Skip to content

Latest commit

 

History

History
560 lines (487 loc) · 24.4 KB

API_service.md

File metadata and controls

560 lines (487 loc) · 24.4 KB

grobid-medical-report API services

Raw text to TEI conversion services

The services in this subsection are provided to receive plain text input and send the extraction results in TEI/XML format.

Response status codes are:

HTTP Status code Signification
200 Successful operation.
204 Process was completed, but no content could be extracted and structured
400 Wrong request, missing parameters, missing header
500 Indicate an internal service error, further described by a provided message
503 The service is not available, which usually means that all the threads are currently used. The client need to re-send the query after a wait time that will allow the server to free some threads.

/api/processDateline

Parse a raw dateline string and return the extracted dateline.

Method Request type Response type Parameters Requirement Description
POST, PUT application/x-www-form-urlencoded application/xml dateline required dateline to be parsed

For testing the service, we can use the cURL command line. For example:

$ curl -X POST -d "dateline=Intervention du 14/03/2017. Paris, le 20.9.2018" localhost:8090/api/processDateline

The successful operation will return:

<dateline>
    <note type="date">Intervention</note> du <date>14/03/2017</date>. <placeName>Paris</placeName>, le <date>20.9.2018</date>
</dateline>

/api/processMedic

Parse a raw patient string and return the extracted patient data.

Method Request type Response type Parameters Requirement Description
POST, PUT application/x-www-form-urlencoded application/xml patient required patient to be parsed

For testing the service, we can use the cURL command line. For example:

$ curl -X POST -d "medic=Chef de Service Pr. Abagael ZOSIMA. Assistant Dr Woody WOOD." localhost:8090/api/processMedic

The successful operation will return:

<medic>
    <roleName>Chef de Service</roleName> <persName>Pr. Abagael ZOSIMA</persName>. <roleName>Assistant</roleName> <persName>Dr Woody WOOD</persName>.
</medic>

/api/processPatient

Parse a raw medic string and return the extracted medical personnel.

Method Request type Response type Parameters Requirement Description
POST, PUT application/x-www-form-urlencoded application/xml patient required patient to be parsed

For testing the service, we can use the cURL command line. For example:

$ curl -X POST -d "patient=Madame Eva GOODRICH 666, RUE DU MARRANT 92290 CHATENAY MALABRY" localhost:8090/api/processPatient

The successful operation will return:

<patient>
    <persName>Madame Eva GOODRICH</persName> <address>666, RUE DU MARRANT 92290 CHATENAY MALABRY</address>
</patient>

/api/processNER

Parse a raw medic string and return the extracted medical personnel.

Method Request type Response type Parameters Requirement Description
POST, PUT application/x-www-form-urlencoded application/xml ner required ner to be parsed

For testing the service, we can use the cURL command line. For example:

$ curl -X POST -d "ner=Madame Renee MASSON ayant présenté une arthrite septique du genou droit à Corynebacterium documentée sur fonction de genou traitée par Daptomycine 1500 mg puis relais par Linézolide 600 mg *2" localhost:8090/api/processNER

The successful operation will return:

<listEntity>
    <persName>Madame Renee MASSON</persName> ayant présenté une <pathology>arthrite septique</pathology> du <anatomy>genou droit</anatomy> à <substance>Corynebacterium</substance> documentée sur fonction de <anatomy>genou</anatomy> traitée par <medicament>Daptomycine 1500 mg</medicament> puis relais par <medicament>Linézolide 600 mg *2</medicament>
</listEntity>

Results using a web-based application: API Results

PDF to TEI conversion services

The services in this subsection are provided to receive PDF file input and send the extraction results in TEI/XML format.

Response status codes:

HTTP Status code Signification
200 Successful operation.
204 Process was completed, but no content could be extracted and structured
400 Wrong request, missing parameters, missing header
500 Indicate an internal service error, further described by a provided message
503 The service is not available, which usually means that all the threads are currently used. The client need to re-send the query after a wait time that will allow the server to free some threads.

/api/processHeaderDocument

Extract the header of the input PDF document, normalize it and convert it into a TEI XML format.

Method Request type Response type Parameters Requirement Description
POST, PUT multipart/form-data application/xml input required PDF file to be processed

For testing the service, we can use the cURL command line. For example:

$ curl -v --form input=@./Example.pdf localhost:8090/api/processHeaderDocument

The successful operation will return:

*   Trying 127.0.0.1...
* TCP_NODELAY set
* Connected to localhost (127.0.0.1) port 8090 (#0)
> POST /api/processHeaderDocument HTTP/1.1
> Host: localhost:8090
> User-Agent: curl/7.64.1
> Accept: */*
> Content-Length: 473311
> Content-Type: multipart/form-data; boundary=------------------------cbd8d6dc8d0c9c75
> Expect: 100-continue
> 
< HTTP/1.1 100 Continue
* We are completely uploaded and fine
< HTTP/1.1 200 OK
< Date: Mon, 29 Aug 2022 13:18:12 GMT
< Content-Type: application/xml; charset=UTF-8
< Content-Length: 1978
< 

<?xml version="1.0" encoding="UTF-8"?>
<TEI xml:space="preserve" xmlns="http://www.tei-c.org/ns/1.0" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xmlns:xlink="http://www.w3.org/1999/xlink">
	<teiHeader xml:lang="fr">
		<encodingDesc>
			<appInfo>
				<application version="0.0.1" name="grobid-medical-report" access="2022-08-29T13:18+0000">
					<desc>grobid-medical-report is a GROBID (https://github.com/kermitt2/grobid) module for extracting and structuring French medical reports into structured XML/TEI encoded documents.</desc>
					<ref target="https://github.com/tantikristanti/grobid-medical-report"/>
				</application>
			</appInfo>
		</encodingDesc>
		<fileDesc>
			<titleStmt>
				<title type="main">COMPTE RENDU OPÉRATOIRE</title>
				<extent>
					<measure unit="pages">1</measure>
				</extent>
			</titleStmt>
				<availability>
					<p>Copyright : ©grobid-medical-report (INRIA-Project)</p>
				</availability>
			<publicationStmt>
				<date type="issued" when="2000-04-29">2000-04-29</date>
				<publisher>
					<affiliation>Pôle Femmes -Adolescents -Mères -Enfants SERVICE DE GYNECOLOGIEOBSTETRIQUE ET MEDECINE DE LA REPRODUCTION</affiliation>
					<address>
						<addrLine>51, Avenue du Mal de Lattre de Tassigny 94010 CRETEIL Cedex</addrLine>
					</address>
				</publisher>
			</publicationStmt>
			<sourceDesc>
				<listPerson type="medics">
					<medic>
						<persName>Dr Mathieu MERLIN; Dr Leroy BLANC; Dr Jolie MASSON</persName>
						<roleName>Opérateur	Assistant	Anesthésiste</roleName>
					</medic>
				</listPerson>
				<listPerson type="patients">
					<patient>
						<idType>IPP</idType>
						<idno>800099001; 231456001</idno>
						<persName>Madame Abba Voletta DUPONT</persName>
						<birth when="01/01/1990">01/01/1990</birth>
						<age>27 ans</age>
						<address>666, Avenue de la République 94270 LE KREMLIN BICETRE;</address>
					</patient>
				</listPerson>
			</sourceDesc>
		</fileDesc>
	</teiHeader>
</TEI>
* Connection #0 to host localhost left intact
* Closing connection 0

/api/processLeftNoteDocument

Extract the header of the input PDF document, normalize it and convert it into a TEI XML format.

Method Request type Response type Parameters Requirement Description
POST, PUT multipart/form-data application/xml input required PDF file to be processed

For testing the service, we can use the cURL command line. For example:

$ curl -v --form input=@./Example.pdf localhost:8090/api/processLeftNoteDocument

The successful operation will return:

*   Trying 127.0.0.1...
    * TCP_NODELAY set
    * Connected to localhost (127.0.0.1) port 8090 (#0)
    > POST /api/processLeftNoteDocument HTTP/1.1
    > Host: localhost:8090
    > User-Agent: curl/7.64.1
    > Accept: */*
    > Content-Length: 473311
    > Content-Type: multipart/form-data; boundary=------------------------6c098ff4c6457696
    > Expect: 100-continue
    >
< HTTP/1.1 100 Continue
    * We are completely uploaded and fine
< HTTP/1.1 200 OK
< Date: Mon, 29 Aug 2022 13:23:13 GMT
< Content-Type: application/xml; charset=UTF-8
< Content-Length: 1463
<

<?xml version="1.0" encoding="UTF-8"?>
<TEI xml:space="preserve" xmlns="http://www.tei-c.org/ns/1.0"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xmlns:xlink="http://www.w3.org/1999/xlink">
	<note place="left" type="hospital-structure" xml:lang="fr">
        <encodingDesc>
            <appInfo>
                <application version="0.0.1" name="grobid-medical-report" access="2022-08-29T13:23+0000">
                    <desc>grobid-medical-report is a GROBID (https://github.com/kermitt2/grobid) module for extracting and structuring French medical reports into structured XML/TEI encoded documents.</desc>
                    <ref target="https://github.com/tantikristanti/grobid-medical-report"/>
                </application>
			</appInfo>
		</encodingDesc>
            <fileDesc>
                <titleStmt>
                    <extent>
                        <measure unit="pages">1</measure>
                    </extent>
			    </titleStmt>
                <availability>
                    <p>Copyright : ©grobid-medical-report (INRIA-Project)</p>
                 </availability>
                <sourceDesc>
                    <listOrg>				
                        <medic>
                            <roleName>Chef de Service</roleName> : 
                            <persName>Pr. A. Gautier Pr Robin HOOD</persName> 
                            <orgName>Secrétariat</orgName> : <phone>01 41 12 34 56</phone> 
                            <persName>Dr Caroline GENTILE</persName> 
                            <orgName>Secrétariat</orgName> : <phone>01 41 12 34 57</phone> 
                            <persName>Mme Pauline</persName> 
                            <roleName>Kinésithérapeute Rééducation périnéale et abdominale</roleName> 
                            <orgName>Secrétariat</orgName> : <phone>01 41 12 34 59</phone>
                        </medic>
                    </listOrg>
                </sourceDesc>
            </fileDesc>
	</note>
</TEI>
* Connection #0 to host localhost left intact
* Closing connection 0

/api/processFullMedicalText

Extract the header of the input PDF document, normalize it and convert it into a TEI XML format.

Method Request type Response type Parameters Requirement Description
POST, PUT multipart/form-data application/xml input required PDF file to be processed

For testing the service, we can use the cURL command line. For example:

$ curl -v --form input=@./Example.pdf localhost:8090/api/processFullMedicalText

The successful operation will return:

*   Trying 127.0.0.1...
* TCP_NODELAY set
* Connected to localhost (127.0.0.1) port 8090 (#0)
> POST /api/processFullMedicalText HTTP/1.1
> Host: localhost:8090
> User-Agent: curl/7.64.1
> Accept: */*
> Content-Length: 473311
> Content-Type: multipart/form-data; boundary=------------------------d710215784f6a51c
> Expect: 100-continue
> 
< HTTP/1.1 100 Continue
* We are completely uploaded and fine
< HTTP/1.1 200 OK
< Date: Tue, 30 Aug 2022 09:01:49 GMT
< Content-Type: application/xml; charset=UTF-8
< Content-Length: 3346
< 

<?xml version="1.0" encoding="UTF-8"?>
<TEI xml:space="preserve" xmlns="http://www.tei-c.org/ns/1.0" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xmlns:xlink="http://www.w3.org/1999/xlink">
    <teiHeader xml:lang="fr">
        <encodingDesc>
            <appInfo>
                <application version="0.0.1" name="grobid-medical-report" access="2022-08-30T09:01+0000">
                    <desc>grobid-medical-report is a GROBID (https://github.com/kermitt2/grobid) module for extracting and structuring French medical reports into structured XML/TEI encoded documents.</desc>
                    <ref target="https://github.com/tantikristanti/grobid-medical-report"/>
                </application>
            </appInfo>
        </encodingDesc>
        <fileDesc>
            <titleStmt>
                <title type="main">COMPTE RENDU OPÉRATOIRE</title>
                <extent>
                    <measure unit="pages">1</measure>
                </extent>
            </titleStmt>
            <availability>
                <p>Copyright : ©grobid-medical-report (INRIA-Project)</p>
            </availability>
            <publicationStmt>
                <date type="issued" when="2000-04-29">2000-04-29</date>
                <publisher>
                    <affiliation>Pôle Femmes -Adolescents -Mères -Enfants SERVICE DE GYNECOLOGIEOBSTETRIQUE ET MEDECINE DE LA REPRODUCTION</affiliation>
                    <address>
                        <addrLine>51, Avenue du Mal de Lattre de Tassigny 94010 CRETEIL Cedex</addrLine>
                    </address>
                </publisher>
            </publicationStmt>
            <sourceDesc>
                <listPerson type="medics">
                    <medic>
                        <persName>Dr Mathieu MERLIN; Dr Leroy BLANC; Dr Jolie MASSON</persName>
                        <roleName>Opérateur	Assistant	Anesthésiste</roleName>
                    </medic>
                </listPerson>
                <listOrg>				
                    <medic><roleName>Chef de Service</roleName> : <persName>Pr. A. Gautier Pr Robin HOOD</persName> <orgName>Secrétariat</orgName> : <phone>01 41 12 34 56</phone> <persName>Dr Caroline GENTILE</persName> <orgName>Secrétariat</orgName> : <phone>01 41 12 34 57</phone> <persName>Mme Pauline</persName> <roleName>Kinésithérapeute Rééducation périnéale et abdominale</roleName> <orgName>Secrétariat</orgName> : <phone>01 41 12 34 59</phone></medic>
                </listOrg>
                <listPerson type="patients">
                    <patient>
                        <idType>IPP</idType>
                        <idno>800099001; 231456001</idno>
                        <persName>Madame Abba Voletta DUPONT</persName>
                        <birth when="01/01/1990">01/01/1990</birth>
                        <age>27 ans</age>
                        <address>666, Avenue de la République LE KREMLIN BICETRE;</address>
                    </patient>
                </listPerson>
            </sourceDesc>
        </fileDesc>
    </teiHeader>
    <body>
        <div>
            <head level="1">DIAGNOSTIC :</head>
            <p>Injection in situ de Methotrexate sur cicatrice de césarienne</p>
        </div>
        <div>
            <head level="1">RAPPEL CLINIQUE :</head>
        </div>
        <div>
            <head level="2">Antécédents :</head>
            <p>G4P2 (2 césariennes, )</p>
        </div>
        <div>
            <head level="2">Histoire de la maladie :</head>
            <p>Échographie du 10/02 (</p>
            <medic>Dr Martinez</medic>
            <p>) : diagnostic de grossesse isthmique à 5 SA au niveau de la cicatrice de césarienne. Patiente adressée aux urgences. Douleurs pelviennes intermittentes en regard de la cicatrice de césarienne. Abdomen souple.</p>
        </div>
        <div>
            <head level="1">DESCRIPTION DETAILLEE :</head>
            <p>Gestes effectués :</p>
            <p>Injection in situ de Methotrexate </p>
        </div>
        <div>
            <head level="1">COMPTE RENDU OPÉRATOIRE :</head>
            <medic>Docteur Margo COCO</medic>
            <p>le 29/04/2000</p>
        </div>
        <div>
            <p>______________</p>
            <medic>Docteur Margo COCO</medic>
        </div>
    </body>
</TEI>
* Connection #0 to host localhost left intact
* Closing connection 0

/api/processFrenchMedicalNER

Extract the header of the input PDF document, normalize it and convert it into a TEI XML format.

Method Request type Response type Parameters Requirement Description
POST, PUT multipart/form-data application/xml input required PDF file to be processed

For testing the service, we can use the cURL command line. For example:

$ curl -v --form input=@./Example.pdf localhost:8090/api/processFrenchMedicalNER

The successful operation will return:

*   Trying 127.0.0.1...
* TCP_NODELAY set
* Connected to localhost (127.0.0.1) port 8090 (#0)
> POST /api/processFrenchMedicalNER HTTP/1.1
> Host: localhost:8090
> User-Agent: curl/7.64.1
> Accept: */*
> Content-Length: 473311
> Content-Type: multipart/form-data; boundary=------------------------fc7282241fd7c2b3
> Expect: 100-continue
>
< HTTP/1.1 100 Continue
* We are completely uploaded and fine
  < HTTP/1.1 200 OK
  < Date: Tue, 30 Aug 2022 08:57:16 GMT
  < Content-Type: application/xml; charset=UTF-8
  < Content-Length: 2864
  <

<?xml version="1.0" encoding="UTF-8"?>
<TEI xml:space="preserve" xmlns="http://www.tei-c.org/ns/1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xlink="http://www.w3.org/1999/xlink">
<text>
    <encodingDesc>
    <appInfo>
    <application version="0.0.1" name="grobid-medical-report" access="2022-08-30T08:57+0000">
    <desc>grobid-medical-report is a GROBID (https://github.com/kermitt2/grobid) module for extracting and structuring French medical reports into structured XML/TEI encoded documents.</desc>
    <ref target="https://github.com/tantikristanti/grobid-medical-report"/>
    </application>
    </appInfo>
    </encodingDesc>
        <fileDesc>
            <titleStmt>
                <extent>
                    <measure unit="pages">1</measure>
                </extent>
            </titleStmt>
            <availability>
                <p>Copyright : ©grobid-medical-report (INRIA-Project)</p>
            </availability>
            <sourceDesc>
                <listEntity>
                    DIAGNOSTIC :
                    <procedure>Injection in situ</procedure> de
                    <medicament>Methotrexate</medicament> sur
                    <symptom>cicatrice de césarienne</symptom>

                    RAPPEL CLINIQUE :
                    Antécédents :
                    G4P2 (
                    <value>2</value>
                    <procedure>césariennes</procedure>, )

                    Histoire de la maladie :
                    Échographie du
                    <date>10/02</date> (
                    <persName>Dr Martinez</persName>) :
                    <procedure>diagnostic</procedure> de
                    <physiology>grossesse isthmique</physiology> à
                    <value>5</value>
                    <unit>SA</unit> au
                    niveau de la cicatrice de césarienne.

                    <roleName>Patiente</roleName> adressée aux
                    <location>urgences.</location>
                    <symptom>Douleurs pelviennes</symptom> intermittentes en regard de la cicatrice de césarienne.

                    <symptom>Abdomen souple</symptom>.

                    DESCRIPTION DETAILLEE :

                    Gestes effectués :

                    <procedure>Injection in situ</procedure> de
                    <medicament>Methotrexate</medicament>

                    COMPTE RENDU OPÉRATOIRE :
                    Rachi-anesthésie.

                    <roleName>Patiente</roleName> en position gynécologique.
                    Badigeonnage à la
                    <medicament>bétadine</medicament> et pose de champs stériles.

                    <procedure>Sondage vésical</procedure> évacuateur.
                    Repérage à l'
                    <procedure>échographie</procedure> de la
                    <physiology>grossesse ectopique</physiology> sur cicatrice de césarienne.
                    Vérification de l'absence de vaisseaux en regard du point de ponction.
                    Ponction à l'aiguille à l'aide d'un
                    <anatomy>guide</anatomy> et
                    <device>aspiration du sac gestationnel.</device>
                    <procedure>Injection de 120mg</procedure> de
                    <medicament>Methotrexate</medicament> au niveau du sac gestationnel.
                    Suivi à J7 puis toutes les semaines jusqu'à négativation.
                    Anesthésie pratiquée :
                    Rachi-
                    <procedure>anesthésie</procedure>

                    Courrier validé électroniquement par
                    <persName>Docteur Margo COCO</persName> le
                    <date>29/04/2000</date>

                    ______________

                    <persName>Docteur Margo COCO</persName>
                </listEntity>
            </sourceDesc>
        </fileDesc>
	</text>
</TEI>
* Connection #0 to host localhost left intact
* Closing connection 0