Spaces:
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Update api/routes.py
Browse files- api/routes.py +25 -14
api/routes.py
CHANGED
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@@ -139,7 +139,6 @@ def hyphenate_long_strings(text: str, max_length: int = 10) -> str:
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"""Insert LaTeX hyphenation points into long strings to prevent overfull hboxes."""
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if not isinstance(text, str) or len(text) <= max_length:
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return text
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-
# Insert a discretionary hyphen (\-) every max_length characters
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result = ""
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for i, char in enumerate(text):
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result += char
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@@ -147,6 +146,18 @@ def hyphenate_long_strings(text: str, max_length: int = 10) -> str:
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result += "\\-"
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return result
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async def process_synthea_patient(bundle: dict, file_path: str) -> Optional[dict]:
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logger.debug(f"Processing patient from file: {file_path}")
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patient_data = {}
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@@ -602,45 +613,45 @@ async def generate_patient_pdf(patient_id: str, current_user: dict = Depends(get
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# Format rows safely, ensuring proper column counts and hyphenation
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note_rows = " \\\\\n".join(
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"{} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(n.get("date", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(n.get("type", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(n.get("text", "") or ""))
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)
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for n in patient.get("notes", [])
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) or "No notes available \\\\"
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condition_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(c.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("code", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("onset_date", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("verification_status", "") or ""))
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)
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for c in patient.get("conditions", [])
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) or "No conditions available \\\\"
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medication_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(m.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("name", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("prescribed_date", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("dosage", "") or ""))
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)
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for m in patient.get("medications", [])
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) or "No medications available \\\\"
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encounter_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(e.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("type", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("period", {}).get("start", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("service_provider", "") or ""))
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)
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for e in patient.get("encounters", [])
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) or "No encounters available \\\\"
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# Use Template for safe insertion
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latex_template = Template(r"""
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@@ -689,7 +700,7 @@ $notes
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\end{longtable}
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\section*{Conditions}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{3cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{
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\toprule
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\textbf{ID} & \textbf{Code} & \textbf{Status} & \textbf{Onset} & \textbf{Verification} \\
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\midrule
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@@ -699,7 +710,7 @@ $conditions
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\end{longtable}
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\section*{Medications}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{4cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{
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\toprule
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\textbf{ID} & \textbf{Name} & \textbf{Status} & \textbf{Date} & \textbf{Dosage} \\
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\midrule
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@@ -709,7 +720,7 @@ $medications
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\end{longtable}
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\section*{Encounters}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{4cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{
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\toprule
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\textbf{ID} & \textbf{Type} & \textbf{Status} & \textbf{Start} & \textbf{Provider} \\
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\midrule
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@@ -721,8 +732,8 @@ $encounters
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\end{document}
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""")
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# Set the generated_on date to 03:
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generated_on = datetime.strptime("2025-05-16 15:
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latex_filled = latex_template.substitute(
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generated_on=generated_on,
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"""Insert LaTeX hyphenation points into long strings to prevent overfull hboxes."""
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if not isinstance(text, str) or len(text) <= max_length:
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return text
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result = ""
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for i, char in enumerate(text):
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result += char
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result += "\\-"
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return result
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def format_timestamp(timestamp: str) -> str:
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"""Shorten a timestamp to YYYY-MM-DD format."""
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if not isinstance(timestamp, str):
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return ""
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try:
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# Parse the timestamp and extract just the date part
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dt = datetime.strptime(timestamp, "%Y-%m-%dT%H:%M:%S%z")
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return dt.strftime("%Y-%m-%d")
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except ValueError:
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# If parsing fails, return the original string (safely escaped later)
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return timestamp
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async def process_synthea_patient(bundle: dict, file_path: str) -> Optional[dict]:
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logger.debug(f"Processing patient from file: {file_path}")
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patient_data = {}
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# Format rows safely, ensuring proper column counts and hyphenation
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note_rows = " \\\\\n".join(
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"{} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(format_timestamp(n.get("date", "") or ""))),
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escape_latex_special_chars(hyphenate_long_strings(n.get("type", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(n.get("text", "") or ""))
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)
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for n in patient.get("notes", [])
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) or "\\multicolumn{3}{l}{No notes available} \\\\"
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condition_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(c.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("code", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(c.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(format_timestamp(c.get("onset_date", "") or ""))),
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escape_latex_special_chars(hyphenate_long_strings(c.get("verification_status", "") or ""))
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)
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for c in patient.get("conditions", [])
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) or "\\multicolumn{5}{l}{No conditions available} \\\\"
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medication_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(m.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("name", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(m.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(format_timestamp(m.get("prescribed_date", "") or ""))),
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escape_latex_special_chars(hyphenate_long_strings(m.get("dosage", "") or ""))
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)
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for m in patient.get("medications", [])
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) or "\\multicolumn{5}{l}{No medications available} \\\\"
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encounter_rows = " \\\\\n".join(
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"{} & {} & {} & {} & {}".format(
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escape_latex_special_chars(hyphenate_long_strings(e.get("id", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("type", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(e.get("status", "") or "")),
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escape_latex_special_chars(hyphenate_long_strings(format_timestamp(e.get("period", {}).get("start", "") or ""))),
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escape_latex_special_chars(hyphenate_long_strings(e.get("service_provider", "") or ""))
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)
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for e in patient.get("encounters", [])
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) or "\\multicolumn{5}{l}{No encounters available} \\\\"
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# Use Template for safe insertion
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latex_template = Template(r"""
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\end{longtable}
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\section*{Conditions}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{3cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{3cm}>{\raggedright\arraybackslash}p{3cm}}
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\toprule
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\textbf{ID} & \textbf{Code} & \textbf{Status} & \textbf{Onset} & \textbf{Verification} \\
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\midrule
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\end{longtable}
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\section*{Medications}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{4cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{3cm}>{\raggedright\arraybackslash}p{2cm}}
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\toprule
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\textbf{ID} & \textbf{Name} & \textbf{Status} & \textbf{Date} & \textbf{Dosage} \\
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\midrule
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\end{longtable}
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\section*{Encounters}
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\begin{longtable}{>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{4cm}>{\raggedright\arraybackslash}p{2cm}>{\raggedright\arraybackslash}p{4cm}>{\raggedright\arraybackslash}p{3cm}}
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\toprule
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\textbf{ID} & \textbf{Type} & \textbf{Status} & \textbf{Start} & \textbf{Provider} \\
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\midrule
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\end{document}
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""")
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# Set the generated_on date to 03:59 PM CET, May 16, 2025
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generated_on = datetime.strptime("2025-05-16 15:59:00+01:00", "%Y-%m-%d %H:%M:%S%z").strftime("%A, %B %d, %Y at %I:%M %p")
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latex_filled = latex_template.substitute(
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generated_on=generated_on,
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