#77 ptd structure data v2

Structured_data_template/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

Structured_data_template/.github/ISSUE_TEMPLATE/CAPA.md

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+---
+name: CAPA
+about: File a corrective action or preventative action (CAPA) report
+title: "[CAPA]: "
+labels: ''
+assignees: ''
+
+---
+
+*This template is used to file a corrective action or preventative action (CAPA) report as specified by [CSC-QMS: SOP-016](https://github.com/GSTT-CSC/CSC-QMS)*
+
+*Please complete all of the following fields*
+
+**Type**
+*Is this a corrective action or a preventative action? (delete as appropriate)*
+
+Corrective/Preventative action
+
+**Datix ID**
+*If this CAPA has an associated Datix report, please enter the Datix ID here.*
+
+**Description**
+*Please describe the action. e.g., No contact details provided as part of product information*
+
+**Immediate Actions**
+*Describe any immeadiate actions needed to ensure safe control of the product/QMS process etc.* 
+
+**Root Cause**
+*Please describe the root cause. e.g., Loss of information during development*
+
+**Potentially Adverse Implications**
+*Describe any potentially adverse implications to the action e.g., Release of product version and process update*
+
+**Time Frame for Completion**
+*Confirm the time frame within which the actions must be completed, confirmed by the QMO.*
+*Consult CSC PR.014 for Incident Reporting timeframes*

Structured_data_template/.github/ISSUE_TEMPLATE/meeting-minutes.md

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+---
+name: Meeting Minutes
+about: Log agenda and minutes
+title: "[Minutes] - Weekly Meeting - DD-MM-YYYY"
+labels: minutes
+assignees: ''
+
+---
+
+**Attendance/Apologies**
+
+**Agenda**
+
+**Actions**
+
+- [ ] Action 1
+- [ ] Action 2

Structured_data_template/.github/ISSUE_TEMPLATE/systematic_review.md

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+---
+name: Systematic Review
+about: Log outcomes of systematic review of documentation at key project milestones 
+title: "[Systematic Review] - DD-MM-YYYY"
+labels: minutes
+assignees: ''
+
+---
+
+### Stakeholders
+
+| Name | Role |
+|------|------|
+|      |      |
+
+### Project Milestone
+> At which milestone is this review taking place?
+
+Requirements /  Proof of Concept / Deployment / Before Prospective Study / Clinical release / Other
+
+
+### Requirements Review
+
+> Are requirements still adequate and non-conflicting?
+
+### Hazard log review - CRM
+
+> Have any new hazards been identified?
+
+### Design specification review
+
+> Have extra design spec items been identified?
+
+### Verification and validation review 
+
+> Have any unit tests or manual tests failed?
+
+### Outstanding issues 
+
+
+### Resource issues

Structured_data_template/.github/PULL_REQUEST_TEMPLATE.md

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+### Linked Issue(s)
+> Explicitly tag the issue linked to this pull request, if any.
+
+### Summary of changes
+*Briefly describe the changes in this PR.*
+
+### Reason for changes
+*Explain why these changes are being made*
+
+<!-- Fill out the following section if this PR is related to a medical device. -->
+<!-- Delete this section if your changes are not related to medical devices. -->
+### Clinical Risk Management Review 
+#### Summary of the clinical risk management review:
+Briefly describe the outcome of the review and any actions taken.
+
+#### Hazard Impact
+**Related Hazards:** *Include references to the Hazard Log e.g. HZ-xxx, HZ-yyy*
+
+**Impact on Hazards:** 
+- Mitigates: *List hazards it helps mitigate (e.g., HZ-xxx, HZ-yyy)*.
+- Induces: *List hazards it might induce (e.g., HZ-xxx, HZ-yyy)*.
+
+## Quality Assurance
+- [ ] Unit tests added

Structured_data_template/.github/hooks/pre-commit

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+#!/bin/sh
+
+# REGEX PATTERNS 
+FORBIDDEN_ADDRESS="^[A-PR-UWYZ]([0-9]{1,2}|([A-HK-Y][0-9]([0-9ABEHMNPRV-Y])?)|[0-9][A-HJKPS-UW])?[[:space:]]?[0-9][ABD-HJLNP-UW-Z]{2}$"
+FORBIDDEN_PATIENT_ID="^[a-zA-Z][0-9]{6}$|^[0-9]{7}[a-zA-Z]$"
+FORBIDDEN_PHONE="(\+44|07)[0-9]{9}"
+FORBIDDEN_ACCESSION_NUMBER="sp-[0-9]{2}-[0-9]{7}"
+FORBIDDEN_DOB="[0-1][0-9]/[0-3][0-9]/[1-2][0-9]{3}"
+FORBIDDEN_DATE_TIME="[0-1][0-9]/[0-3][0-9]/[1-2][0-9]{3}\s[0-2][0-9]:[0-5][0-9]:[0-5][0-9]"
+FORBIDDEN_NHS="[0-9]{10}"
+
+git_verification_patterns=( $FORBIDDEN_ADDRESS $FORBIDDEN_PATIENT_ID $FORBIDDEN_PHONE $FORBIDDEN_ACCESSION_NUMBER $FORBIDDEN_DATE_TIME $FORBIDDEN_DOB $FORBIDDEN_NHS)
+git_verification_patterns_desc=("Address" "Patient ID" "Phone number" "Accession Number" "Date and Time" "Date of Birth" "NHS Number")
+
+# Get modified files
+FILES_MODIFIED=$(git diff --cached --name-only)
+
+NUM_FILES_CHECKED=0
+NUM_FILES_OFFENCES=0
+
+# Exceptions
+exception_file=".sensitive_exceptions"
+exclusion_file=".files_exceptions"
+
+echo "-- RUNNING SENSITIVE DATA CHECKS ----------------------------------------"
+
+for F in $FILES_MODIFIED
+do
+  F_basename=$(basename $F)
+  if grep -Fiq -- "$F_basename" $exclusion_file; then
+    continue
+  fi
+
+  for i in "${!git_verification_patterns[@]}"; do
+    MATCHES=$(egrep -i --line-number "${git_verification_patterns[$i]}" "$F" || true)
+
+    for MATCH in $MATCHES; do
+      IFS=':' read -ra PARTS <<< "$MATCH"
+      LINE_NUMBER=${PARTS[0]}
+      CONTENT=${PARTS[1]}
+
+      # Skip exceptions
+      if echo "$CONTENT" | grep -Fiq -f $exception_file; then
+        continue
+      fi
+
+      echo "FILE: $F"
+      echo "   DESC: ${git_verification_patterns_desc[$i]}"
+      echo "   MATCH: $MATCH"      
+      echo "  "
+
+      NUM_FILES_OFFENCES=$((NUM_FILES_OFFENCES+1))
+    done
+  done
+
+  NUM_FILES_CHECKED=$((NUM_FILES_CHECKED+1))
+done
+
+echo "-- SUMMARY --------------------------------------------------------------"
+echo ""
+echo "   Files Checked: $NUM_FILES_CHECKED"
+echo "   Num File Offences: $NUM_FILES_OFFENCES"
+if [ $NUM_FILES_OFFENCES -gt 0 ]; then
+  echo "   Status: FAIL"  
+  echo "   "
+else
+  echo "   Status: OK"
+  echo "   "
+fi
+
+if [ $NUM_FILES_OFFENCES -gt 0 ]; then
+  exit 1
+else
+  exit 0
+fi

Structured_data_template/.github/workflows/development_test.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Development tests
+
+on:
+  pull_request:
+
+env:
+  PROJECT_NAME: template  # the project name
+  APPLICATION_DIR: project  # the name of the main directory that contains the project code
+  TEST_DIR: tests  # the name of the directory that contains the tests
+
+jobs:
+
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+
+      - name: Build and tag image
+        run: docker build -t $PROJECT_NAME:latest .
+
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          docker run --mount type=bind,source=$(pwd),target=/$APPLICATION_DIR $PROJECT_NAME flake8 /$APPLICATION_DIR --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          docker run --mount type=bind,source=$(pwd),target=/$APPLICATION_DIR $PROJECT_NAME flake8 /$APPLICATION_DIR --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test with pytest
+        run: |
+          coverage run -m --source=project pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=$APPLICATION_DIR $TEST_DIR/ | tee pytest-coverage.txt
+
+      - name: Pytest coverage comment
+        id: coverageComment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: ./pytest-coverage.txt
+          junitxml-path: ./pytest.xml

Structured_data_template/.github/workflows/production_test.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Production tests
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'master'
+      - 'release/*'
+
+env:
+  PROJECT_NAME: template  # the project name
+  APPLICATION_DIR: project  # the name of the main directory that contains the project code
+  TEST_DIR: tests  # the name of the directory that contains the tests
+  COV_GIST_BADGEID: COV_GIST_BADGEID  # this github repo secret should define a gist token see https://github.com/Schneegans/dynamic-badges-action
+  COV_GIST_NAME: COV_GIST_NAME  # this github repo secret should contain the filename of the gist see https://github.com/Schneegans/dynamic-badges-action
+
+jobs:
+
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+
+      - name: Build and tag image
+        run: docker build -t $PROJECT_NAME:latest .
+
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          docker run --mount type=bind,source=$(pwd),target=/$APPLICATION_DIR $PROJECT_NAME flake8 /$APPLICATION_DIR --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          docker run --mount type=bind,source=$(pwd),target=/$APPLICATION_DIR $PROJECT_NAME flake8 /$APPLICATION_DIR --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test with pytest
+        run: |
+          coverage run -m --source=project pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=$APPLICATION_DIR $TEST_DIR/ | tee pytest-coverage.txt
+
+      - name: Pytest coverage comment
+        id: coverageComment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: ./pytest-coverage.txt
+          junitxml-path: ./pytest.xml
+
+      - name: Create coverage Badge
+        uses: schneegans/dynamic-badges-action@v1.0.0
+        with:
+          auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+          gistID: COV_GIST_BADGEID
+          filename: $COV_GIST_NAME
+          label: Test coverage
+          message: ${{ steps.coverageComment.outputs.coverage }}
+          color: ${{ steps.coverageComment.outputs.color }}
+          namedLogo: python