Releases: OHDSI/MedlineXmlToDatabase
Correct jar file version
Ignoring XML elements with names having illegal characters
Ignoring XML elements with names having illegal characters when analyzing.
For example, pubmed18n1239.xml erroneously contains the XML element 'mml:math', which led to errors when trying to create the database structure. Now these elements are skipped. When parsing and inserting the data, these elements will also be ignored since no matching field is present in the schema.
More informative error messages
More informative error messages when something goes wrong when talking to the server. Also, now stopping at first error.
Bugfix for commentscorrections table
This fixes issue #8
The PMID and PMID_Version fields for the referenced PMIDs are renamed to Other_PMID and Other_PMID_Version to avoid collision with the PMID and PMID_Version of the referencing article.
Bugfix when creating tables
Fix of bug introduced in latest bugfix
Bugfix when adding MeSH in PostgreSQL
- Bugfix when adding MeSH in PostgreSQL
Bugfix in classpath
Fixed the classpath, JAR should now run.
MEDLINE 2017
In 2017 MEDLINE started including inline tags in text fields. For example, abstracts can contain <I> and <B> tags. I decided to completely ignore these. The alternative would have been to keep the tags, but that would mean the user would need to parse them when using the database. Also, for consistency it would have made sense to keep the entire text fields in XML, including XML encoding of international characters, etc.. As a consequence, all text fields like journal name and author name would then also need to be in XML, and all would need to be parsed when using the database. Since I couldn't think of a use case for the tags, I removed them altogether. The resulting database is therefore still XML-free.
Enforcing processing of XML files in order
This version enforces processing the XML files in order, which is a requirement (later files may contain corrections for earlier records).
Release generated using Ant file
v0.2.0 Update README.md