clowder-framework / extractors-s2orc-pdf2text

Extractor to convert pdf to text
Apache License 2.0
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Have sentence coordinates in the json file #19

Closed minump closed 5 months ago

minump commented 8 months ago

Have sentence coordinates in the output json file from grobid. Change the s2orc-pdf2text code to get the below json file:

 "pdf_parse": {
        "paper_id": "main",
        "_pdf_hash": "",
        "abstract": [
            {
                 "section": "Abstract",
"text": [
{"sentence": "Background In a previous randomised controlled phase 2 trial, intravenous infusion of salbutamol for up to 7 days in patients with acute respiratory distress syndrome (ARDS) reduced extravascular lung water and plateau airway pressure.", "coords":"1,399.22,689.56,82.67,9.32;1,268.21,701.56,213.69,9.32;1,268.21,713.56,213.67,9.32;1,42.52,98.76,360.30,18.36;1,42.52,121.76,394.00,18.36;1,42.52,144.76,371.80,18.36;1,42.52,167.76,319.08,18.36;1,42.52,190.76,386.62,18.36;2,113.39,72.80,113.98,9.73" }, 
{"sentence": We assessed the effects of this intervention on mortality in patients with ARDS.", "coords": "1,399.22,689.56,82.67,9.32;1,268.21,701.56,213.69,9.32;1,268.21,713.56,213.67,9.32;1,42.52,98.76,360.30,18.36"},
],   
            },
            {
               "section": "Abstract",
                "text": [
{"sentence":"Interpretation Treatment with intravenous salbutamol early in the course of ARDS was poorly tolerated.Treatment is unlikely to be beneficial, and could worsen outcomes.", "coords":"1,42.52,167.76,319.08,18.36;1,42.52,190.76,386.62,18.36;2,113.39,72.80,113.98,9.73"},
{"sentence": "Routine use of \u03b2-2 agonist treatment in ventilated patients with this disorder cannot be recommended.", "coords":"1,399.22,689.56,82.67,9.32;1,268.21,701.56,213.69,9.32;" }
],
              }
        ],    // end of abstract
        "body_text": [
            {
                "section": "Introduction",
                "text": [
{"sentence": " \u03b2-2 agonists could be a potential pharma cological intervention because they act on the many pulmonary cellular pathways thought to be associated with the pathophysiology of ARDS.]", "coords": "1,399.22,689.56,82.67,9.32;" },
{"sentence": "In patients with ARDS given salbutamol, we reported invivo evidence of reduced permeability of alveolar capillaries, and in-vitro evidence of enhanced wound repair in epithelial monolayers.", "coords":  "1,399.22,689.56,82.67,9.32;" },
],
            },
            {
              "section": "Study design and participants",
                "text": [
{"sentence": "We undertook a multicentre, pragmatic, double-blind, placebo-controlled, parallel-group, randomised trial at 46 UK intensive-care units between December, 2006, and March, 2010." , "coords": "1,268.21,713.56,213.67,9.32;" }, 
{"sentence": "Eligible participants were intubated and mechanically ventilated adults aged 16 years and older within 72 h of ARDS onset.", "coords": "1,268.21,713.56,213.67,9.32;" },
                ],
            },
] // end of body_text
} // end of pdf-parse