a,a,5.4,6,99.65,7,valid,https://www.google.com/,1738,1738,8085,98085,,6549,str1,70,32-984,7
 MockComponent,invalid list values,ab cd ef,q,m,0,c,99,5.63,94,http://googlef.com/,7163,51100,9965,71738,,32851,str1,30,notADate,9.5
-MockComponent,"ab,cd","ab,cd,ef",b,b,683902,6.5,62.3,2,valid,https://github.com/Sage-Bionetworks/schematic,8085,8085,1738,210065,,6550,str1,90,84-43-094,Not Applicable
\ No newline at end of file
+MockComponent,"ab,cd","ab,cd,ef",b,b,683902,6.5,62.3,2,valid,https://github.com/Sage-Bionetworks/schematic,8085,8085,1738,210065,,6550,str1,90,84-43-094,Not Applicable
+,,,,,,,,,,,,,,,,,,,
\ No newline at end of file
diff --git a/tests/test_utils.py b/tests/test_utils.py
index d9f06c845..2efee6aa9 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -255,6 +255,31 @@ def test_load_schema_org(self):
 
 
 class TestDfUtils:
+    @pytest.mark.parametrize("preserve_raw_input", [True, False], ids=["Do not infer datatypes", "Infer datatypes"])
+    def test_load_df(self, helpers, preserve_raw_input):
+        test_col = "Check NA"
+        file_path = helpers.get_data_path("mock_manifests", "Invalid_Test_Manifest.csv")
+
+        unprocessed_df = pd.read_csv(file_path, encoding="utf8")
+        df = df_utils.load_df(file_path, preserve_raw_input=preserve_raw_input, data_model=False)
+
+        assert df["Component"].dtype == "object"
+
+        n_unprocessed_rows = unprocessed_df.shape[0]
+        n_processed_rows = df.shape[0]
+
+        assert n_unprocessed_rows == 4
+        assert n_processed_rows == 3
+
+        if preserve_raw_input:
+            assert isinstance(df[test_col].iloc[0], str)
+            assert isinstance(df[test_col].iloc[1], str)
+            assert isinstance(df[test_col].iloc[2], str)
+        else:
+            assert isinstance(df[test_col].iloc[0], np.int64)
+            assert isinstance(df[test_col].iloc[1], float)
+            assert isinstance(df[test_col].iloc[2], str)
+
     def test_update_df_col_present(self, helpers):
 
         synapse_manifest = helpers.get_data_frame(