grobid-client-python 0.0.7__tar.gz → 0.0.9__tar.gz

grobid_client_python-0.0.9/.github/workflows/ci-build.yml

@@ -0,0 +1,39 @@
+name: Build unstable
+
+on: [push]
+
+concurrency: 
+  group: unstable
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12', '3.13' ]
+      fail-fast: true
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Cleanup more disk space
+        run: sudo rm -rf /usr/share/dotnet && sudo rm -rf /opt/ghc && sudo rm -rf "/usr/local/share/boost" && sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install --upgrade flake8 pytest pycodestyle pytest-cov
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+#      - name: Test with pytest
+#        run: |
+#          pytest

grobid_client_python-0.0.9/.github/workflows/ci-release.yml

@@ -0,0 +1,43 @@
+name: Build release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'v*'
+
+concurrency:
+  group: docker
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+          cache: 'pip'
+      - name: Cleanup more disk space
+        run: sudo rm -rf /usr/share/dotnet && sudo rm -rf /opt/ghc && sudo rm -rf "/usr/local/share/boost" && sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install --upgrade flake8 pytest pycodestyle
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    #    - name: Test with pytest
+    #      run: |
+    #        pytest
+
+      - name: Build and Publish to PyPI
+        uses: conchylicultor/pypi-build-publish@v1
+        with:
+          pypi-token: ${{ secrets.PYPI_API_TOKEN }}

grobid_client_python-0.0.9/.gitignore

@@ -0,0 +1,23 @@
+target
+.DS_Store
+.project
+.settings
+.classpath
+.idea
+*.iml
+*.log
+*.log.*
+*.old
+*.obj
+*.zip
+data/doi
+data/entries
+data/fail
+data/*.pdf
+data/*.png
+my_config.json
+__pycache__
+doc/
+build/
+dist/
+grobid_client_python.egg-info/

{grobid_client_python-0.0.7 → grobid_client_python-0.0.9}/LICENSE

@@ -187,7 +187,7 @@
      same "printed page" as the copyright notice for easier
      identification within third-party archives.
 
-  Copyright 2018-2023 The Contributors
+  Copyright 2018-2024 The Contributors
 
   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.

grobid_client_python-0.0.9/PKG-INFO

@@ -0,0 +1,431 @@
+Metadata-Version: 2.1
+Name: grobid-client-python
+Version: 0.0.9
+Summary: Simple python client for GROBID REST services
+Author-email: Patrice Lopez <patrice.lopez@science-miner.com>
+Maintainer-email: Patrice Lopez <patrice.lopez@science-miner.com>, Luca Foppiano <lucanoro@duck.com>
+License: 
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+          Copyright 2018-2024 The Contributors
+        
+          Licensed under the Apache License, Version 2.0 (the "License");
+          you may not use this file except in compliance with the License.
+          You may obtain a copy of the License at
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+        
+Project-URL: Homepage, https://github.com/kermitt2/grobid_client_python
+Project-URL: Repository, https://github.com/kermitt2/grobid_client_python
+Project-URL: Changelog, https://github.com/kermitt2/grobid_client_python
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+
+[![PyPI version](https://badge.fury.io/py/grobid_client_python.svg)](https://badge.fury.io/py/grobid_client_python)
+[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/kermitt2/grobid_client_python/)](https://archive.softwareheritage.org/browse/origin/https://github.com/kermitt2/grobid_client_python/)
+[![License](http://img.shields.io/:license-apache-blue.svg)](http://www.apache.org/licenses/LICENSE-2.0.html)
+
+# Simple python client for GROBID REST services
+
+This Python client can be used to process in an efficient concurrent manner a set of PDF in a given directory by the [GROBID](https://github.com/kermitt2/grobid) service. It includes a command line for processing PDF on a file system and write results in a given output directory and a library for import in other python scripts. The client can also process similarly a list of files with reference strings (one per line) and patents in XML ST36 formats.
+
+## Before you start
+
+Please be aware that, at the moment, [grobid does not support Windows](https://grobid.readthedocs.io/en/latest/Troubleshooting/#windows-related-issues).
+If you are a Windows user, don't worry. You can still [run grobid 
+via Docker](https://grobid.readthedocs.io/en/latest/Grobid-docker/).
+
+## Build and run
+
+You need first a running *grobid* service, latest stable version, see the [documentation](http://grobid.readthedocs.io/) for installation. 
+By default, it is assumed that the server will run on the address `http://localhost:8070`. 
+You can change the server address by editing the file `config.json`, see below.
+
+## Requirements
+
+This client has been developed and was tested with Python `3.5`-`3.9` and should work with any higher `3.*` versions. It uses `requests` as dependency beyond the Standard Python Library.
+
+## Install
+
+The client can be installed with any of the following ways:
+
+* Install *latest stable release* from PyPI:
+
+```console
+python3 -m pip install grobid-client-python
+```
+
+* Install *current master development version* from GitHub:
+
+```console
+python3 -m pip install git+https://github.com/kermitt2/grobid_client_python.git
+```
+
+* Install and build from a clone of the repo (*current master development version*): 
+
+```
+git clone https://github.com/kermitt2/grobid_client_python
+cd grobid_client_python
+python3 setup.py install
+```
+
+There is nothing more needed to start using the python command lines, see the next section. 
+
+## Usage and options
+
+The call to the script can normally be realized interchangeably with `python3 -m grobid_client.grobid_client` or simply `grobid_client`. 
+
+```
+usage: grobid_client [-h] [--input INPUT] [--output OUTPUT] [--config CONFIG]
+                     [--n N] [--generateIDs] [--consolidate_header]
+                     [--consolidate_citations] [--include_raw_citations]
+                     [--include_raw_affiliations] [--force] [--teiCoordinates]
+                     [--verbose]
+                     service
+
+Client for GROBID services
+
+positional arguments:
+  service               one of ['processFulltextDocument',
+                        'processHeaderDocument', 'processReferences',
+                        'processCitationList','processCitationPatentST36',
+                        'processCitationPatentPDF']
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --input INPUT         path to the directory containing PDF files or .txt
+                        (for processCitationList only, one reference per line)
+                        to process
+  --output OUTPUT       path to the directory where to put the results
+                        (optional)
+  --config CONFIG       path to the config file, default is ./config.json
+  --n N                 concurrency for service usage
+  --generateIDs         generate random xml:id to textual XML elements of the
+                        result files
+  --consolidate_header  call GROBID with consolidation of the metadata
+                        extracted from the header
+  --consolidate_citations
+                        call GROBID with consolidation of the extracted
+                        bibliographical references
+  --include_raw_citations
+                        call GROBID requesting the extraction of raw citations
+  --include_raw_affiliations
+                        call GROBID requestiong the extraciton of raw
+                        affiliations
+  --force               force re-processing pdf input files when tei output
+                        files already exist
+  --teiCoordinates      add the original PDF coordinates (bounding boxes) to
+                        the extracted elements
+  --segmentSentences    segment sentences in the text content of the document
+                        with additional <s> elements
+  --verbose             print information about processed files in the console
+
+
+```
+
+Examples:
+
+```console
+> grobid_client --input ~/tmp/in2 --output ~/tmp/out processFulltextDocument
+```
+
+This command will process all the PDF files present under the input directory recursively (files with extension `.pdf` only) with the `processFulltextDocument` service of GROBID, and write the resulting XML TEI files under the output directory, reusing the file name with a different file extension (`.grobid.tei.xml`), using the default `10` concurrent workers. 
+
+If `--output` is omitted, the resulting XML TEI documents will be produced alongside the PDF in the `--input` directory.
+
+```console
+> grobid_client --input ~/tmp/in2 --output ~/tmp/out --n 20 processHeaderDocument
+```
+
+This command will process all the PDF files present in the input directory (files with extension `.pdf` only) with the `processHeaderDocument` service of GROBID, and write the resulting XML TEI files under the output directory, reusing the file name with a different file extension (`.grobid.tei.xml`), using `20` concurrent workers. 
+
+By default if an existing `.grobid.tei.xml` file is present in the output directory corresponding to a PDF in the input directory, this PDF will be skipped to avoid reprocessing several times the same PDF. To force the processing of PDF and over-write of existing TEI files, use the parameter `--force`.   
+
+`processCitationList` does not take a repertory of PDF as input, but a repertory of `.txt` files, with one reference raw string per line, for example:
+
+```console
+> grobid_client --input resources/test_txt/ --output resources/test_out/ --n 20 processCitationList
+```
+
+The following command example will process all the PDF files present in the input directory and add bounding box coordinates (`--teiCoordinates`) relative to the original PDFs for the elements listed in the config file. It will also segment the sentences (`--segmentSentences`, this is a "layout aware" sentence segmentation) in the identified paragraphs with bounding box coordinates for the sentences. 
+
+```console
+> grobid_client --input ~/tmp/in2 --output ~/tmp/out --teiCoordinates --segmentSentences processFulltextDocument
+```
+
+The file `example.py` gives an example of usage as a library, from a another python script. 
+
+## Using the client in your python
+
+Import and call the client as follow:
+
+```python
+from grobid_client.grobid_client import GrobidClient
+
+client = GrobidClient(config_path="./config.json")
+client.process("processFulltextDocument", "/mnt/data/covid/pdfs", n=20)
+```
+
+See also `example.py`.
+
+## Configuration of the client
+
+There are a few parameters that can be set with the `config.json` file. 
+
+- `grobid_server` indicates the URL of the GROBID server to be used by the client. 
+
+- `batch_size` is the the size of the pool of threads used by ThreadPoolExecutor, you normally don't want to change this. This should be a high number (default 1000) - but not too high to protect the memory on the machine running the client. This should not be confused with the concurrency parameter `n` which indicates how many parallel requests can be send to GROBID.
+
+- `sleep_time` indicates in seconds the time to wait for sending a new request to GROBID when the server indicates that all its 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. This wait time usually depends on the service and the capacities of the server, we suggest 5-10 seconds for the `processFulltextDocument` service and 2 seconds for `processHeaderDocument` service.
+
+- `timeout` is a client side timeout - the process on server side will still be running until the server finished the task or the server timeout is reached.
+
+- `coordinates` indicates the structure XML elements that should contains PDF coordinates when the parameters `--teiCoordinates` is used see [here](https://grobid.readthedocs.io/en/latest/Coordinates-in-PDF/) for more details.
+
+Here is the default `config.json` file for the client:
+
+```
+{
+    "grobid_server": "http://localhost:8070",
+    "batch_size": 1000,
+    "sleep_time": 5,
+    "timeout": 60,
+    "coordinates": [ "persName", "figure", "ref", "biblStruct", "formula", "s" ]
+}
+```
+
+## Benchmarking
+
+Full text processing of __136 PDF__ (total 3443 pages, in average 25 pages per PDF) on Intel Core i7-4790K CPU 4.00GHz, 4 cores (8 threads), 16GB memory, `n` being the concurrency parameter:
+
+| n  | runtime (s)| s/PDF | PDF/s |
+|----|------------|-------|-------|
+| 1  | 209.0      | 1.54  | 0.65  |
+| 2  | 112.0      | 0.82  | 1.21  |
+| 3  | 80.4       | 0.59  | 1.69  |
+| 5  | 62.9       | 0.46  | 2.16  |
+| 8  | 55.7       | 0.41  | 2.44  |
+| 10 | 55.3       | 0.40  | 2.45  |
+
+![Runtime Plot](resources/20180928112135.png)
+
+As complementary info, GROBID processing of header of the 136 PDF and with `n=10` takes 3.74 s (15 times faster than the complete full text processing because only the two first pages of the PDF are considered), 36 PDF/s. 
+
+In similar conditions, extraction and structuring of bibliographical references takes 26.9 s (5.1 PDF/s).
+
+Processing of 3500 raw bibliographical take 4.3 s with `n=10` (814 references parsed per second).
+
+
+## Developer notes 
+
+### New release 
+
+New releases can be published by using `bump-my-version`:
+
+```shell
+pip install bump-my-version
+bump-my-version bump patch 
+```
+
+Use of  `major`, `minor`, or `patch` or  will increment the first, second or the third digit of the version, respectively.  
+The release will be published automatically on pypy. 
+
+## License and contact
+
+Distributed under [Apache 2.0 license](http://www.apache.org/licenses/LICENSE-2.0). 
+
+Main author and contact: Patrice Lopez (<patrice.lopez@science-miner.com>)

grobid_client_python-0.0.7/grobid_client_python.egg-info/PKG-INFO → grobid_client_python-0.0.9/Readme.md

@@ -1,20 +1,10 @@
-Metadata-Version: 2.1
-Name: grobid-client-python
-Version: 0.0.7
-Summary: Simple python client for GROBID REST services
-Home-page: https://github.com/kermitt2/grobid_client_python
-Author: kermitt2
-License: LICENSE
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
 [![PyPI version](https://badge.fury.io/py/grobid_client_python.svg)](https://badge.fury.io/py/grobid_client_python)
 [![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/kermitt2/grobid_client_python/)](https://archive.softwareheritage.org/browse/origin/https://github.com/kermitt2/grobid_client_python/)
 [![License](http://img.shields.io/:license-apache-blue.svg)](http://www.apache.org/licenses/LICENSE-2.0.html)
 
 # Simple python client for GROBID REST services
 
-This Python client can be used to process in an efficient concurrent manner a set of PDF in a given directory by the [GROBID](https://github.com/kermitt2/grobid) service. It includes a command line for processing PDF on a file system and write results in a given output directory and a library for import in other python scripts. The client can also process similarly a list of files with reference strings (one per line).
+This Python client can be used to process in an efficient concurrent manner a set of PDF in a given directory by the [GROBID](https://github.com/kermitt2/grobid) service. It includes a command line for processing PDF on a file system and write results in a given output directory and a library for import in other python scripts. The client can also process similarly a list of files with reference strings (one per line) and patents in XML ST36 formats.
 
 ## Before you start
 
@@ -30,13 +20,27 @@ You can change the server address by editing the file `config.json`, see below.
 
 ## Requirements
 
-This client has been developed and was tested with Python `3.5`-`3.8` and should work with any higher `3.*` versions. It does not require any dependencies beyond the standard Python ones.
+This client has been developed and was tested with Python `3.5`-`3.9` and should work with any higher `3.*` versions. It uses `requests` as dependency beyond the Standard Python Library.
 
 ## Install
 
-Get the github repo:
+The client can be installed with any of the following ways:
+
+* Install *latest stable release* from PyPI:
 
 ```console
+python3 -m pip install grobid-client-python
+```
+
+* Install *current master development version* from GitHub:
+
+```console
+python3 -m pip install git+https://github.com/kermitt2/grobid_client_python.git
+```
+
+* Install and build from a clone of the repo (*current master development version*): 
+
+```
 git clone https://github.com/kermitt2/grobid_client_python
 cd grobid_client_python
 python3 setup.py install
@@ -44,9 +48,10 @@ python3 setup.py install
 
 There is nothing more needed to start using the python command lines, see the next section. 
 
-
 ## Usage and options
 
+The call to the script can normally be realized interchangeably with `python3 -m grobid_client.grobid_client` or simply `grobid_client`. 
+
 ```
 usage: grobid_client [-h] [--input INPUT] [--output OUTPUT] [--config CONFIG]
                      [--n N] [--generateIDs] [--consolidate_header]
@@ -60,7 +65,8 @@ Client for GROBID services
 positional arguments:
   service               one of ['processFulltextDocument',
                         'processHeaderDocument', 'processReferences',
-                        'processCitationList']
+                        'processCitationList','processCitationPatentST36',
+                        'processCitationPatentPDF']
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -187,6 +193,20 @@ In similar conditions, extraction and structuring of bibliographical references
 Processing of 3500 raw bibliographical take 4.3 s with `n=10` (814 references parsed per second).
 
 
+## Developer notes 
+
+### New release 
+
+New releases can be published by using `bump-my-version`:
+
+```shell
+pip install bump-my-version
+bump-my-version bump patch 
+```
+
+Use of  `major`, `minor`, or `patch` or  will increment the first, second or the third digit of the version, respectively.  
+The release will be published automatically on pypy. 
+
 ## License and contact
 
 Distributed under [Apache 2.0 license](http://www.apache.org/licenses/LICENSE-2.0). 

grobid_client_python-0.0.9/config.json

@@ -0,0 +1,7 @@
+{
+    "grobid_server": "http://localhost:8070",
+    "batch_size": 100,
+    "sleep_time": 5,
+    "timeout": 60,
+    "coordinates": [ "persName", "figure", "ref", "biblStruct", "formula", "s", "note", "title" ]
+}

grobid_client_python-0.0.9/example.py

@@ -0,0 +1,5 @@
+from grobid_client.grobid_client import GrobidClient
+
+if __name__ == "__main__":
+    client = GrobidClient(config_path="./config.json")
+    client.process("processFulltextDocument", "./resources/test_pdf", output="./resources/test_out/", consolidate_citations=True, tei_coordinates=True, force=True)