Beta version

.gitignore

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+.idea/*
+__pycache__/*
+*.pyc

README.md

@@ -1,2 +1,3 @@
-# data-quality
-This repository contains all materials tied to the Data Quality Framework Project.
+# Development version
+
+Run the app by executing the script "gui.py."

mmci_convertor/export_graphs_fhir.py

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+from reportlab.lib.pagesizes import letter
+from reportlab.pdfgen import canvas
+import quality_checks_fhir as qc
+
+
+# disclaimer: parts of this function were generated by ChatGPT.
+def create_report_fhir(server):
+    """
+    Create dataframes, run quality checks and create report.
+
+    :param server: FHIR server.
+    :return:
+        None
+    """
+    pdf = qc.create_patient_data_frame(server)
+    sdf = qc.create_specimen_data_frame(server)
+    cdf = qc.create_condition_data_frame(server)
+
+    # Create canvas
+    can = canvas.Canvas("plots_fhir.pdf", pagesize=letter)
+    # create pages
+    create_dq_checks(can, pdf, cdf, sdf, server)
+    create_warnings(can, pdf, cdf, sdf)
+    create_reports(can, pdf, cdf, sdf)
+    # Save PDF
+    can.save()
+
+
+# disclaimer: parts of this function were generated by ChatGPT.
+def create_page(can, header, fig, graph_image_name, graph_size):
+    """
+    Helper function of create_report_fhir. Draw page.
+
+    :param can: Canvas.
+    :param header: Header in page.
+    :param fig: Figure in page.
+    :param graph_image_name: Path to save figure.
+    :param graph_size: Size of figure.
+    :return:
+        None
+    """
+    # Add text to canvas for page 1
+    text_page = "FHIR data quality checks"
+    can.setFont("Helvetica-Bold", 14)
+    can.drawString(50, 750, text_page)
+
+    # header
+    can.drawString(50, 700, header)
+
+    # Save Plotly graph as PNG
+    fig.write_image("graphs/fhir/" + graph_image_name + ".png")
+
+    # Add Plotly graph to the PDF
+    can.drawImage("graphs/fhir/" + graph_image_name + ".png", 50, 50, width=graph_size[0], height=graph_size[1])
+
+    can.showPage()
+
+def create_dq_checks(can, pdf, cdf, sdf, server):
+    """
+    Helper function of create_report_fhir. Run basic data quality checks.
+
+    :param can: Canvas.
+    :param pdf: Patient data frame.
+    :param cdf: Condition data frame.
+    :param sdf: Specimen data frame.
+    :param server: FHIR server.
+    :return:
+        None
+    """
+    completeness = "completeness"
+
+    person = qc.completeness(pdf)
+    person.update_layout(width=400, height=400)
+    create_page(can, completeness + " person", person,
+                completeness + "_person", (500,500))
+
+    condition = qc.completeness(cdf)
+    condition.update_layout(width=400, height=400)
+    create_page(can, completeness + " condition", condition, completeness + "_condition", (500, 500))
+
+    specimens = qc.completeness(sdf)
+    specimens.update_layout(width=400, height=400)
+    create_page(can, completeness + " specimen", specimens, completeness + "_specimens", (500, 500))
+
+    uniqueness = "uniqueness"
+
+    person = qc.uniqueness(pdf, "person")
+    person.update_layout(width=400, height=400)
+    create_page(can, uniqueness + " person", person, uniqueness + "_person", (500, 500))
+
+    condition = qc.uniqueness(cdf, "condition")
+    condition.update_layout(width=400, height=400)
+    create_page(can, uniqueness + " condition", condition, uniqueness + "_condition", (500, 500))
+
+    specimens = qc.uniqueness(sdf, "specimen")
+    specimens.update_layout(width=400, height=400)
+    create_page(can, uniqueness + " specimen", specimens, uniqueness + "_specimens", (500, 500))
+
+    qc.conformance_patient(pdf)
+    qc.conformance_condition(cdf)
+    qc.conformance_specimen(sdf)
+
+    qc.conformance_relational(sdf, server)
+    qc.conformance_relational(cdf, server)
+    qc.conformance_computational(pdf, sdf, cdf)
+    # TODO proč tady není vykreslení?
+
+def create_warnings(can, pdf, cdf, sdf):
+    """
+    Helper function of create_report_fhir. Run warnings.
+
+    :param can: Canvas.
+    :param pdf: Patient data frame.
+    :param cdf: Condition data frame.
+    :param sdf: Specimen data frame.
+    :return:
+        None
+    """
+    young = qc.age_at_primary_diagnosis(pdf, cdf)
+    young.update_layout(width=400, height=400)
+    create_page(can, "age_at_primary_diagnosis",
+                young, "age_at_primary_diagnosis",
+                (500, 500))
+
+    diagnosis_in_future = qc.diagnosis_in_future(cdf)
+    diagnosis_in_future.update_layout(width=400, height=400)
+    create_page(can, "diagnosis_in_future",
+                diagnosis_in_future, "diagnosis_in_future",
+                (500, 500))
+
+
+def create_reports(can, pdf, cdf, sdf):
+    """
+    Helper function of create_report_fhir. Run reports.
+
+    :param can: Canvas.
+    :param pdf: Patient data frame.
+    :param cdf: Condition data frame.
+    :param sdf: Specimen data frame.
+    :return:
+        None
+    """
+    missing_collection_collectedDateTime = qc.missing_collection_collectedDateTime(pdf, sdf)
+    missing_collection_collectedDateTime.update_layout(width=400, height=400)
+    create_page(can, "missing_collection_collectedDateTime",
+                missing_collection_collectedDateTime, "missing_collection_collectedDateTime",
+                (500, 500))
+
+    patients_without_specimen_type_text = qc.patients_without_specimen_type_text(pdf, sdf)
+    patients_without_specimen_type_text.update_layout(width=400, height=400)
+    create_page(can, "patients_without_specimen_type_text",
+                patients_without_specimen_type_text, "patients_without_specimen_type_text",
+                (500, 500))
+
+    patients_without_specimen_type_text = qc.patients_without_condition_values(pdf, cdf)
+    patients_without_specimen_type_text.update_layout(width=400, height=400)
+    create_page(can, "patients_without_condition_values",
+                patients_without_specimen_type_text, "patients_without_condition_values",
+                (500, 500))