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#alt_skripte/inject_pseudonym.py
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#alt_skripte/inject_pseudonym.py
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#!/usr/bin/env python3
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"""Injects pseudonym-based matching into every Diagnostik-App Shiny app.R.
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Usage (run from the "formr" folder that directly contains all the app
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subfolders, next to server.py / get_pseudo.R / pseudonyme.db):
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python inject_pseudonym.py # dry run: reports what WOULD happen
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python inject_pseudonym.py --apply # actually writes the changes
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Finds every "<app-folder>/app.R" itself (no shell globbing needed, so this
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works the same from Windows cmd.exe as from bash). Idempotent (marker-based -
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safe to rerun), makes a .bak next to each file it actually changes, and
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leaves a file completely untouched if any of the required anchors can't be
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found unambiguously - such files are reported with a reason instead of being
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guessed at.
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"""
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import re
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import shutil
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import sys
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from pathlib import Path
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MARKER = "# --- pseudonym-support-injection v1 ---"
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def inject(path, write=True):
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path = str(path)
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raw = open(path, encoding="utf-8", newline="").read()
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uses_crlf = raw.count("\r\n") > raw.count("\n") - raw.count("\r\n")
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text = raw.replace("\r\n", "\n")
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if MARKER in text:
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return "skip: already patched", text
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orig = text
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warnings = []
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notes = []
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# 1. UI field: a pseudonym textInput with a small italic hint instead of
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# a bulky bold label. If textInput("chiffre", ...) is directly preceded
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# by a simple single-purpose `div(style = "...",` wrapper (the common
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# shape), clone a sibling div so both fields sit side by side in the
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# same flex row instead of stacking. Otherwise fall back to a plain
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# inline sibling insert (functional, just possibly stacked) and note it.
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label_block = (
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'tagList(\n'
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'{i} "Pseudonym",\n'
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'{i} tags$span(style = "font-weight: normal; font-style: italic; '
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'font-size: 0.78em; color: #888; margin-left: 4px; white-space: nowrap;",\n'
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'{i} "optional, hat Vorrang vor Chiffre")\n'
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'{i} )'
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)
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m_wrapped = re.search(
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r'^([ \t]*)div\(style\s*=\s*"[^"]*"\s*,\s*\n([ \t]*)textInput\("chiffre"',
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text, re.MULTILINE,
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)
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if m_wrapped:
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outer_indent, inner_indent = m_wrapped.group(1), m_wrapped.group(2)
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label = label_block.format(i=inner_indent)
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insertion = (
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f'{outer_indent}div(style = "min-width: 360px; white-space: nowrap;",\n'
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f'{inner_indent}textInput("pseudonym",\n'
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f'{inner_indent} label = {label},\n'
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f'{inner_indent} placeholder = "optional", width = "340px")\n'
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f'{outer_indent}),\n'
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)
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text = text[: m_wrapped.start()] + insertion + text[m_wrapped.start() :]
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else:
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m = re.search(r'^([ \t]*)textInput\("chiffre"', text, re.MULTILINE)
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if not m:
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warnings.append('UI: textInput("chiffre" not found')
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else:
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indent = m.group(1)
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label = label_block.format(i=indent)
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insertion = (
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f'{indent}textInput("pseudonym",\n'
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f'{indent} label = {label},\n'
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f'{indent} placeholder = "optional", width = "340px"),\n'
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)
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text = text[: m.start()] + insertion + text[m.start() :]
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notes.append(
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"UI: no simple preceding div(style=...) wrapper found around "
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"textInput(\"chiffre\" - pseudonym field inserted inline; layout "
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"may need a manual look (may stack instead of sitting side by side)"
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)
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# 2. URL prefill: new observe() block right after the server function
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# signature, independent of/in addition to the existing chiffre one.
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m = re.search(r"server\s*=\s*function\(input,\s*output,\s*session\)\s*\{\n", text)
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if not m:
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warnings.append("server = function(input, output, session) { not found")
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else:
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block = (
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f" {MARKER}\n"
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" observe({\n"
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" query = parseQueryString(session$clientData$url_search)\n"
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" if (!is.null(query$pseudonym) && nchar(trimws(query$pseudonym)) > 0) {\n"
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' updateTextInput(session, "pseudonym", value = trimws(query$pseudonym))\n'
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" }\n"
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" })\n\n"
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)
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idx = m.end()
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text = text[:idx] + block + text[idx:]
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# Some apps run their chiffre-empty/format checks inside a dedicated
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# top-level helper function (e.g. desii_validiere_chiffre(),
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# validiere_chiffre()) defined OUTSIDE server() - such a function has no
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# `input` in scope. Blindly rewriting a check there would compile fine
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# but throw "object 'input' not found" at runtime on every single click,
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# for every patient, whether pseudonym is used or not. So items 3 and 4
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# only ever touch occurrences that are reachable from inside server()
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# (i.e. at/after the server function's opening brace); anything found
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# only earlier in the file is left completely untouched and reported as
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# a note instead - pseudonym-only entry (no chiffre at all) just won't
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# work for that one app, but the chiffre+pseudonym disambiguation (the
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# actual bug this whole thing fixes) is unaffected either way.
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m_anchor = re.search(r"server\s*=\s*function\(input,\s*output,\s*session\)\s*\{", text)
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reactive_start = m_anchor.start() if m_anchor else None
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def patch_reachable(text, target, replacement):
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matches = list(re.finditer(re.escape(target), text))
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reachable = [
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mm for mm in matches
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if reactive_start is not None and mm.start() >= reactive_start
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]
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for mm in reversed(reachable):
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text = text[: mm.start()] + replacement + text[mm.end() :]
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return text, len(matches), len(reachable)
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# 3. Relax the "chiffre leer" gate - phrasing varies (some apps check
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# `chiffre`, others read into `chiffre_roh` first).
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empty_gate_variants = [
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("nchar(chiffre) == 0",
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"(nchar(trimws(input$pseudonym)) == 0 && nchar(chiffre) == 0)"),
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("nchar(trimws(chiffre_roh)) == 0",
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"(nchar(trimws(input$pseudonym)) == 0 && nchar(trimws(chiffre_roh)) == 0)"),
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('trimws(chiffre_roh) == ""',
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'(nchar(trimws(input$pseudonym)) == 0 && trimws(chiffre_roh) == "")'),
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]
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any_empty_gate_patched = False
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for target, replacement in empty_gate_variants:
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text, total, reachable = patch_reachable(text, target, replacement)
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if reachable:
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any_empty_gate_patched = True
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if not any_empty_gate_patched:
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notes.append(
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"no reachable chiffre-empty gate found (the format-check gate below "
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"usually already covers an empty chiffre too, so this is often fine)"
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)
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# 4. Relax the chiffre-format gate.
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target = 'grepl("^[A-Z][0-9]{6}$", chiffre)'
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replacement = '(nchar(trimws(input$pseudonym)) > 0 || grepl("^[A-Z][0-9]{6}$", chiffre))'
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text, total, reachable = patch_reachable(text, target, replacement)
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if reachable == 0:
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if total > 0:
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notes.append(
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"chiffre-format check only exists inside a top-level helper function "
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"with no access to the pseudonym input - pseudonym-only entry (no "
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"chiffre at all) won't work for this app, but chiffre+pseudonym "
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"disambiguation (the main fix) is unaffected"
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)
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else:
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warnings.append(f'gate not found: "{target}"')
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# 5. Backfill `chiffre` from the pseudonym right after the pseudonym
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# script is sourced (pseudo now exists in .GlobalEnv - guaranteed
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# name, set by the one shared get_pseudo.R).
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target = "source(PFAD_PSEUDONYM_SKRIPT, local = FALSE)"
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occurrences = [mm.start() for mm in re.finditer(re.escape(target), text)]
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if len(occurrences) != 1:
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warnings.append(
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f'expected exactly 1 occurrence of source(PFAD_PSEUDONYM_SKRIPT...), found {len(occurrences)}'
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)
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else:
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pos = occurrences[0]
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line_start = text.rfind("\n", 0, pos) + 1
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indent = re.match(r"[ \t]*", text[line_start:pos]).group(0)
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end = pos + len(target)
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backfill = (
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f"\n{indent}if (nchar(trimws(input$pseudonym)) > 0) {{\n"
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f'{indent} .pw_wert = trimws(input$pseudonym)\n'
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f'{indent} .pw_tab = get("pseudo", envir = .GlobalEnv)\n'
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f"{indent} .pw_treffer = .pw_tab[.pw_tab$pseudonym == .pw_wert, ]\n"
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f"{indent} if (nrow(.pw_treffer) > 0) chiffre = toupper(trimws(.pw_treffer$chiffre[1]))\n"
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f"{indent}}}"
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)
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text = text[:end] + backfill + text[end:]
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# 6. Override the final session-id(s) with the exact pseudonym, so an
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# ambiguous chiffre (multiple pseudonyms) doesn't silently pick the
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# wrong / most-recent entry.
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sid_pattern = re.compile(
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r"^([ \t]*)([A-Za-z_][A-Za-z0-9_.]*)\s*=\s*"
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r"(unique\(as\.character\(\w+\$pseudonym\)\)|unique\(\w+\$pseudonym\)|\w+\$pseudonym\[1\])[ \t]*$",
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re.MULTILINE,
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)
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matches = list(sid_pattern.finditer(text))
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if len(matches) == 0:
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warnings.append("session-id assignment (X = unique(Y$pseudonym) / Y$pseudonym[1]) not found")
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else:
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for mm in reversed(matches):
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indent, varname = mm.group(1), mm.group(2)
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override = f"\n{indent}if (nchar(trimws(input$pseudonym)) > 0) {varname} = trimws(input$pseudonym)"
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text = text[: mm.end()] + override + text[mm.end() :]
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if warnings:
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return "skip: " + "; ".join(warnings), orig
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out = text.replace("\n", "\r\n") if uses_crlf else text
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if write:
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shutil.copy(path, path + ".bak")
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with open(path, "w", encoding="utf-8", newline="") as f:
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f.write(out)
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status = "patched"
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if notes:
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status += " (note: " + "; ".join(notes) + ")"
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return status, out
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def main():
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args = sys.argv[1:]
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apply_changes = "--apply" in args
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args = [a for a in args if a != "--apply"]
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if args:
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paths = [Path(a) for a in args]
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else:
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paths = sorted(Path(".").glob("*/app.R"))
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if not paths:
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print('No "*/app.R" files found in the current directory. '
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"Run this from the folder that directly contains all the app "
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"subfolders (next to server.py / get_pseudo.R / pseudonyme.db), "
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"or pass explicit paths.")
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sys.exit(1)
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print(f"{'DRY RUN (no files will be changed - pass --apply to write)' if not apply_changes else 'APPLYING CHANGES'}")
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print(f"{len(paths)} app(s) found.\n")
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counts = {"patched": 0, "patched-with-note": 0, "skip-already-patched": 0, "skip": 0}
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for p in paths:
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try:
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status, _ = inject(p, write=apply_changes)
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except Exception as e:
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status = f"skip: UNEXPECTED ERROR ({type(e).__name__}: {e}) - file left untouched, please report this"
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if status.startswith("skip: already patched"):
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counts["skip-already-patched"] += 1
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elif status.startswith("skip:"):
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counts["skip"] += 1
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elif "(note:" in status:
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counts["patched-with-note"] += 1
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else:
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counts["patched"] += 1
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print(f"{p}: {status}")
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print(
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f"\n{counts['patched']} clean, {counts['patched-with-note']} patched-with-note, "
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f"{counts['skip']} skipped, {counts['skip-already-patched']} already patched."
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)
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if not apply_changes:
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print("This was a dry run - nothing was written. Rerun with --apply once you're happy.")
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if __name__ == "__main__":
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main()
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