Link to webvowl

7d3ca756 · David Rouquet · 8950fd60 · 7d3ca756
Commit 7d3ca756 authored 2 years ago by David Rouquet
--- a/selfContainedDemo.ipynb
+++ b/selfContainedDemo.ipynb
@@ -279,7 +279,7 @@
    "                [\n",
    "                    \"You can click a class to see its instances in the right panel, they are not shown in the graph.\",\n",
    "                    html.Br(),\n",
-    "                    '''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace(\"/opt/webvowl/\",\"\").replace(\".json\",\"\")),\n",
+    "                    html.A(children=\"Open ontology browser in separate tab.\", href='''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace(\"/opt/webvowl/\",\"\").replace(\".json\",\"\")), target=\"_blank\",id=\"webvowl-link\"),\n",
    "                    html.Br(),\n",
    "                    html.Iframe(src='''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace(\"/opt/webvowl/\",\"\").replace(\".json\",\"\")),style={\"height\": \"800px\", \"width\": \"100%\"}),\n",
    "                ],\n",

 %% Cell type:code id:0d91640d-23ea-4079-b765-2eea030926c5 tags:
 ``` python
 import importlib.util
 import re
 import amrlib
 from amrlib.graph_processing.amr_plot import AMRPlot
 import uuid
 from IPython.display import SVG, display
 import os
 import shutil
 import subprocess
 from subprocess import Popen, PIPE, STDOUT
 from glob import glob
 import sys
 import os
 from IPython.display import HTML,IFrame
 import ipywidgets
 import dash_bootstrap_components as dbc
 from dash import dcc, html, Input, Output
 from jupyter_dash import JupyterDash as Dash
 from dash.dependencies import Input, Output, State
 import base64
 import xml.etree.ElementTree as ET
 AMR_BATCH_PATH = "/opt/lib/TetrasMARS/amrbatch/"
 sys.path.insert(0, os.path.abspath(AMR_BATCH_PATH))
 import amrbatch
 TENET_PATH = "/opt/lib/TetrasMARS/tenet/"
 sys.path.insert(0, os.path.abspath(TENET_PATH))
 import tenet
 AMR_MODEL_PATH="/opt/lib/TetrasMARS/corpus/cm-tool/amrModel/model_parse_xfm_bart_large-v0_1_0"
 MEDIA_PATH = "/opt/dashboards/media/17/"
 MEDIA_URL = "https://unsel.tetras-lab.io/dashboard/17/media/"
 ROOT_PATH = "/opt/dashboards/TetrasMARS/tetras-mars-demo-prod/"
 AMRLD_PATH = "/opt/lib/TetrasMARS/amrld/"
 owl2vowlPath = '/opt/dashboards/tools/owl2vowl_0.3.7/owl2vowl.jar'
 WEBVOWL_PATH = '/opt/webvowl/'
 onto_prefix="ontologyTarget"
 # The following is basically `import tenet`
 #spec=importlib.util.spec_from_file_location("tenet",TENET_PATH+'tenet/__init__.py')
 #tenet = importlib.util.module_from_spec(spec)
 #spec.loader.exec_module(tenet)
 ```
 %% Cell type:code id:295e4aef-bbd8-40f0-8d84-0b8032b7b039 tags:
 ``` python
 #stog = amrlib.load_stog_model(model_dir="/opt/dashboards/TetrasMARS/corpus/cm-tool/amrModel/model_parse_xfm_bart_large-v0_1_0")
 #prefixPath = uuidDirPath+"file"
 #penmanPath = prefixPath+".amr.penman"
 #svgPath = prefixPath+".amr.svg"
 #ttlFilePath = uuidDirPath+onto_prefix+"-0/"+onto_prefix+"_factoid.ttl"
 ```
 %% Cell type:code id:a410a6b3-865d-441f-9b83-90a1badae291 tags:
 ``` python
 def clean_sting(string):
    """ Sentence cleanup as needed """
    return re.sub("(\.)*\\n", "", string)
 def string2amr(string,stog):
    stog_result = stog.parse_sents([clean_sting(string)], add_metadata=True)
    return stog_result[0]
 def show_svg(path):
    display(SVG(filename=path))
 def add_id_in_penman_if_needed(penmanStr,uuidStr):
    if not(penmanStr.startswith('# ::id')):
        penmanStr = '# ::id '+uuidStr+'\n'+penmanStr
    return penmanStr
 def owl2vowl(ttlFilePath, webvowlFileName, webvowlFilePath, uuid='', importList=[]):
    # Run java parser
    if importList == []:
        cmd = ['java', '-jar', owl2vowlPath,
           '-file', ttlFilePath]
    else:
        cmd = ['java', '-jar', owl2vowlPath,
           '-file', ttlFilePath,
           '-dependencies'] + importList
    with Popen(cmd, stdout=PIPE, stderr=STDOUT) as p:
        p.wait()
        p.stdout.flush()
        if p.returncode != 0:
            print("Error in owl2vowl: \n\n"+p.stdout.read().decode())
    os.rename(webvowlFileName, webvowlFilePath)
 def localImage2htmlImg(imgPath):
    with open(imgPath, "rb") as image_file:
        imageStr = image_file.read()
        root = ET.fromstring(imageStr)
        widthInt = int(root.attrib['width'].replace("pt",""))
        if widthInt > 1700 :
            widthStr = "100%"
        else:
            widthStr = str(widthInt)+"pt"
        img_data = base64.b64encode(imageStr)
        img_data = img_data.decode()
        img_data = "data:image/svg+xml;base64,{}".format(img_data)
        # ...
        return html.Img(id="tag_id", src=img_data, width=widthStr, height="100%", className="img_class")#, alt="my image"
 ```
 %% Cell type:code id:5fd9cf0c-990a-4776-b206-8cc94f87c7be tags:
 ``` python
 def processStr(input):
    # Define usefull variable and paths based on a uuid
    uuidStr = str(uuid.uuid4())
    uuidDirPath = "/opt/data/tmp/demo-tetras-mars/"+uuidStr+'/'
    os.mkdir(uuidDirPath)
    fullOntoPath = uuidDirPath+'full-ontology.ttl'
    ontoBySentencePath = uuidDirPath+'onto-by-sentence/'
    webvowlFileName = fullOntoPath.split('/')[-1].replace('ttl','json')
    webvowlFilePath = WEBVOWL_PATH+uuidStr+'_'+webvowlFileName
    uuidZipPath = MEDIA_PATH+uuidStr # without the .zip extention
    uuidZipUrl = MEDIA_URL+uuidStr+".zip"
    # Generate an AMR graph by sentence in a subfolder (with companion files such as images of the graphs)
    amr_graph_list = amrbatch.parse_document_string_to_produce_amr_graph(
                         input, None, amr_model_path=AMR_MODEL_PATH, output_dirpath=uuidDirPath,
                         amrld_serialization=True)
    # Construct ontologies from each AMR graph plus a "full" one that is the union
    factoids = tenet.create_ontology_from_amrld_dir(
                    uuidDirPath,
                    onto_prefix="http://ontologies",
                    out_file_path=fullOntoPath,
                    technical_dir_path=ontoBySentencePath)
    # Create a zip file so the user can download all generated files
    owl2vowl(fullOntoPath, webvowlFileName, webvowlFilePath, uuid=uuidStr)
    shutil.make_archive(uuidZipPath, 'zip', uuidDirPath)
    return uuidDirPath, uuidZipUrl, webvowlFilePath
 ```
 %% Cell type:code id:0cd10e8b-cf7a-4fd4-b8ac-540fcb943325 tags:
 ``` python
 ##################################################################################################
 # THE FOLLOWING PART IS SPECIFIC TO TÉTRAS LAB
 #
 # The _get_tl_config function gets configuration parameters for your
 # Tétras Lab instance.
 # Those parameters are passed when initialising the Dash app.
 ##################################################################################################
 def _get_tl_config():
    import socket, errno, os
    # Find a free port
    host = "0.0.0.0"
    port = 8050
    end = 9999
    found = False
    while not found:
        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
            try:
                s.bind((host, port))
                found = True
            except socket.error as e:
                if e.errno == errno.EADDRINUSE:
                    port = port + 1
                    if (port > end):
                        raise "No available APP port"
                else:
                    raise e
    if (os.getenv("HOST", None) is not None):
        proto = os.getenv("PROTO")
        actualhost = os.getenv("JUPYTER_HOST", os.getenv("VOILA_HOST", ""))
        localport = os.getenv("PORT", 80)
        intermediatehost = os.getenv("HOST", "localhost")
        base_path = f"/{actualhost}/app_proxy/{port}/"
        proxified= f"{proto}://{intermediatehost}:{localport}{base_path}"
        localurl = f"http://{host}:{port}"
        proxy = f"{localurl}::{proxified}"
        return ((proxified, host, port, proxy, base_path))
    return ((f"http://localhost:{port}", host, port, None, "/"))
 server_url, host, port, proxy, base_path = _get_tl_config()
 app = Dash(
    server_url=server_url,
    requests_pathname_prefix=base_path,
    external_stylesheets=[dbc.themes.BOOTSTRAP]
 )
 ##################################################################################################
 ##################################################################################################
 # THE FOLLOWING PART IS GENERIC (JUPYTER)-DASH CODE FROM https://dash.plotly.com/basic-callbacks
 #
 # The _get_tl_config function gets configuration parameters for your
 # Tétras Lab instance.
 # Those parameters are passed when initialising the Dash app.
 ##################################################################################################
 app.layout = html.Div([
    html.H4("Enter an english text and click on the button bellow to construct an ontology.", style={'text-align': 'center'}),
    html.Br(),
    html.P("It should take about 10 sec/sentence. You can then browse the results online or download them as a zip file.", style={'text-align': 'center'}),
    html.P("The text must be a simple succession of sentences. Fancy formating is not supported at the moment. ", style={'text-align': 'center'}),
    html.Br(),
    html.Br(),
    html.Div(dbc.Textarea(
        id='textarea-state',
        value='Jupiter is a gas giant. Earth is a rock planet.',style={'width': '100%', 'height': 130}),
        style={'width': '60%', 'height': 130, 'margin-left': 'auto', 'margin-right': 'auto'},
    ),
    html.Br(), html.Br(),
    html.Div(
        dbc.Button('Construct AMR graphs and ontology', id='textarea-state-button', n_clicks=0, outline=True, color="primary"),
        className="text-center"),
    html.Br(),
    dcc.Loading(html.Div(html.A(children="", href='', target="_blank",id="download-link"), className="text-center")),
    html.Br(),
    html.Br(),
    dcc.Loading(html.Div(id='my-output'), type='circle'),
 ])
 @app.callback(
    #Output('textarea-state-output', 'children'),
    Output(component_id='my-output', component_property='children'),
    Output(component_id='download-link', component_property='children'),
    Output(component_id='download-link', component_property='href'),
    Input('textarea-state-button', 'n_clicks'),
    State('textarea-state', 'value'),
    prevent_initial_call=True,
 )
 def update_output(n_clicks, value):
    if n_clicks > 0:
        uuidDirPath, uuidZipUrl, webvowlFilePath = processStr(value)
        #show_svg(svgPath)
        #display(IFrame('''https://unsel.tetras-lab.io/webvowl/#{}">'''.format(webvowlFilePath.replace("/opt/webvowl/","").replace(".json","")),800,1200))
        return  [dbc.Row([dbc.Col(),
        dbc.Col(dbc.Accordion(
            [dbc.AccordionItem(
                [
                    localImage2htmlImg(svgPath)
                ],
                title="AMR Graph for sentence "+re.sub(r'.document.*', '', svgPath.replace(uuidDirPath+"document-","")),
            )
             for svgPath in sorted(glob(uuidDirPath+"document-*/*.svg"))
            ]+
            [dbc.AccordionItem(
                [
                    "You can click a class to see its instances in the right panel, they are not shown in the graph.",
                    html.Br(),
-                    '''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace("/opt/webvowl/","").replace(".json","")),
+                    html.A(children="Open ontology browser in separate tab.", href='''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace("/opt/webvowl/","").replace(".json","")), target="_blank",id="webvowl-link"),
                    html.Br(),
                    html.Iframe(src='''https://unsel.tetras-lab.io/webvowl/#{}'''.format(webvowlFilePath.replace("/opt/webvowl/","").replace(".json","")),style={"height": "800px", "width": "100%"}),
                ],
                title="Browse ontology", item_id='onto'
            )
        ] , active_item='onto'), width=10), dbc.Col()
                         ]),
                 "Download Zip File", uuidZipUrl
                ]
 #@app.callback(
 #    Output("download-zip", "data"),
 #    Input("download-zip-button", "n_clicks"),
 #    prevent_initial_call=True,
 #)
 #def func(n_clicks):
 #    if n_clicks > 0:
 #        return dcc.send_file('https://unsel.tetras-lab.io/dashboard/17/media/9f7287d0-e7b2-4328-9137-7a7c44225b68.zip')
 app.run_server(mode="inline",
               #mode="external",
               host=host, port=port, proxy=proxy, height=2000)
 ##################################################################################################
 ```