ENH: Apply security fixes (#912)

hi-ml-azure/src/health_azure/traverse.py

@@ -8,7 +8,7 @@ from io import StringIO
 from typing import Any, Dict, Iterable, Union, List, Optional
 
 import param
-from ruamel import yaml
+from ruamel.yaml import YAML
 
 
 def is_basic_type(o: Any) -> bool:
@@ -138,7 +138,13 @@ def object_to_yaml(o: Any) -> str:
     :param o: The object to inspect.
     :return: A string in YAML format.
     """
-    return yaml.safe_dump(object_to_dict(o), default_flow_style=False)  # type: ignore
+    yaml = YAML(typ='safe', pure=True)
+    stream = StringIO()
+    yaml.default_flow_style = False
+    yaml.dump(object_to_dict(o), stream)
+    result = stream.getvalue()
+    stream.close()
+    return result
 
 
 def yaml_to_dict(s: str) -> Dict[str, Any]:
@@ -150,7 +156,8 @@ def yaml_to_dict(s: str) -> Dict[str, Any]:
     or dictionaries again.
     """
     stream = StringIO(s)
-    return yaml.safe_load(stream=stream)
+    yaml = YAML(typ='safe', pure=True)
+    return yaml.load(stream=stream)
 
 
 def _write_dict_to_object(o: Any, d: Dict[str, Any], traversed_fields: Optional[List] = None) -> List[str]:

hi-ml-azure/testazure/testazure/test_himl.py

@@ -77,7 +77,7 @@ from testazure.utils_testazure import (
 )
 
 INEXPENSIVE_TESTING_CLUSTER_NAME = "lite-testing-ds2"
-EXPECTED_QUEUED = "This command will be run in AzureML:"
+EXPECTED_QUEUED = "Successfully queued run"
 GITHUB_SHIBBOLETH = "GITHUB_RUN_ID"  # https://docs.github.com/en/actions/reference/environment-variables
 AZUREML_FLAG = himl.AZUREML_FLAG
 

hi-ml-cpath/requirements_run.txt

@@ -10,7 +10,7 @@ numpy==1.22.0
 pillow==9.3.0
 pydicom==2.3.0
 scikit-image==0.19.3
-scipy==1.7.3
+scipy==1.10.0
 seaborn==0.10.1
 simpleitk==2.1.1.2
 tifffile==2022.10.10

hi-ml-cpath/testSSL/testSSL/test_ssl_containers.py

@@ -143,7 +143,7 @@ def test_ssl_container_cifar10_resnet_simclr() -> None:
     # Note: It is possible that after the PyTorch 1.10 upgrade, we can't get parity between local runs and runs on
     # the hosted build agents. If that suspicion is confirmed, we need to add branching for local and cloud results.
     expected_metrics = {
-        'simclr/val/loss': 2.8596301078796387,
+        'simclr/val/loss': 2.859630584716797,
         'ssl_online_evaluator/val/loss': 2.2664988040924072,
         'ssl_online_evaluator/val/AccuracyAtThreshold05': 0.20000000298023224,
         'simclr/train/loss': 3.6261773109436035,

hi-ml-multimodal/requirements_test.txt

@@ -2,7 +2,7 @@ bump2version==1.0.1
 coverage==6.3.2
 flake8==5.0.2
 ipykernel==6.15.0
-ipython==7.34.0
+ipython==8.11.0
 mypy==0.931
 papermill==2.3.4
 pycobertura==2.0.1

hi-ml/src/health_ml/utils/reports.py

@@ -13,7 +13,7 @@ from pathlib import Path
 from typing import Any, Dict, List, Optional, OrderedDict, Tuple
 
 import jinja2
-import ruamel.yaml
+from ruamel.yaml import YAML
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -407,7 +407,8 @@ class HTMLReport:
         # TODO: add option to overwrite report title with entry here
         assert report_config_path.suffix == ".yml", f"Expected a .yml file but found {report_config_path.suffix}"
         with open(report_config_path, "r") as f_path:
-            yaml_contents = ruamel.yaml.load(f_path)
+            yaml = YAML(typ='safe', pure=True)
+            yaml_contents = yaml.load(f_path)
 
         return yaml_contents
 

hi-ml/testhiml/testhiml/utils/test_reports.py

@@ -11,7 +11,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import pytest
-import ruamel.yaml
+from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap as OrderedDict, CommentedSeq as OrderedList
 
 from health_ml.utils.reports import HTMLReport, IMAGE_KEY_HTML, TABLE_KEY_HTML, REPORT_CONTENTS_KEY, ReportComponentKey
@@ -226,28 +226,25 @@ def test_html_report_read_config(html_report: HTMLReport, dummy_df: pd.DataFrame
 
     plt.plot(dummy_df[[dummy_df_cols[0]]], dummy_df[[dummy_df_cols[1]]])
 
-    report_config_contents = OrderedDict(
-        {
-            REPORT_CONTENTS_KEY: OrderedList(
-                [
-                    {
-                        ReportComponentKey.TYPE.value: ReportComponentKey.TABLE.value,
-                        ReportComponentKey.VALUE.value: table_path,
-                    }
-                ]
-            )
-        }
-    )
+    report_config_contents = {
+        REPORT_CONTENTS_KEY: [
+            {
+                ReportComponentKey.TYPE.value: ReportComponentKey.TABLE.value,
+                ReportComponentKey.VALUE.value: str(table_path),
+            }
+        ]
+    }
     report_config_path = tmp_path / "report_config.yml"
-    with open(report_config_path, "w+") as f_path:
-        ruamel.yaml.dump(report_config_contents, f_path)
+    with open(report_config_path, "w+", encoding="utf-8") as f_path:
+        yaml = YAML(typ='safe', pure=True)
+        yaml.dump(report_config_contents, f_path)
 
     report_config = html_report.read_config_yaml(report_config_path)
     assert list(report_config.keys()) == [REPORT_CONTENTS_KEY]
     assert len(report_config[REPORT_CONTENTS_KEY]) == 1
     report_contents_first_entry = report_config[REPORT_CONTENTS_KEY][0]
     assert report_contents_first_entry[ReportComponentKey.TYPE.value] == ReportComponentKey.TABLE.value
-    assert report_contents_first_entry[ReportComponentKey.VALUE.value] == table_path
+    assert report_contents_first_entry[ReportComponentKey.VALUE.value] == str(table_path)
 
     html_report.add_yaml_contents_to_report(report_config)
     html_template_difference = html_report.template.replace(html_template_before, "")