Inti

Capture system from non scrapping data sources

Description

Package to download data and process datasets, not related to scrapping, like Microsoft Academic MAG and Scielo. For MAG, this package allows to download the data from azure and in parallel, dumps the data to MongDB collections. This allows too, create indexes for ElasticSearch database to perform search using the title of the document.

Azure account

https://docs.microsoft.com/en-us/academic-services/graph/get-started-setup-provisioning

Installation

Dependencies

• Install MongoDB:
  • Debian Based systems: apt install mongodb
  • RedHat Based systems: here
• Install ElasticSearch: here
• The other dependecies can be installed with pip installing this package.

Package

pip install inti

MongoDB requirement

Very importan for MA, other way it won't work. https://docs.mongodb.com/manual/reference/ulimit/ max opened files have to be updated.

Usage

Exaple running save MAG in MongoDB

inti_maloader --ma_dir=/storage/colav/mag_sample/ --db=MA --all

Exaple running save MAG in ElasticSearch

inti_maesloader --mag_dir=/home/colav/mag/ --col_name=Papers --field_name=PaperTitle --index_name=mag

MongoDB Options requirement

There is a special requirement for mongodb server to allow run multithread sessions To avoid the error ok" : 0, "errmsg" : "cannot add session into the cache", "code" : 261, "codeName" : "TooManyLogicalSessions",

you need to start the server with the option

mongod --setParameter maxSessions=10000000 --config /etc/mongodb.conf

ElasticSearch Options requirement

in the file /etc/elasticsearch/elasticsearch.yml add

thread_pool.get.queue_size: 10000

thread_pool.write.queue_size: 10000

ElasticSearch disk options

With low disk space, this error can appear

('1 document(s) failed to index.', [{'index': {'_index': 'mag', '_type': '_doc', '_id': '9915517', 'status': 429, 'error': {'type': 'cluster_block_exception', 'reason': 'index [mag] blocked by: [TOO_MANY_REQUESTS/12/disk usage exceeded flood-stage watermark, index has read-only-allow-delete block];'}, 'data': {'PaperTitle': '...'}}}])

solver it with this.

curl -XPUT -H "Content-Type: application/json" http://localhost:9200/_cluster/settings -d '{ "transient": { "cluster.routing.allocation.disk.threshold_enabled": false } }'

curl -XPUT -H "Content-Type: application/json" http://localhost:9200/_all/_settings -d '{"index.blocks.read_only_allow_delete": null}'

MongoDB optimizations

increase the index creation memory to 6G of RAM to improve the performance(use this with caution)

db.adminCommand({getParameter: 1, maxIndexBuildMemoryUsageMegabytes: 1})

db.adminCommand({setParameter: 1, maxIndexBuildMemoryUsageMegabytes: 6144})

Final notes

Be aware that running this package, mongodb producess a huge amount of informtation in the logs, please clean the file /var/log/mongodb.log (it could be more that 65G)

This is required to perform massive insertions in parallel!

License

BSD-3-Clause License

Links

http://colav.udea.edu.co/