Python client for using the Softcite software mention recognition service at scale. It can be applied to:
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individual PDF or XML fulltext file
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recursively to a local directory, processing all the encountered PDF and XML fulltext files
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to a collection of documents harvested by biblio-glutton-harvester and article-dataset-builder. The collection can be stored locally or on a S3 storage.
The client will handle parallel requests and availability of the server to optimize the processing of a large collection of full texts.
For convenience, the client works also with a DataStet server to run this service at scale similarly as a Softcite software mention recognition service. DataStet extracts dataset mentions from full texts.
The client has been tested with Python 3.5-3.10.
The client requires a working Softcite software mention recognition service or a working Datastet service. The easiest is to use a docker image for these services, see the documentation and latest images at https://hub.docker.com/r/grobid/software-mentions/tags and https://hub.docker.com/r/grobid/datastet/tags.
Service host and port can be changed in the config.json file of the client.
> git clone https://github.com/softcite/software_mentions_client.git
> cd software_mentions_client/It is advised to setup first a virtual environment to avoid falling into one of these gloomy python dependency marshlands:
> virtualenv --system-site-packages -p python3 env
> source env/bin/activateInstall the dependencies, use:
> python3 -m pip install -r requirements.txtFinally install the project in editable state
> python3 -m pip install -e .usage: client.py [-h] [--repo-in REPO_IN] [--file-in FILE_IN] [--file-out FILE_OUT] [--config CONFIG]
[--reprocess] [--reset] [--load] [--diagnostic-mongo] [--diagnostic-files]
[--scorched-earth] [--datastet]
Softcite software mention recognizer client
optional arguments:
-h, --help show this help message and exit
--repo-in REPO_IN path to a directory of PDF or XML fulltext files to be processed by the
Softcite software mention recognizer
--file-in FILE_IN a single PDF or XML input file to be processed by the Softcite software mention
recognizer
--file-out FILE_OUT path to a single output the software mentions in JSON format, extracted from
the PDF file-in
--config CONFIG path to the config file, default is ./config.json
--reprocess reprocessed failed PDF or XML fulltexts
--reset ignore previous processing states and re-init the annotation process from the
beginning
--load load json files into the MongoDB instance, the --repo-in or --data-path
parameter must indicate the path to the directory of resulting json files to be
loaded, --dump must indicate the path to the json dump file of document
metadata
--diagnostic-mongo perform a full count of annotations and diagnostic using MongoDB regarding the
harvesting and annotation process
--diagnostic-files perform a full count of annotations and diagnostic using repository files
regarding the harvesting and annotation process
--scorched-earth remove the PDF or XML fulltext files file after their sucessful processing in
order to save storage space, careful with this!
--datastet call the DataStet service instead of the software mention extraction service.
It requires a DataStet server running instead of the Softcite server, and
indicating the Datastet server url in the config file
The logs are written by default in a file ./client.log, but the location of the logs can be changed in the configuration file (default ./config.json).
For processing a single file, the resulting json being written as file at the indicated output path:
python3 -m software_mentions_client.client --file-in toto.pdf --file-out toto.jsonThe default config file is ./config.json, but could also be specified via the parameter --config:
python3 -m software_mentions_client.client --file-in toto.pdf --file-out toto.json --config ./my_config.jsonFor processing recursively a directory of PDF files, the results will be:
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written to a mongodb server and database indicated in the config file
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and in the directory of PDF files, as json files, together with each processed PDF
python3 -m software_mentions_client.client --repo-in /mnt/data/biblio/pmc_oa_dir/The default config file is ./config.json, but could also be specified via the parameter --config:
python3 -m software_mentions_client.client --repo-in /mnt/data/biblio/pmc_oa_dir/ --config ./my_config.jsonIf, for any reason, the process is stopped, it can be resumed by entering the exact same command:
python3 -m software_mentions_client.client --repo-in /mnt/data/biblio/pmc_oa_dir/This will continue the processing of the input PDF and XML files not yet processed.
Anntations will be added along the PDF and XML files, with extension *.software.json, e.g.:
-rw-rw-r-- 1 lopez lopez 1.1M Aug 8 03:26 0100a44b-6f3f-4cf7-86f9-8ef5e8401567.pdf
-rw-rw-r-- 1 lopez lopez 485 Aug 8 03:41 0100a44b-6f3f-4cf7-86f9-8ef5e8401567.software.json
Just add --reprocess to the command line, the processing will be limited to the PDF and XML files that failed when processing them:
python3 -m software_mentions_client.client --repo-in /mnt/data/biblio/pmc_oa_dir/ --reprocessFor using the DataStet service instead of the Softcite Software Mention service, use the --datastet command line parameter (be sure to indicate the server URL in the configuration file). This alternative mode is provided for convenience and will write results in files with extension *.dataset.json instead of *.software.json. All the other parameters are similar, just the service to be used and the result files will be different.
Using --load option will trigger the loading of all the produced annotations into a MongoDB server indicated in the configuration file.
python3 -m software_mentions_client.client --load After the processing of a repository of PDF and XML files, it is possible to get detailed statistics about the produced annotations.
The --diagnostic-files option performs a full count of annotations and diagnostic using repository files regarding the existing file and the annotation process.
python3 -m software_mentions_client.client --diagnostic-file The --diagnostic-mongo option performs a full count of annotations and diagnostic using MongoDB regarding the existing files and the annotation process. It supposes that the annotations have been loaded into a MongoDB instance, but it is faster and more complete than the --diagnostic-files option.
python3 -m software_mentions_client.client --diagnostic-mongo By default, the concurreny of the parallelized calls to a service is 8. This parameter can be changed in the configuration file config.json.
Other important configuration parameter are the URL of the Software mention recognition web service software_mention_url, the optional URL of a DataStet server if used dataset_mention_url, the MongoDb instance information if you wish to load the produced annotations in MongoDB.
Normally, the configuration parameters sleep_time, timeout and batch_size do not need to be modified to ensure a robust processing.
Distributed under Apache 2.0 license. The dependencies used in the project are either themselves also distributed under Apache 2.0 license or distributed under a compatible license.
If you contribute to Softcite software mention recognizer client project, you agree to share your contribution following these licenses.
Main author and contact: Patrice Lopez (patrice.lopez@science-miner.com)