Factor Value

condaEnv.yaml

@@ -6,7 +6,7 @@ channels:
 dependencies:
    - python=3.10 # required for in-house codebase compatibility
    - pandas
-   - samtools
+  # - samtools
    - isatools
    - multiqc
    - schema

dp_tools/demo.py

@@ -0,0 +1,140 @@
+from dp_tools.core.check_model import ValidationProtocol, FlagCode
+
+#########################################
+# DATA MODEL INIT
+#########################################
+
+car = {
+    "wheels": [
+        {"isFlat": False},
+        {"isFlat": False},
+        {"isFlat": True},  # uh oh
+        {"isFlat": False},
+    ],
+    "engineOkay": True,
+    "gasTank": 100,
+    "isElectric": False,
+    # doesn't apply so this entry isn't included
+    # "charge":0
+}
+
+
+#########################################
+# Check function definitions
+#########################################
+
+
+def check_if_wheel_flat(wheel: dict):
+    if not wheel["isFlat"]:
+        code = FlagCode.GREEN
+        message = "Wheel is ready to go!"
+    else:
+        code = FlagCode.HALT
+        message = "This wheel is flat!"
+    return {"code": code, "message": message}
+
+
+def check_engine_okay(car: dict):
+    if car["engineOkay"]:
+        code = FlagCode.GREEN
+        message = "Engine looks good"
+    else:
+        code = FlagCode.HALT
+        message = "Engine needs work!"
+    return {"code": code, "message": message}
+
+
+def check_gas(cur_gas: float, minimum_gas: float):
+    if cur_gas >= minimum_gas:
+        code = FlagCode.GREEN
+        message = f"Gas tank is at {cur_gas}. Which is above {minimum_gas}"
+    else:
+        code = FlagCode.HALT
+        message = (
+            f"Gas tank needs a fill up! Current: {cur_gas}. Minimum: {minimum_gas}"
+        )
+    return {"code": code, "message": message}
+
+
+def check_charge(cur_charge: float, minimum_charge: float):
+    if cur_charge >= minimum_charge:
+        code = FlagCode.GREEN
+        message = "Charge looks good"
+    else:
+        code = FlagCode.HALT
+        message = "Needs a charge!"
+    return {"code": code, "message": message}
+
+
+#########################################
+# Protocol definition
+#########################################
+
+vp = ValidationProtocol()
+with vp.component_start(
+    name="PreDrive Check",
+    description="Make sure the car is ready for the trip",
+):
+
+    with vp.component_start(
+        name="Engine",
+        description="Make sure the engine is running fine",
+    ):
+        with vp.payload(payloads=[{"car": car}]):
+            vp.add(check_engine_okay)
+
+    with vp.component_start(
+        name="Tires",
+        description="Make sure the tires are road ready",
+    ):
+        with vp.payload(
+            payloads=[
+                {"wheel": car["wheels"][0]},
+                {"wheel": car["wheels"][1]},
+                {"wheel": car["wheels"][2]},
+                {"wheel": car["wheels"][3]},
+            ]
+        ):
+            vp.add(check_if_wheel_flat)
+
+    with vp.component_start(
+        name="Fuel",
+        description="Check gas or charge is sufficent",
+    ):
+        # NOTE: lambda is used in payload to defer evaluation conditioned
+        #   on whether the check is run or skipped.
+        with vp.payload(payloads=[{"cur_gas": lambda: car["gasTank"]}]):
+            vp.add(check_gas, config={"minimum_gas": 95}, skip=(car["isElectric"]))
+
+        with vp.payload(payloads=[{"cur_charge": lambda: car["charge"]}]):
+            vp.add(
+                check_charge,
+                config={"minimum_charge": 95},
+                skip=(not car["isElectric"]),
+            )
+
+
+#########################################
+# Running Protocol
+#########################################
+
+# Now printing the queued checks
+print(vp.queued_checks())
+
+print("********************************")
+# Running the checks
+vp.run()
+vp.run(skip_components = ["Tires"])
+
+# And showing the results
+print(vp.report()["flag_table"])
+
+print("Individual Flag Row")
+print(vp.report()["flag_table"].iloc[5].to_dict())
+
+
+#########################################
+# Exporting Protocol Results to File
+#########################################
+
+vp.report()["flag_table"].to_csv("VV_log.tsv", sep = "\t")

dp_tools/microarray/checks.py

@@ -1,34 +1,43 @@
-def check_if_valid_extensions(file, valid_ext):
-    """description
-    params (description + data type)
-    return (description + data type)"""
-    pass
-def check_factor():
-    """description"""
-    pass
-
-def check_if_extensions_valid(file, valid_ext):
-    """ Description of the function
-    Description Line 2
-
-    :param file: Input raw data file
-    :type file: Path
-    :param valid_ext: Extensions that are allow for the raw data files
-    :type valid_ext: list[str]
-    :return: A required fields-only flag entry dictionary
+from enum import Flag
+from dp_tools.core.check_model import FlagCode, FlagEntry
+import pandas as pd
+
+def check_factor_values_in_runsheet(runsheet_file: str) -> FlagEntry: 
+    """Verifies inclusion of factor values in runsheet
+
+    :param runsheet_file: Path to runsheet file
+    :type runsheet_file: str
+    :return: determination if factor value was located
     :rtype: FlagEntry
     """
-    pass # Does nothing (... is equivalent)
+    runsheet = pd.read_csv(runsheet_file)
+    code = FlagCode.HALT
+    message = f"Runsheet does not have a Factor Value column"
+    for col_name in runsheet.columns:
+        if "Factor Value" in col_name:
+            code = FlagCode.GREEN
+            message = f"Factor Value column detected in runsheet"
+    return {"code": code, "message": message}
 
-def check_factor_values_in_runsheet():
-    """ Description of the function
-    Description Line 2
+def check_html_file(html_file: str) -> FlagEntry:
+    """Verifies if the rendered Rmarkdown file has a valid html extension
 
-    :param file: Input raw data file
-    :type file: Path
-    :param valid_ext: Extensions that are allow for the raw data files
-    :type valid_ext: list[str]
-    :return: A required fields-only flag entry dictionary
+    :param html_file: Path to rendered Rmarkdown
+    :type html_file: str
+    :return: determination if the file has a valid extension
     :rtype: FlagEntry
     """
-    pass # Does nothing (... is equivalent)
+    if html_file[-4:] == "html":
+        code = FlagCode.GREEN
+        message = f"File is an html file"
+    else:
+        code = FlagCode.HALT
+        message = f"File is not an html file"
+    return {"code": code, "message": message}
+
+
+
+
+
+
+

tests/checks/test_microarray_checks.py

@@ -0,0 +1,9 @@
+from dp_tools.microarray.checks import check_factor_values_in_runsheet
+
+from dp_tools.core.check_model import FlagCode
+
+
+def test_check_factor_values_in_runsheet():
+    res = check_factor_values_in_runsheet(r"C:\Users\linde\rmarkdown\affy_processing\data_runsheets\GLDS_6_runsheet.csv")
+    assert res["code"] == FlagCode.GREEN
+    assert res["message"]