Deploy Clinical GraphRAG Pro backend and UI

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.venv/bin/Activate.ps1

@@ -0,0 +1,247 @@
+<#
+.Synopsis
+Activate a Python virtual environment for the current PowerShell session.
+
+.Description
+Pushes the python executable for a virtual environment to the front of the
+$Env:PATH environment variable and sets the prompt to signify that you are
+in a Python virtual environment. Makes use of the command line switches as
+well as the `pyvenv.cfg` file values present in the virtual environment.
+
+.Parameter VenvDir
+Path to the directory that contains the virtual environment to activate. The
+default value for this is the parent of the directory that the Activate.ps1
+script is located within.
+
+.Parameter Prompt
+The prompt prefix to display when this virtual environment is activated. By
+default, this prompt is the name of the virtual environment folder (VenvDir)
+surrounded by parentheses and followed by a single space (ie. '(.venv) ').
+
+.Example
+Activate.ps1
+Activates the Python virtual environment that contains the Activate.ps1 script.
+
+.Example
+Activate.ps1 -Verbose
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and shows extra information about the activation as it executes.
+
+.Example
+Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv
+Activates the Python virtual environment located in the specified location.
+
+.Example
+Activate.ps1 -Prompt "MyPython"
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and prefixes the current prompt with the specified string (surrounded in
+parentheses) while the virtual environment is active.
+
+.Notes
+On Windows, it may be required to enable this Activate.ps1 script by setting the
+execution policy for the user. You can do this by issuing the following PowerShell
+command:
+
+PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
+
+For more information on Execution Policies: 
+https://go.microsoft.com/fwlink/?LinkID=135170
+
+#>
+Param(
+    [Parameter(Mandatory = $false)]
+    [String]
+    $VenvDir,
+    [Parameter(Mandatory = $false)]
+    [String]
+    $Prompt
+)
+
+<# Function declarations --------------------------------------------------- #>
+
+<#
+.Synopsis
+Remove all shell session elements added by the Activate script, including the
+addition of the virtual environment's Python executable from the beginning of
+the PATH variable.
+
+.Parameter NonDestructive
+If present, do not remove this function from the global namespace for the
+session.
+
+#>
+function global:deactivate ([switch]$NonDestructive) {
+    # Revert to original values
+
+    # The prior prompt:
+    if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) {
+        Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt
+        Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT
+    }
+
+    # The prior PYTHONHOME:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME
+        Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME
+    }
+
+    # The prior PATH:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH
+        Remove-Item -Path Env:_OLD_VIRTUAL_PATH
+    }
+
+    # Just remove the VIRTUAL_ENV altogether:
+    if (Test-Path -Path Env:VIRTUAL_ENV) {
+        Remove-Item -Path env:VIRTUAL_ENV
+    }
+
+    # Just remove VIRTUAL_ENV_PROMPT altogether.
+    if (Test-Path -Path Env:VIRTUAL_ENV_PROMPT) {
+        Remove-Item -Path env:VIRTUAL_ENV_PROMPT
+    }
+
+    # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether:
+    if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) {
+        Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force
+    }
+
+    # Leave deactivate function in the global namespace if requested:
+    if (-not $NonDestructive) {
+        Remove-Item -Path function:deactivate
+    }
+}
+
+<#
+.Description
+Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the
+given folder, and returns them in a map.
+
+For each line in the pyvenv.cfg file, if that line can be parsed into exactly
+two strings separated by `=` (with any amount of whitespace surrounding the =)
+then it is considered a `key = value` line. The left hand string is the key,
+the right hand is the value.
+
+If the value starts with a `'` or a `"` then the first and last character is
+stripped from the value before being captured.
+
+.Parameter ConfigDir
+Path to the directory that contains the `pyvenv.cfg` file.
+#>
+function Get-PyVenvConfig(
+    [String]
+    $ConfigDir
+) {
+    Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg"
+
+    # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue).
+    $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue
+
+    # An empty map will be returned if no config file is found.
+    $pyvenvConfig = @{ }
+
+    if ($pyvenvConfigPath) {
+
+        Write-Verbose "File exists, parse `key = value` lines"
+        $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath
+
+        $pyvenvConfigContent | ForEach-Object {
+            $keyval = $PSItem -split "\s*=\s*", 2
+            if ($keyval[0] -and $keyval[1]) {
+                $val = $keyval[1]
+
+                # Remove extraneous quotations around a string value.
+                if ("'""".Contains($val.Substring(0, 1))) {
+                    $val = $val.Substring(1, $val.Length - 2)
+                }
+
+                $pyvenvConfig[$keyval[0]] = $val
+                Write-Verbose "Adding Key: '$($keyval[0])'='$val'"
+            }
+        }
+    }
+    return $pyvenvConfig
+}
+
+
+<# Begin Activate script --------------------------------------------------- #>
+
+# Determine the containing directory of this script
+$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition
+$VenvExecDir = Get-Item -Path $VenvExecPath
+
+Write-Verbose "Activation script is located in path: '$VenvExecPath'"
+Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)"
+Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)"
+
+# Set values required in priority: CmdLine, ConfigFile, Default
+# First, get the location of the virtual environment, it might not be
+# VenvExecDir if specified on the command line.
+if ($VenvDir) {
+    Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values"
+}
+else {
+    Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir."
+    $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/")
+    Write-Verbose "VenvDir=$VenvDir"
+}
+
+# Next, read the `pyvenv.cfg` file to determine any required value such
+# as `prompt`.
+$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir
+
+# Next, set the prompt from the command line, or the config file, or
+# just use the name of the virtual environment folder.
+if ($Prompt) {
+    Write-Verbose "Prompt specified as argument, using '$Prompt'"
+}
+else {
+    Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value"
+    if ($pyvenvCfg -and $pyvenvCfg['prompt']) {
+        Write-Verbose "  Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'"
+        $Prompt = $pyvenvCfg['prompt'];
+    }
+    else {
+        Write-Verbose "  Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virtual environment)"
+        Write-Verbose "  Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'"
+        $Prompt = Split-Path -Path $venvDir -Leaf
+    }
+}
+
+Write-Verbose "Prompt = '$Prompt'"
+Write-Verbose "VenvDir='$VenvDir'"
+
+# Deactivate any currently active virtual environment, but leave the
+# deactivate function in place.
+deactivate -nondestructive
+
+# Now set the environment variable VIRTUAL_ENV, used by many tools to determine
+# that there is an activated venv.
+$env:VIRTUAL_ENV = $VenvDir
+
+if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) {
+
+    Write-Verbose "Setting prompt to '$Prompt'"
+
+    # Set the prompt to include the env name
+    # Make sure _OLD_VIRTUAL_PROMPT is global
+    function global:_OLD_VIRTUAL_PROMPT { "" }
+    Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT
+    New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt
+
+    function global:prompt {
+        Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) "
+        _OLD_VIRTUAL_PROMPT
+    }
+    $env:VIRTUAL_ENV_PROMPT = $Prompt
+}
+
+# Clear PYTHONHOME
+if (Test-Path -Path Env:PYTHONHOME) {
+    Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME
+    Remove-Item -Path Env:PYTHONHOME
+}
+
+# Add the venv to the PATH
+Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH
+$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH"

.venv/bin/activate

@@ -0,0 +1,76 @@
+# This file must be used with "source bin/activate" *from bash*
+# You cannot run it directly
+
+deactivate () {
+    # reset old environment variables
+    if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
+        PATH="${_OLD_VIRTUAL_PATH:-}"
+        export PATH
+        unset _OLD_VIRTUAL_PATH
+    fi
+    if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
+        PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
+        export PYTHONHOME
+        unset _OLD_VIRTUAL_PYTHONHOME
+    fi
+
+    # Call hash to forget past locations. Without forgetting
+    # past locations the $PATH changes we made may not be respected.
+    # See "man bash" for more details. hash is usually a builtin of your shell
+    hash -r 2> /dev/null
+
+    if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
+        PS1="${_OLD_VIRTUAL_PS1:-}"
+        export PS1
+        unset _OLD_VIRTUAL_PS1
+    fi
+
+    unset VIRTUAL_ENV
+    unset VIRTUAL_ENV_PROMPT
+    if [ ! "${1:-}" = "nondestructive" ] ; then
+    # Self destruct!
+        unset -f deactivate
+    fi
+}
+
+# unset irrelevant variables
+deactivate nondestructive
+
+# on Windows, a path can contain colons and backslashes and has to be converted:
+case "$(uname)" in
+    CYGWIN*|MSYS*|MINGW*)
+        # transform D:\path\to\venv to /d/path/to/venv on MSYS and MINGW
+        # and to /cygdrive/d/path/to/venv on Cygwin
+        VIRTUAL_ENV=$(cygpath /Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv)
+        export VIRTUAL_ENV
+        ;;
+    *)
+        # use the path as-is
+        export VIRTUAL_ENV=/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv
+        ;;
+esac
+
+_OLD_VIRTUAL_PATH="$PATH"
+PATH="$VIRTUAL_ENV/"bin":$PATH"
+export PATH
+
+VIRTUAL_ENV_PROMPT='(.venv) '
+export VIRTUAL_ENV_PROMPT
+
+# unset PYTHONHOME if set
+# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
+# could use `if (set -u; : $PYTHONHOME) ;` in bash
+if [ -n "${PYTHONHOME:-}" ] ; then
+    _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
+    unset PYTHONHOME
+fi
+
+if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
+    _OLD_VIRTUAL_PS1="${PS1:-}"
+    PS1="("'(.venv) '") ${PS1:-}"
+    export PS1
+fi
+
+# Call hash to forget past commands. Without forgetting
+# past commands the $PATH changes we made may not be respected
+hash -r 2> /dev/null

.venv/bin/activate.csh

@@ -0,0 +1,27 @@
+# This file must be used with "source bin/activate.csh" *from csh*.
+# You cannot run it directly.
+
+# Created by Davide Di Blasi <davidedb@gmail.com>.
+# Ported to Python 3.3 venv by Andrew Svetlov <andrew.svetlov@gmail.com>
+
+alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; unsetenv VIRTUAL_ENV_PROMPT; test "\!:*" != "nondestructive" && unalias deactivate'
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+setenv VIRTUAL_ENV /Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv
+
+set _OLD_VIRTUAL_PATH="$PATH"
+setenv PATH "$VIRTUAL_ENV/"bin":$PATH"
+
+
+set _OLD_VIRTUAL_PROMPT="$prompt"
+
+if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
+    set prompt = '(.venv) '"$prompt"
+    setenv VIRTUAL_ENV_PROMPT '(.venv) '
+endif
+
+alias pydoc python -m pydoc
+
+rehash

.venv/bin/activate.fish

@@ -0,0 +1,69 @@
+# This file must be used with "source <venv>/bin/activate.fish" *from fish*
+# (https://fishshell.com/). You cannot run it directly.
+
+function deactivate  -d "Exit virtual environment and return to normal shell environment"
+    # reset old environment variables
+    if test -n "$_OLD_VIRTUAL_PATH"
+        set -gx PATH $_OLD_VIRTUAL_PATH
+        set -e _OLD_VIRTUAL_PATH
+    end
+    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
+        set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
+        set -e _OLD_VIRTUAL_PYTHONHOME
+    end
+
+    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
+        set -e _OLD_FISH_PROMPT_OVERRIDE
+        # prevents error when using nested fish instances (Issue #93858)
+        if functions -q _old_fish_prompt
+            functions -e fish_prompt
+            functions -c _old_fish_prompt fish_prompt
+            functions -e _old_fish_prompt
+        end
+    end
+
+    set -e VIRTUAL_ENV
+    set -e VIRTUAL_ENV_PROMPT
+    if test "$argv[1]" != "nondestructive"
+        # Self-destruct!
+        functions -e deactivate
+    end
+end
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+set -gx VIRTUAL_ENV /Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv
+
+set -gx _OLD_VIRTUAL_PATH $PATH
+set -gx PATH "$VIRTUAL_ENV/"bin $PATH
+
+# Unset PYTHONHOME if set.
+if set -q PYTHONHOME
+    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
+    set -e PYTHONHOME
+end
+
+if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
+    # fish uses a function instead of an env var to generate the prompt.
+
+    # Save the current fish_prompt function as the function _old_fish_prompt.
+    functions -c fish_prompt _old_fish_prompt
+
+    # With the original prompt function renamed, we can override with our own.
+    function fish_prompt
+        # Save the return status of the last command.
+        set -l old_status $status
+
+        # Output the venv prompt; color taken from the blue of the Python logo.
+        printf "%s%s%s" (set_color 4B8BBE) '(.venv) ' (set_color normal)
+
+        # Restore the return status of the previous command.
+        echo "exit $old_status" | .
+        # Output the original/"old" prompt.
+        _old_fish_prompt
+    end
+
+    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
+    set -gx VIRTUAL_ENV_PROMPT '(.venv) '
+end

.venv/bin/alembic

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from alembic.config import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/celery

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from celery.__main__ import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/convert-caffe2-to-onnx

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from caffe2.python.onnx.bin.conversion import caffe2_to_onnx
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(caffe2_to_onnx())

.venv/bin/convert-onnx-to-caffe2

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from caffe2.python.onnx.bin.conversion import onnx_to_caffe2
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(onnx_to_caffe2())

.venv/bin/coverage

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from coverage.cmdline import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/coverage-3.12

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from coverage.cmdline import main_deprecated
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main_deprecated())

.venv/bin/coverage3

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from coverage.cmdline import main_deprecated
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main_deprecated())

.venv/bin/dotenv

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from dotenv.__main__ import cli
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(cli())

.venv/bin/f2py

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from numpy.f2py.f2py2e import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/fastapi

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from fastapi.cli import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/fonttools

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from fontTools.__main__ import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/hf

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from huggingface_hub.cli.hf import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/httpx

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from httpx import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/huggingface-cli

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from huggingface_hub.commands.huggingface_cli import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/idna

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from idna.cli import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/isympy

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from isympy import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/jsondiff

@@ -0,0 +1,41 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+# -*- coding: utf-8 -*-
+
+from __future__ import print_function
+
+import sys
+import json
+import jsonpatch
+import argparse
+
+
+parser = argparse.ArgumentParser(description='Diff two JSON files')
+parser.add_argument('FILE1', type=argparse.FileType('r'))
+parser.add_argument('FILE2', type=argparse.FileType('r'))
+parser.add_argument('--indent', type=int, default=None,
+                    help='Indent output by n spaces')
+parser.add_argument('-u', '--preserve-unicode', action='store_true',
+                    help='Output Unicode character as-is without using Code Point')
+parser.add_argument('-v', '--version', action='version',
+                    version='%(prog)s ' + jsonpatch.__version__)
+
+
+def main():
+    try:
+        diff_files()
+    except KeyboardInterrupt:
+        sys.exit(1)
+
+
+def diff_files():
+    """ Diffs two JSON files and prints a patch """
+    args = parser.parse_args()
+    doc1 = json.load(args.FILE1)
+    doc2 = json.load(args.FILE2)
+    patch = jsonpatch.make_patch(doc1, doc2)
+    if patch.patch:
+        print(json.dumps(patch.patch, indent=args.indent, ensure_ascii=not(args.preserve_unicode)))
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()

.venv/bin/jsonpatch

@@ -0,0 +1,107 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+# -*- coding: utf-8 -*-
+
+import sys
+import os.path
+import json
+import jsonpatch
+import tempfile
+import argparse
+
+
+parser = argparse.ArgumentParser(
+    description='Apply a JSON patch on a JSON file')
+parser.add_argument('ORIGINAL', type=argparse.FileType('r'),
+                    help='Original file')
+parser.add_argument('PATCH', type=argparse.FileType('r'),
+                    nargs='?', default=sys.stdin,
+                    help='Patch file (read from stdin if omitted)')
+parser.add_argument('--indent', type=int, default=None,
+                    help='Indent output by n spaces')
+parser.add_argument('-b', '--backup', action='store_true',
+                    help='Back up ORIGINAL if modifying in-place')
+parser.add_argument('-i', '--in-place', action='store_true',
+                    help='Modify ORIGINAL in-place instead of to stdout')
+parser.add_argument('-v', '--version', action='version',
+                    version='%(prog)s ' + jsonpatch.__version__)
+parser.add_argument('-u', '--preserve-unicode', action='store_true',
+                    help='Output Unicode character as-is without using Code Point')
+
+def main():
+    try:
+        patch_files()
+    except KeyboardInterrupt:
+        sys.exit(1)
+
+
+def patch_files():
+    """ Diffs two JSON files and prints a patch """
+    args = parser.parse_args()
+    doc = json.load(args.ORIGINAL)
+    patch = json.load(args.PATCH)
+    result = jsonpatch.apply_patch(doc, patch)
+
+    if args.in_place:
+        dirname = os.path.abspath(os.path.dirname(args.ORIGINAL.name))
+
+        try:
+            # Attempt to replace the file atomically.  We do this by
+            # creating a temporary file in the same directory as the
+            # original file so we can atomically move the new file over
+            # the original later.  (This is done in the same directory
+	    # because atomic renames do not work across mount points.)
+
+            fd, pathname = tempfile.mkstemp(dir=dirname)
+            fp = os.fdopen(fd, 'w')
+            atomic = True
+
+        except OSError:
+            # We failed to create the temporary file for an atomic
+            # replace, so fall back to non-atomic mode by backing up
+            # the original (if desired) and writing a new file.
+
+            if args.backup:
+                os.rename(args.ORIGINAL.name, args.ORIGINAL.name + '.orig')
+            fp = open(args.ORIGINAL.name, 'w')
+            atomic = False
+
+    else:
+        # Since we're not replacing the original file in-place, write
+        # the modified JSON to stdout instead.
+
+        fp = sys.stdout
+
+    # By this point we have some sort of file object we can write the 
+    # modified JSON to.
+    
+    json.dump(result, fp, indent=args.indent, ensure_ascii=not(args.preserve_unicode))
+    fp.write('\n')
+
+    if args.in_place:
+        # Close the new file.  If we aren't replacing atomically, this
+        # is our last step, since everything else is already in place.
+
+        fp.close()
+
+        if atomic:
+            try:
+                # Complete the atomic replace by linking the original
+                # to a backup (if desired), fixing up the permissions
+                # on the temporary file, and moving it into place.
+
+                if args.backup:
+                    os.link(args.ORIGINAL.name, args.ORIGINAL.name + '.orig')
+                os.chmod(pathname, os.stat(args.ORIGINAL.name).st_mode)
+                os.rename(pathname, args.ORIGINAL.name)
+
+            except OSError:
+                # In the event we could not actually do the atomic
+                # replace, unlink the original to move it out of the
+                # way and finally move the temporary file into place.
+                
+                os.unlink(args.ORIGINAL.name)
+                os.rename(pathname, args.ORIGINAL.name)
+
+
+if __name__ == "__main__":
+    main()

.venv/bin/jsonpointer

@@ -0,0 +1,66 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+
+
+import argparse
+import json
+import sys
+
+import jsonpointer
+
+parser = argparse.ArgumentParser(
+    description='Resolve a JSON pointer on JSON files')
+
+# Accept pointer as argument or as file
+ptr_group = parser.add_mutually_exclusive_group(required=True)
+
+ptr_group.add_argument('-f', '--pointer-file', type=argparse.FileType('r'),
+                       nargs='?',
+                       help='File containing a JSON pointer expression')
+
+ptr_group.add_argument('POINTER', type=str, nargs='?',
+                       help='A JSON pointer expression')
+
+parser.add_argument('FILE', type=argparse.FileType('r'), nargs='+',
+                    help='Files for which the pointer should be resolved')
+parser.add_argument('--indent', type=int, default=None,
+                    help='Indent output by n spaces')
+parser.add_argument('-v', '--version', action='version',
+                    version='%(prog)s ' + jsonpointer.__version__)
+
+
+def main():
+    try:
+        resolve_files()
+    except KeyboardInterrupt:
+        sys.exit(1)
+
+
+def parse_pointer(args):
+    if args.POINTER:
+        ptr = args.POINTER
+    elif args.pointer_file:
+        ptr = args.pointer_file.read().strip()
+    else:
+        parser.print_usage()
+        sys.exit(1)
+
+    return ptr
+
+
+def resolve_files():
+    """ Resolve a JSON pointer on JSON files """
+    args = parser.parse_args()
+
+    ptr = parse_pointer(args)
+
+    for f in args.FILE:
+        doc = json.load(f)
+        try:
+            result = jsonpointer.resolve_pointer(doc, ptr)
+            print(json.dumps(result, indent=args.indent))
+        except jsonpointer.JsonPointerException as e:
+            print('Could not resolve pointer: %s' % str(e), file=sys.stderr)
+
+
+if __name__ == "__main__":
+    main()

.venv/bin/mako-render

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from mako.cmd import cmdline
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(cmdline())

.venv/bin/markdown-it

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from markdown_it.cli.parse import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/nodeenv

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from nodeenv import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/normalizer

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from charset_normalizer.cli import cli_detect
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(cli_detect())

.venv/bin/pip

@@ -0,0 +1,8 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

.venv/bin/pip3

@@ -0,0 +1,8 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

.venv/bin/pip3.12

@@ -0,0 +1,8 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

.venv/bin/py.test

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pytest import console_main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(console_main())

.venv/bin/pybind11-config

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pybind11.__main__ import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/pydicom

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pydicom.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/pyftmerge

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from fontTools.merge import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/pyftsubset

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from fontTools.subset import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/pygmentize

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pygments.cmdline import main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(main())

.venv/bin/pyright

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pyright.cli import entrypoint
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(entrypoint())

.venv/bin/pyright-langserver

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pyright.langserver import entrypoint
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(entrypoint())

.venv/bin/pyright-python

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pyright.cli import entrypoint
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(entrypoint())

.venv/bin/pyright-python-langserver

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pyright.langserver import entrypoint
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(entrypoint())

.venv/bin/pytest

@@ -0,0 +1,6 @@
+#!/Users/mohsenshamsijazeb/.gemini/antigravity/scratch/clinical-graphrag-pro/backend/.venv/bin/python3.12
+import sys
+from pytest import console_main
+if __name__ == '__main__':
+    sys.argv[0] = sys.argv[0].removesuffix('.exe')
+    sys.exit(console_main())

.venv/bin/ruff

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7558e90e169048f7f32821b621bcddb3da57899b2e54d99f53d0df06cefc6df4
+size 28785872