### Start Monitoring Stack

Source: https://grobid.readthedocs.io/en/latest/Monitoring

Execute this command to start the services defined in the docker-compose.yml file.

```bash
docker compose up -d
```

--------------------------------

### Install JEP Library

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Execute the provided script to install the native JEP library required for the Java-Python bridge.

```bash
./grobid-home/scripts/install_jep_lib.sh 
```

--------------------------------

### Run GROBID Service

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Start the GROBID service using Gradle.

```bash
./gradlew run
```

--------------------------------

### Verify Java Installation

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Commands to verify the installed versions of the Java runtime and compiler.

```bash
# Check Java version
java -version

# Check JDK version (should show 21+ for building)
javac -version
```

--------------------------------

### Install OpenJDK 21 on Linux (CentOS/RHEL/Fedora)

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Command to install the OpenJDK 21 development kit using the dnf package manager.

```bash
# For JDK 21
sudo dnf install java-21-openjdk-devel
```

--------------------------------

### Test DeLFT Installation

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Verify the DeLFT environment by running the citation tagger application.

```bash
cd delft/
python -m delft.applications.grobidTagger citation tag --architecture BidLSTM_CRF
```

--------------------------------

### Run the PDF-TEI-Editor with Docker

Source: https://grobid.readthedocs.io/en/latest/PDF-TEI-Editor

Starts the editor container, configuring the admin password and the GROBID server URL.

```bash
docker run -p 8000:8000 \
  -e APP_ADMIN_PASSWORD=secure_password \
  -e GROBID_SERVER_URL=https://grobidOrg-grobid-full.hf.space \
  cboulanger/pdf-tei-editor:latest
```

--------------------------------

### GET /api/isalive

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Checks if the service has completed initialization successfully.

```APIDOC
## GET /api/isalive

### Description
Returns true/false as plain text indicating whether the service completed initialization successfully. Suitable for use as a liveness probe.

### Method
GET

### Endpoint
/api/isalive

### Response
#### Success Response (200)
- **body** (string) - Returns 'true' if alive.

#### Error Response (503)
- **status** (integer) - Returns 503 when not initialized or initialization failed.
```

--------------------------------

### Standalone installation directory structure

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Expected directory layout after extracting the standalone service distributions.

```text
.
├── grobid-home
└── grobid-service
```

--------------------------------

### Install JNI JAR

Source: https://grobid.readthedocs.io/en/latest/Recompiling-and-integrating-CRF-libraries

Deploy the JNI JAR file to the local repository within grobid-core.

```bash
> mvn install:install-file -Dfile=wapiti-1.5.0.jar -DgroupId="fr.limsi.wapiti" -DartifactId="wapiti" -Dversion="1.5.0" -Dpackaging="jar" -DlocalRepositoryPath="GROBID-ROOT-DIRECTORY/grobid-core/lib"
```

--------------------------------

### Install OpenJDK 21 on Linux (Ubuntu/Debian)

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Commands to update package lists and install the OpenJDK 21 development kit on Debian-based systems.

```bash
# Ubuntu 22.04+ or Debian 12+
sudo apt update
sudo apt install openjdk-21-jdk
```

--------------------------------

### TEI Citation Output Example

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Example of the TEI-structured output returned by the service, including raw reference notes.

```xml
<biblStruct >
    <analytic>
        <title/>
        <author>
            <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">T</forename><forename type="middle">J</forename><surname>Vaughan</surname></persName>
        </author>
    </analytic>
    <monogr>
        <title level="j">Nat.Biotech</title>
        <imprint>
            <biblScope unit="volume">14</biblScope>
            <biblScope unit="page" from="309" to="314" />
            <date type="published" when="1996" />
        </imprint>
    </monogr>
    <note type="raw_reference"> Vaughan, T.J. et al., Nat.Biotech., 14:309-314(1996)</note>
</biblStruct>


<biblStruct >
    <monogr>
        <title/>
        <author>
            <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">Perkin</forename><surname>Elmer</surname></persName>
        </author>
        <imprint>
            <biblScope unit="volume">1</biblScope>
            <biblScope unit="page">1000</biblScope>
        </imprint>
    </monogr>
    <note type="report_type">Cat.1244-360</note>
    <note type="raw_reference">Perkin Elmer, Cat.1244-360, 1:1000</note>
</biblStruct>
```

--------------------------------

### Install OpenJDK 21 on macOS

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Commands to install OpenJDK 21 via Homebrew and configure the JAVA_HOME environment variable.

```bash
# Install JDK 21
brew install openjdk@21

# Set JAVA_HOME (add to ~/.zshrc or ~/.bash_profile)
export JAVA_HOME=$(brew --prefix)/opt/openjdk@21/libexec/openjdk.jdk/Contents/Home
```

--------------------------------

### Build and run standalone service

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Commands to build the distribution, create an installation directory, and execute the standalone service binary.

```bash
./gradlew clean assemble
cd ..
mkdir grobid-installation
cd grobid-installation
unzip ../grobid/grobid-service/build/distributions/grobid-service-0.9.1.zip
mv grobid-service-0.9.1 grobid-service
unzip ../grobid/grobid-home/build/distributions/grobid-home-0.9.1.zip
./grobid-service/bin/grobid-service
```

--------------------------------

### Running the Grobid container

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Commands to start the Grobid container with default or custom port mappings.

```bash
> docker run --rm --init --ulimit core=0 -p 8070:8070 grobid/grobid:${latest_grobid_version}-crf
```

```bash
> docker run --rm --init --ulimit core=0 -p 8070:8070 grobid/grobid:0.9.1-crf
```

```bash
docker run --rm --init --ulimit core=0 -p 8080:8070 -p 8081:8071 grobid/grobid:${latest_grobid_version}-crf
```

--------------------------------

### GET /api/allTraining

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Lists all training tokens currently running in the server instance.

```APIDOC
## GET /api/allTraining

### Description
List the tokens of the trainings currently running in this server instance.

### Method
GET

### Endpoint
/api/allTraining

### Response
#### Success Response (200)
- **tokens** (array) - List of active training tokens

#### Error Handling
- 500: Internal service error
```

--------------------------------

### Run Deep Learning GROBID Container

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Starts a container with GPU support and optional configuration mounting.

```bash
docker run --rm --gpus all --init --ulimit core=0 -p 8080:8070 -p 8081:8071 grobid/grobid:0.9.2-SNAPSHOT
```

```bash
docker run --rm --gpus all --init --ulimit core=0 -p 8080:8070 -p 8081:8071 -v /home/lopez/grobid/grobid-home/config/grobid.yaml:/opt/grobid/grobid-home/config/grobid.yaml:ro grobid/grobid:0.9.2-SNAPSHOT
```

--------------------------------

### Run a full GROBID instance with Docker

Source: https://grobid.readthedocs.io/en/latest/PDF-TEI-Editor

Starts a GROBID server container with deep learning models enabled on port 8070.

```bash
docker run --rm --gpus all --init --ulimit core=0 -p 8070:8070 grobid/grobid:0.9.1-full
```

--------------------------------

### Install native libraries

Source: https://grobid.readthedocs.io/en/latest/Recompiling-and-integrating-CRF-libraries

Copy the compiled native libraries to the appropriate Grobid home directory for Linux or Mac OS X.

```bash
> cp ld-linux-x86-64.so.2 libc.so.6 libgcc_s.so.1 libm.so.6 libstdc++.so.6 libwapiti.so GROBID-ROOT-DIRECTORY/grobid-home/lib/lin-<nb bits of the OS>
```

```bash
> cp libwapiti.dylib GROBID-ROOT-DIRECTORY/grobid-home/lib/mac-64/
```

--------------------------------

### Run Grobid Container

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Standard command to start the Grobid container with GPU support and core dump limits.

```bash
> docker run --rm --gpus all --init --ulimit core=0 -p 8070:8070 grobid/grobid:0.9.1-full
```

--------------------------------

### Start the GROBID service via Docker

Source: https://grobid.readthedocs.io/en/latest/Upgrading

Command to launch the GROBID service using a Docker container.

```bash
docker run ... grobid/grobid:0.9.1-full
```

--------------------------------

### Example CXXABI Linker Error

Source: https://grobid.readthedocs.io/en/latest/Frequently-asked-questions

An example of the ImportError encountered when the system's libstdc++ version is incompatible with the Python environment's requirements.

```text
ImportError: /home/user/miniconda3/envs/myenv/lib/python3.10/lib-dynload/../../libicui18n.so.78:
  version `CXXABI_1.3.15' not found (required by .../libstdc++.so.6)
```

--------------------------------

### GET /metrics/prometheus

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Retrieves application and JVM metrics in Prometheus exposition format.

```APIDOC
## GET /metrics/prometheus

### Description
Returns application metrics (rate/throughput per entry point) and JVM/process metrics (heap, GC, threads, CPU) in Prometheus exposition format.

### Method
GET

### Endpoint
/metrics/prometheus
```

--------------------------------

### Create Anaconda environment

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Initializes a new conda environment named grobidDelft with pip installed.

```bash
conda create --name grobidDelft pip
```

--------------------------------

### Start Model Training with cURL

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Initiates a training process for a specified model using the /api/modelTraining endpoint.

```bash
curl -v -X POST -d "model=date" -d "type=holdout" localhost:8070/api/modelTraining
```

--------------------------------

### Tagging Web References

Source: https://grobid.readthedocs.io/en/latest/training/Bibliographical-references

Example of tagging a web-based reference including publisher, date, and URL pointer.

```xml
<?xml version="1.0" encoding="UTF-8"?>
<tei xmlns="http://www.tei-c.org/ns/1.0" 
      xmlns:xlink="http://www.w3.org/1999/xlink" 
      xmlns:mml="http://www.w3.org/1998/Math/MathML">

    <listBibl>
        <bibl>
            <publisher>Microsoft</publisher>. <date>2019</date>.
            <title level="m">Azure REST API Specifications</title>.
            <ptr type="web">https://github.com/Azure/azurerest-api-specs</ptr> Last accessed <date>2019-11-22</date>.
        </bibl>
    </listBibl>

</tei>
```

--------------------------------

### Run GROBID Lightweight Docker Image

Source: https://grobid.readthedocs.io/en/latest/getting_started

Starts the CPU-only lightweight container for high-performance, low-resource environments. Suitable for processing large volumes of PDFs where maximum accuracy is not the primary requirement.

```bash
docker run --rm --init --ulimit core=0 -p 8070:8070 grobid/grobid:0.9.1-crf
```

--------------------------------

### Configure DeLFT Global Parameters

Source: https://grobid.readthedocs.io/en/latest/Configuration

Defines the installation path and virtual environment for the DeLFT library. Required when using Deep Learning architectures.

```yaml
  delft:
    # delft installation path if Deep Learning architectures are used to implement one of the sequence labeling model, 
    # embeddings are usually compiled as lmdb under delft/data (this parameter is ignored if only featured-engineered CRF are used)
    install: "../delft"
    pythonVirtualEnv: "../delft/env"

```

--------------------------------

### Run CRF-only GROBID Container

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Starts a container configured for CRF-only model execution.

```bash
docker run --rm --init --ulimit core=0 -p 8080:8070 -p 8081:8071 grobid/grobid:0.9.2-SNAPSHOT
```

--------------------------------

### Labeling Keywords

Source: https://grobid.readthedocs.io/en/latest/training/header

Examples of tagging keywords and classification schemes, excluding generic labels.

```xml
<keyword>Mathematics Subject Classification: 83C15, 81U15, 81V80, 17B80, 81R12<lb/></keyword> 

<keywords type="pacs">PACS numbers: 02.30.Ik, 03.65.Fd Fd<lb/></keywords>
```

```xml
<date>17 July 2007<lb/></date>

Keywords: 
<keyword>body mass index; weight change; coronary heart disease; 
    follow-up study; Japanese Japanese<lb/></keyword>
```

--------------------------------

### Configure GROBID for DeLFT

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Define the DeLFT installation path and model architectures in the grobid.yaml configuration file.

```yaml
  delft:
    install: "../delft"
```

```yaml
  models:
    - name: "citation"
      engine: "delft"
      architecture: "BidLSTM_CRF_FEATURES"
```

```yaml
  models:
    - name: "citation"
      engine: "delft"
      architecture: "BERT_CRF"
      transformer: "allenai/scibert_scivocab_cased"
```

```yaml
  delft:
    pythonVirtualEnv: /where/my/damned/python/virtualenv/is/ 
```

--------------------------------

### GET /api/version

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Retrieves the current version and revision of the running GROBID service.

```APIDOC
## GET /api/version

### Description
Returns the current version and the revision of the running service.

### Method
GET

### Endpoint
/api/version
```

--------------------------------

### Configure model engine and architecture

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Example configuration block to set the citation model to use the delft engine with BidLSTM_CRF_FEATURES architecture.

```yaml
  models:
    - name: "citation"
      engine: "delft"
      architecture: "BidLSTM_CRF_FEATURES"
```

--------------------------------

### Example Prometheus metrics output

Source: https://grobid.readthedocs.io/en/latest/Monitoring

Sample of the plain-text format returned by the metrics endpoint, including JVM memory usage.

```text
# HELP jvm_memory_bytes_used Used bytes of a given JVM memory area.
# TYPE jvm_memory_bytes_used gauge
jvm_memory_bytes_used{area="heap",} 1.34217728E8
...
```

--------------------------------

### Example of range citation callout text

Source: https://grobid.readthedocs.io/en/latest/End-to-end-evaluation

Shows a citation range in plain text format.

```text
Recent studies have described the use of contrast material with high iodine content (370 mg I/ml or 400 mg I/ml) for coronary CT angiography (CCTA) (1 – 4).
```

--------------------------------

### Resolve GLIBCXX library errors

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Commands to install libgcc and set the LD_PRELOAD environment variable to resolve library version conflicts.

```bash
conda install libgcc

export export LD_PRELOAD=$anaconda_path/lib/libstdc++.so.6.0.25

./gradlew run
```

--------------------------------

### GET /api/health

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Provides detailed health status and engine pool metrics.

```APIDOC
## GET /api/health

### Description
Returns a JSON object with detailed status including initialization state, engine pool metrics, and configuration checks. Suitable for use as a readiness probe.

### Method
GET

### Endpoint
/api/health

### Response
#### Success Response (200)
- **body** (JSON) - Detailed status object including initialization state and engine pool metrics.

#### Error Response (503)
- **status** (integer) - Returns 503 when not ready to process requests.
```

--------------------------------

### Docker machine inspection output

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Example JSON output from the docker-machine inspect command showing memory allocation.

```json
{
    "ConfigVersion": 3,
    "Driver": {
        "IPAddress": "192.168.99.100",
        "MachineName": "default",
        "SSHUser": "docker",
        "SSHPort": 55933,
        "SSHKeyPath": "/Users/lfoppiano/.docker/machine/machines/default/id_rsa",
        "StorePath": "/Users/lfoppiano/.docker/machine",
        "SwarmMaster": false,
        "SwarmHost": "tcp://0.0.0.0:3376",
        "SwarmDiscovery": "",
        "VBoxManager": {},
        "HostInterfaces": {},
        "CPU": 1,
        "Memory": 2048,     #<---- Memory: 2GB
        "DiskSize": 204800,
        "NatNicType": "82540EM",
        "Boot2DockerURL": "",
        "Boot2DockerImportVM": "",
        "HostDNSResolver": false,
        "HostOnlyCIDR": "192.168.99.1/24",
        "HostOnlyNicType": "82540EM",
        "HostOnlyPromiscMode": "deny",
        "NoShare": false,
        "DNSProxy": true,
        "NoVTXCheck": false
    },
    "DriverName": "virtualbox",
    "HostOptions": {
      [...]
        },
        "SwarmOptions": {
         [...]
        },
        "AuthOptions": {
           [...]
        }
    },
    "Name": "default"
}
```

--------------------------------

### Initialize Grobid Engine

Source: https://grobid.readthedocs.io/en/latest/Grobid-java-library

Demonstrates how to set up the Grobid environment and process a PDF header using the Engine class.

```java
    import org.grobid.core.*;
    import org.grobid.core.data.*;
    import org.grobid.core.factory.*;
    import org.grobid.core.mock.*;
    import org.grobid.core.utilities.*;
    import org.grobid.core.engines.Engine;

    ...
    String pdfPath = "mypdffile.pdf";
    ...

    try {
        String pGrobidHome = "/Users/lopez/grobid/grobid-home";

        // The GrobidHomeFinder can be instantiate without parameters to verify the grobid home in the standard
        // location (classpath, ../grobid-home, ../../grobid-home)

        // If the location is customised: 
        GrobidHomeFinder grobidHomeFinder = new GrobidHomeFinder(Arrays.asList(pGrobidHome));       

        //The grobid yaml config file needs to be instantiate using the correct grobidHomeFinder or it will use the default 
        //locations
        GrobidProperties.getInstance(grobidHomeFinder);

        System.out.println(">>>>>>>> GROBID_HOME="+GrobidProperties.getGrobidHome());

        Engine engine = GrobidFactory.getInstance().createEngine();

        // Biblio object for the result
        BiblioItem resHeader = new BiblioItem();
        String tei = engine.processHeader(pdfPath, 1, resHeader);
    } 
    catch (Exception e) {
        // If an exception is generated, print a stack trace
        e.printStackTrace();
    } 
```

--------------------------------

### Annotate affiliation and address structure

Source: https://grobid.readthedocs.io/en/latest/training/affiliation-address

Example of tagging an affiliation block including department, institution, and address components.

```xml
<affiliation>
    <orgName type="department">Institute of Materials Science</orgName>
    of the 
    <orgName type="institution">Technische Universität Darmstadt</orgName>,
    address:
    <lb/>
    <address>
        <addrLine>Petersenstraße 23</addrLine>,
        <postCode>D-64287</postCode>
        <settlement>Darmstadt</settlement>,
        <country>Germany</country>.
    </address>
</affiliation>
```

--------------------------------

### Deploy the bundled demo

Source: https://grobid.readthedocs.io/en/latest/PDF-TEI-Editor

Clones the repository and runs the demo deployment script.

```bash
git clone https://github.com/mpilhlt/pdf-tei-editor.git
cd pdf-tei-editor
npm run deploy .env.deploy.demo.localhost
```

--------------------------------

### Parse patent citations with cURL

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Example command to send raw text to the processCitationPatentTXT endpoint for citation extraction.

```bash
curl -X POST -d "input=In EP0123456B1 nothing interesting." localhost:8070/api/processCitationPatentTXT
```

--------------------------------

### Process ST.36 Patent Citations via cURL

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Example request to the processCitationPatentST36 endpoint with raw citation inclusion enabled.

```bash
curl --form input=@/home/lopez/grobid/grobid-core/src/test/resources/s/006271747.xml --form includeRawCitations=1 localhost:8070/api/processCitationPatentST36
```

--------------------------------

### TEI Output for Lightweight Article Processing

Source: https://grobid.readthedocs.io/en/latest/Grobid-specialized-processes

Example of the TEI XML structure produced by the lightweight article process, showing a single paragraph body.

```xml
<body>
    <div
        xmlns="http://www.tei-c.org/ns/1.0">
        <p>ONCOLOGY REPORTS 49: 10, 2023 CORRIGENDUM</p>
        <p>Oncol Rep 42: 509-520, 2019; DOI: 10.3892/or.2019.7175 Subsequently to the publication of the above article, and a Corrigendum that has already been published with the intention of showing corrected versions of Figs. 1 and 8 (DOI: 10.3892/or.2022.8348; published online on June 14, 2022), the authors have belatedly realized that the revisions made to Fig. 8 necessitated changes that should have been introduced into Fig. 9, although these were not attended to in the first corrigendum. Essentially, Fig. 8 was revised as the cell apoptosis and cell proliferation assays therein were poorly presented, which made the interpretation of the data difficult; Fig. 9 showed the fractions of apoptotic cells in the SKM-1 and THP-1 cell lines with lncENST00000444102 overexpression as this pertained to Fig. 8. A revised version of Fig. 9, presenting the analysis of the data shown in the revised version of Fig. 8, is shown opposite. In addition to the revision of Fig. 9, the sentence starting on p. 517, left-hand column, line 12 ["The flow cytometric apoptosis assay revealed that lncENST00000444102 overexpression promoted tumor cells to undergo apoptosis compared to control cells (P&lt;0.001, Fig. 9)"] should be replaced with the following text, to reflect the change in the level of statistical significance: 'The flow cytometric apoptosis assay revealed that lncENST00000444102 overexpression promoted tumor cells to undergo apoptosis compared to control cells (P&lt;0.01, Fig. 9)". Note that the revisions made to Figs. 8 and 9 in this paper have not had a major impact on the reported results, and do not affect the overall conclusions reported in the study. All the authors agree to the publication of this corrigendum. The authors are grateful to the Editor of Oncology Reports for allowing them the opportunity to publish this additional Corrigendum; furthermore, they apologize for any inconvenience caused to the readership of the Journal. Figure 9. The fraction of apoptotic cells in the SKM-1 and THP-1 cell lines with lncENST00000444102 overexpression. Data are presented as the means ± standard deviation. ** P&lt;0.01 vs. the controls. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License.</p>
    </div>
</body>
```

--------------------------------

### Annotate Article Title with Front Element

Source: https://grobid.readthedocs.io/en/latest/training/segmentation

Example showing the use of the <front> element to encapsulate the article title and related content within the TEI XML structure.

```xml
virus. <lb/>But is the role of LGP2 in CD8 + T cell <lb/>survival and function cell
intrinsic <lb/></body>

<front>A N T I V I R A L I M U N I T Y <lb/>LGP2 rigs CD8 + T cells for
survival <lb/></front>

<body> or extrinsic? T cell receptor-and <lb/>IFNβ-mediated signalling in CD8 + T
```

--------------------------------

### Fulltext Processing with Page Range

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Process a PDF starting from a specific page index, where the first page is indexed as 1.

```bash
curl -v --form input=@./thefile.pdf --form start=3 localhost:8070/api/processFulltextDocument
```

--------------------------------

### Example of annotated range citation callout in XML

Source: https://grobid.readthedocs.io/en/latest/End-to-end-evaluation

Shows how range citations are annotated in NLM/JATS files, often omitting intermediary references.

```xml
Recent studies have described the use of contrast material with high iodine content (370 mg I/ml or 400 mg I/ml) for coronary CT angiography (CCTA) (<xref ref-type="bibr" rid="b1">1</xref>&#x2013;<xref ref-type="bibr" rid="b4">4</xref>).
```

--------------------------------

### Handle Dropwizard 5 Configuration Parsing Error

Source: https://grobid.readthedocs.io/en/latest/Upgrading

Example of the error message generated when an unrecognized field like maxQueuedRequests is present in the configuration file.

```text
io.dropwizard.configuration.ConfigurationParsingException: grobid.yaml has an error:
  * Unrecognized field at: server.maxQueuedRequests
...
Caused by: com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException:
  Unrecognized field "maxQueuedRequests"
  (class io.dropwizard.core.server.DefaultServerFactory), not marked as ignorable
```

--------------------------------

### Retrieve model archive with cURL

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Download a model archive using either POST or GET requests by specifying the model name and optional architecture.

```bash
curl -v -X POST -d "model=date" "architecture=crf" localhost:8070/api/model > model.zip
```

```bash
curl -v -X GET localhost:8070/api/model?model=date > model.zip
```

--------------------------------

### Navigate to GROBID Directory

Source: https://grobid.readthedocs.io/en/latest/Grobid-batch

Change the current working directory to the project root.

```bash
> cd grobid/
```

--------------------------------

### XML date annotation structure

Source: https://grobid.readthedocs.io/en/latest/training/date

Example of the basic XML format used for date training files, where day, month, and year are tagged within a date element.

```xml
<?xml version="1.0" encoding="UTF-8"?>
<dates>
    <date>Received <month>August</month> <day>17</day>, <year>2005</year>. </date>
</dates>
```

--------------------------------

### Display Batch Command Help

Source: https://grobid.readthedocs.io/en/latest/Grobid-batch

View available batch commands and options for the GROBID core JAR.

```bash
> java -Djava.library.path=grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep -jar grobid-core/build/libs/grobid-core-<current version>-onejar.jar -h
```

```bash
> java -Djava.library.path=grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep -jar grobid-core/build/libs/grobid-core-0.9.0-onejar.jar -h
```

--------------------------------

### Example of raw string citation encoding in NLM XML

Source: https://grobid.readthedocs.io/en/latest/End-to-end-evaluation

Demonstrates citations encoded as raw strings within mixed-citation tags, which can lead to false positives during evaluation.

```xml
      ...
      <ref id="CR9">
        <label>9.</label>
        <mixed-citation publication-type="other">Pira&#xF1;a and PCluster: a modeling environment and cluster infrastructure for NONMEM. Keizer RJ, van Benten M, Beijnen JH, Schellens JH, Huitema AD. Comput Methods Programs Biomed. 2011;101(1):72&#x2013;9.</mixed-citation>
      </ref>
      <ref id="CR10">
        <label>10.</label>
        <mixed-citation publication-type="other">Holford, N. VPC, the visual predictive check&#x2014;superiority to standard diagnostic (Rorschach) plots. In: PAGE 2005. 2005.</mixed-citation>
      </ref>
      ...
```

--------------------------------

### Execute training and evaluation via Gradle

Source: https://grobid.readthedocs.io/en/latest/Training-the-models-of-Grobid

Run the training and evaluation process for a specific model using the Gradle task command.

```bash
> ./gradlew train_<name_of_model>
```

```bash
> ./gradlew train_header
```

```bash
> ./gradlew train_name_header
```

--------------------------------

### TEI Author Coordinates

Source: https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF

Example of the coords attribute in TEI for a single bounding box.

```xml
<author>
    <persName coords="1,53.80,194.57,58.71,9.29">
        <forename type="first">Ron</forename>
        <forename type="middle">J</forename>
        <surname>Keizer</surname>
    </persName>
</author>
```

--------------------------------

### Extract PDF header metadata via cURL

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Use these commands to extract header information from a PDF file. The first example returns TEI XML, while the second returns BibTeX format.

```bash
curl -v -H "Accept: application/xml" --form input=@./thefile.pdf localhost:8070/api/processHeaderDocument
```

```bash
curl -v -H "Accept: application/x-bibtex" --form input=@./thefile.pdf localhost:8070/api/processHeaderDocument
```

--------------------------------

### Configure Model Preloading

Source: https://grobid.readthedocs.io/en/latest/Configuration

Toggle model preloading to balance startup time against memory usage.

```yaml
  # for **service only**: how to load the models, 
  # false -> models are loaded when needed, avoiding putting in memory useless models (only in case of CRF) but slow down 
  #          significantly the service at first call
  # true -> all the models are loaded into memory at the server startup (default), slow the start of the services 
  #         and models not used will take some more memory (only in case of CRF), but server is immediately warm and ready
  modelPreload: true
```

--------------------------------

### Verify OTLP Metrics Startup Log

Source: https://grobid.readthedocs.io/en/latest/Monitoring

Check the application logs for this confirmation line to ensure metrics reporting is active.

```text
OtlpMetricsReporter: OTLP metrics push enabled -> https://otlp-gateway-prod-eu-central-0.grafana.net/otlp (http/protobuf), every 60s, service.name=grobid-service
```

--------------------------------

### Rosetta error message

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Example of the error message encountered when the platform flag is missing on ARM64.

```text
rosetta error: failed to open elf at /lib64/ld-linux-x86-64.so.2
```

--------------------------------

### Build GROBID with Gradle

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Standard command to clean and build the GROBID project from the main directory.

```bash
> ./gradlew clean build
```

--------------------------------

### Initialize a new model programmatically

Source: https://grobid.readthedocs.io/en/latest/Notes-grobid-developers

Load the YAML configuration and register the model with GrobidProperties.

```java
        NewModuleConfiguration newModuleConfiguration = null;
        try {
            ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
            newModuleConfiguration = mapper.readValue(new File("resources/config/config.yml"), NewModuleConfiguration.class);
        } catch(Exception e) {
            LOGGER.error("The config file does not appear valid, see resources/config/config.yml", e);
        }

        if (newModuleConfiguration != null && newModuleConfiguration.getModel() != null)
            GrobidProperties.getInstance().addModel(newModuleConfiguration.getModel());
        LibraryLoader.load();
```

--------------------------------

### GPL FAQ on Mere Aggregation

Source: https://grobid.readthedocs.io/en/latest/Frequently-asked-questions

Excerpt regarding the distribution of GPL and non-GPL software in an aggregate.

```text
The GPL permits you to create and distribute an aggregate, even when the licenses of the
other software are nonfree or GPL-incompatible. The only condition is that you cannot
release the aggregate under a license that prohibits users from exercising rights that
each program's individual license would grant them.
```

--------------------------------

### Tagging Years with Suffixes

Source: https://grobid.readthedocs.io/en/latest/training/Bibliographical-references

Example of tagging a year that includes a letter suffix, common in Harvard-style references.

```xml
<listBibl>
    <bibl>
        <author>Gavazzi G., Piertini D., Boselli A., Tuffs R.</author>, <date>1996c</date>, 
        <title level="j">A&amp;AS</title>, <biblScope unit="volume">120</biblScope>, 
        <biblScope unit="page">489</biblScope>(<note>Paper I</note>) 
    </bibl>
</listBibl>
```

--------------------------------

### Identify GLIBCXX dependency error

Source: https://grobid.readthedocs.io/en/latest/Deep-Learning-models

Example of an ImportError indicating a missing GLIBCXX version required by TensorFlow.

```text
! ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/Luca/.conda/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)
```

--------------------------------

### TEI biblStruct consolidation attributes

Source: https://grobid.readthedocs.io/en/latest/Consolidation

Example of the status and source attributes applied to a biblStruct element after consolidation.

```xml
<biblStruct status="consolidated" source="crossref">
    ...
</biblStruct>
```

--------------------------------

### Run Grobid Docker with custom configuration

Source: https://grobid.readthedocs.io/en/latest/Grobid-docker

Mounts a local grobid.yaml file to the container using an absolute path.

```bash
docker run --rm --gpus all --init --ulimit core=0 -p 8080:8070 -p 8081:8071 -v /home/lopez/grobid/grobid-home/config/grobid.yaml:/opt/grobid/grobid-home/config/grobid.yaml:ro  grobid/grobid:0.9.1
```

--------------------------------

### Generate Training Data with createTraining

Source: https://grobid.readthedocs.io/en/latest/Grobid-batch

Executes the createTraining command to generate training data from PDF files.

```bash
> java -Xmx4G -Djava.library.path=grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep -jar grobid-core/build/libs/grobid-core-0.9.0-onejar.jar -gH grobid-home -dIn /path/to/input/directory -dOut /path/to/output/directory -exe createTraining
```

--------------------------------

### Train specialized header model

Source: https://grobid.readthedocs.io/en/latest/Grobid-specialized-processes

Command to initiate training for the article/light-ref header model.

```bash
./gradlew train_header_article_light_ref
```

--------------------------------

### Execute Gradle Release

Source: https://grobid.readthedocs.io/en/latest/Notes-grobid-developers

Run this command from a release branch to initiate the versioning process and create the release commits and tag.

```bash
git checkout -b release/<X.Y.Z>
./gradlew release \
    -Prelease.useAutomaticVersion=true \
    -Prelease.releaseVersion=<X.Y.Z> \
    -Prelease.newVersion=<X.Y.(Z+1)>-SNAPSHOT
```

--------------------------------

### Generate Blank Training Data with createTrainingBlank

Source: https://grobid.readthedocs.io/en/latest/Grobid-batch

Executes the createTrainingBlank command to generate a blank TEI file and default feature file from PDFs.

```bash
> java -Xmx4G -Djava.library.path=grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep -jar grobid-core/build/libs/grobid-core-0.9.0-onejar.jar -gH grobid-home -dIn /path/to/input/directory -dOut /path/to/output/directory -exe createTrainingBlank
```

--------------------------------

### JSON Bounding Box Structure

Source: https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF

Example of the pos attribute in JSON, representing a list of bounding boxes for an entity.

```json
"pos": [{  "p": 1,
            "x": 20,
            "y": 20,
            "h": 10,
            "w": 30 }, 
        {  "p": 1,
            "x": 30,
            "y": 20,
            "h": 10,
            "w": 30 } ]
```

--------------------------------

### JSON Page Dimensions Structure

Source: https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF

Example of the pages attribute in JSON, defining the height and width of document pages.

```json
    "pages": [  {"page_height":792.0, "page_width":612.0}, 
                {"page_height":792.0, "page_width":612.0}, 
                {"page_height":792.0, "page_width":612.0}  ]
```

--------------------------------

### Build Java artifacts

Source: https://grobid.readthedocs.io/en/latest/Notes-grobid-developers

Checkout the specific release tag and build the project to generate JAR files in subproject build directories.

```bash
git checkout <X.Y.Z>
./gradlew clean build
```

--------------------------------

### Bibliographical Reference Markers

Source: https://grobid.readthedocs.io/en/latest/training/fulltext

Examples of tagging bibliographical references. Note that brackets and parentheses are included within the ref tags.

```xml
Harbaugh and Harbaugh <ref type="biblio">[7]</ref>
```

```xml
in Lolle et al. <ref type="biblio">1</ref>
```

```xml
<p>The clinical entity of cervical flexion myelopa-<lb/>
  thy proposed in the 1960s by Reid <ref type="biblio">[16,17]</ref> and<lb/>
  Breig et al <ref type="biblio">[2,3]</ref> has been neglected for a long time.<lb/>
  ...
  groups of males and females controls.<lb/>
</p>
```

```xml
by <ref type="biblio">Greve et al. [1994]</ref> and <ref type="biblio">Koch et al.<lb/> [1994]</ref>
```

```xml
<ref type="biblio">[Whitham, 1954; Hogg and Pritchard,<lb/> 2004]</ref>
```

```xml
<ref type="biblio">[Abramowitz and Stegun,<lb/> 1964, see pp. 559 – 562] </ref>
```

```xml
<ref type="biblio">LEWANDOWSKI (1982b)</ref> has reported
```

```xml
<ref type="biblio">(STANCZYKOWSKA, 1977)</ref>
```

```xml
(e.g., <ref type="biblio">Bryant<lb/> &amp; Goswami, 1987</ref>) by<lb/>
<ref type="biblio">Smith and Matsoukas [1998]</ref> and <ref type="biblio">Khelifa and Hill [2006b]<lb/></ref>
```

```xml
by <ref type="biblio">Gal [1979]</ref> and<lb/> illustrated further recently by <ref type="biblio">Draper and Lund [2004]</ref>
```

```xml
<ref type="biblio">(ref. 1)</ref>
```

```xml
This was established in<lb/> <ref type="biblio">Thompson v. Lochert (1997)</ref> <ref type="biblio">[114]</ref> in which
```

```xml
such as receptors for IL-1β <ref type="biblio">(REFS 64,65)</ref>,<lb/> TNF <ref type="biblio">66</ref> and IFNγ <ref type="biblio">67</ref> .
```

--------------------------------

### Verify Docker image runtime version

Source: https://grobid.readthedocs.io/en/latest/Notes-grobid-developers

Run the container and query the version API to confirm the application reports the correct version.

```bash
docker run --rm -d --name g-test -p 8070:8070 grobid/grobid:<X.Y.Z>-crf
sleep 30
curl -s http://localhost:8070/api/version
# expected: {"version":"<X.Y.Z>","revision":"<X.Y.Z>"}
docker stop g-test
```

--------------------------------

### TEI Bibliographical Reference Coordinates

Source: https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF

Example of the coords attribute in TEI containing multiple bounding boxes separated by semicolons.

```xml
<biblStruct coords="10,317.03,183.61,223.16,7.55;10,317.03,192.57,223.21,7.55;10,317.03,201.53,223.15,7.55;10,317.03,210.49,52.22,7.55"  xml:id="b19">
```

--------------------------------

### Generate Java bindings with JAXB

Source: https://grobid.readthedocs.io/en/latest/TEI-encoding-of-results

Use the xjc tool with the -extension flag to compile GROBID's XSD schemas into Java classes.

```bash
> xjc -d generated -extension ~/grobid/grobid-home/schemas/xsd/simpleMode.xsd ~/grobid/grobid-home/schemas/xsd/Grobid.xsd
parsing a schema...
compiling a schema...
org/tei_c/ns/_1/Abstract.java
org/tei_c/ns/_1/AddrLine.java
org/tei_c/ns/_1/Address.java
org/tei_c/ns/_1/Affiliation.java
org/tei_c/ns/_1/Analytic.java
org/tei_c/ns/_1/Anchor.java
org/tei_c/ns/_1/Author.java
org/tei_c/ns/_1/Availability.java
org/tei_c/ns/_1/Back.java

etc.
```

--------------------------------

### TEI Facsimile Surface Definition

Source: https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF

Example of the facsimile element in TEI, defining page dimensions using surface attributes.

```xml
    ...
    </teiHeader>
    <facsimile>
        <surface n="1" ulx="0.0" uly="0.0" lrx="612.0" lry="794.0"/>
        <surface n="2" ulx="0.0" uly="0.0" lrx="612.0" lry="794.0"/>
        <surface n="3" ulx="0.0" uly="0.0" lrx="612.0" lry="794.0"/>
        <surface n="4" ulx="0.0" uly="0.0" lrx="612.0" lry="794.0"/>
        <surface n="5" ulx="0.0" uly="0.0" lrx="612.0" lry="794.0"/>
    </facsimile>
    <text xml:lang="en">
    ...
```

--------------------------------

### Search for version strings

Source: https://grobid.readthedocs.io/en/latest/Notes-grobid-developers

Perform a recursive grep to identify remaining references to the previous version before finalizing a release.

```bash
grep -rn '<previous-version>' \
  --include='*.md' --include='*.gradle' --include='*.java' \
  --include='*.kt' --include='*.cff' --include='*.yml' \
  --include='*.properties' .
```

--------------------------------

### Configure Gradle Proxy Settings

Source: https://grobid.readthedocs.io/en/latest/Install-Grobid

Proxy configuration parameters to be added to the grobid/gradle.properties file.

```properties
systemProp.http.proxyHost=host
systemProp.http.proxyPort=port
systemProp.http.proxyUser=username
systemProp.http.proxyPassword=password
systemProp.https.proxyHost=host
systemProp.https.proxyPort=port
systemProp.https.proxyUser=username
systemProp.https.proxyPassword=password
```

--------------------------------

### POST /api/createTraining

Source: https://grobid.readthedocs.io/en/latest/Grobid-service

Generates training data for Grobid models from an input PDF document.

```APIDOC
## POST /api/createTraining

### Description
Generate the training data for the grobid models for a PDF document provided in input. The service returns a ZIP archive with the training data in TEI XML format.

### Method
POST

### Endpoint
/api/createTraining

### Parameters
#### Request Body
- **input** (file) - Required - A PDF document
- **flavor** (string) - Optional - The name of the flavor used to create the training data

### Request Example
curl --location 'http://localhost:8070/api/createTraining' --form 'input=@"PATH_DOCUMENT"' --output output_name.zip

### Response
#### Success Response (200)
- application/zip archive

#### Error Responses
- 400: Wrong request, missing or invalid model name, invalid architecture name, missing header
- 500: Internal service error
```

--------------------------------

### Configure Grobid Maven Project

Source: https://grobid.readthedocs.io/en/latest/Grobid-java-library

Configuration and testing commands for a Maven-based Grobid integration project.

```properties
    grobid_example.pGrobidHome=/Users/lopez/grobid/grobid-home
```

```bash
> mvn test
```

--------------------------------

### Deploy Monitoring Stack with Docker Compose

Source: https://grobid.readthedocs.io/en/latest/Monitoring

Use this configuration to launch GROBID, Prometheus, and Grafana containers simultaneously.

```yaml
services:
  grobid:
    image: grobid/grobid:0.9.1
    ports:
      - "8070:8070"   # REST API
      - "8071:8071"   # admin connector (metrics)

  prometheus:
    image: prom/prometheus:latest
    ports:
      - "9090:9090"
    volumes:
      - ./prometheus.yml:/etc/prometheus/prometheus.yml:ro

  grafana:
    image: grafana/grafana:latest
    ports:
      - "3000:3000"
    depends_on:
      - prometheus
```

--------------------------------

### Integrate CRF++ library

Source: https://grobid.readthedocs.io/en/latest/Recompiling-and-integrating-CRF-libraries

Copy the CRF++ library and its dependencies to the Grobid home directory.

```bash
> cp ld-linux-x86-64.so.2 libwapiti.so libc.so.6 libgcc_s.so.1 libm.so.6 libpthread.so.0 libstdc++.so.6 GROBID-ROOT-DIRECTORY/grobid-home/lib/lin-<nb bits of the OS>
```

--------------------------------

### Tagging Non-Segmented Fields

Source: https://grobid.readthedocs.io/en/latest/training/Bibliographical-references

Example of tagging journal titles and volumes that appear without spacing, ensuring no extra whitespace is introduced.

```xml
<bibl>
    <author>D. Foo, P. Bar</author>, 
    <title level="j">Phys. Rev. D</title><biblScope unit="volume">95</biblScope>, 
    <biblScope unit="page">34</biblScope>(<date>2017</date>)
</bibl>
```

--------------------------------

### Configure biblio-glutton in grobid.yaml

Source: https://grobid.readthedocs.io/en/latest/Consolidation

YAML configuration snippet to enable the glutton service and specify its URL and timeout settings.

```yaml
consolidation:
    service: "glutton"
    glutton:
      url: "http://localhost:8080"
      timeoutSec: 60
```

--------------------------------

### Configure Gradle Repository

Source: https://grobid.readthedocs.io/en/latest/Grobid-java-library

Add the GROBID repository to your build.gradle file.

```groovy
    repositories { 
        maven { url "https://grobid.s3.eu-west-1.amazonaws.com/repo/" }
    }
```

--------------------------------

### Train specialized segmentation model

Source: https://grobid.readthedocs.io/en/latest/Grobid-specialized-processes

Command to initiate training for the article/light segmentation model.

```bash
./gradlew train_segmentation_article_light
```