NEWS.md

In Dainanahan/dbparser: Drugs Databases Parser

dbparser 2.0.3

Enhancements

• Updated unit tests with latest DrugBank DB info v 5.1.12

Bugs Fixes

• Fixed "Drug Targets has two drugbank_id columns" bug (#163)

dbparser 2.0.2

Enhancements

• Replaced "-" with "_" in tibbles column names (#111)
• Renamed "primary_key" to "drugbank_id" in parsed drugs "general_information" tibble (#111)
• Replaced "parent_key" keywords in different tibbles column names with original parent name (#111)
• Updated Vignette to use interactive canvasXpress package plots

dbparser 2.0.1

Bugs Fixes

• Fixed output references (#147)
• Updated parseDrugBanKparameters default values (#146)
• Fixed package documentation references (#144)
• Fixed CRAN error on some of linux info (#145)

dbparser 2.0.0

Breaking changes

• Deprecated saving parsed data into given database (#140)
• Deprecated saving parsed data into a csv file (#140)
• Deprecated old structure public methods (#141)
• Updated minimum R required version to 3.5 (#143)

New features

• Introduced new methods for paring DrugBank DB and returning dvobject (#141)

Major Updates

• Updated unit tests to work with new data structure (#141)

Minor Fixes

• Removed RMariaDB dependency (#129)
• Fix pkgdown configuration for reference (#136)

dbparser 1.2.0

UI Changes

• Introduce progress bar in parser functions

New Parsers

Collective Parsers

• drugs, cett and References Parsers

Elements Parsers

• attachments parsers for drugs and CETT
• drug_pharmacology parser
• Rename drugs_books parser to drugs_textbooks
• Rename drug_all parser to run_all_parsers
• Rename drug parser to drug_general_information

Documentation Update:

• Add returned parsed data structure
• Explain the returned data functionality as a whole and for each elements
• Point out to related/similar parsers

Package design

For those who thinking to contribute in dbparser, now parsers are implemented as R6 classes.

Minor Fixes

• Update database saver functions to accommodate new DrugBank data size.

dbparser 1.1.2

Major Changes

• Enhance many memory and performance issues for many parsers.
• Change the drug classification representations to extract more useful information.

Minor Changes

• Change some drug tibbles features names

DEFUNCT

• Size columns in drugs main table is no longer exist, will do full statistical analysis later using dvminer package.

dbparser 1.1.1

• Fix column size issue while importing into SQL Server (#91)
• Fix dbparser and upcoming CRAN release of dplyr issues (#92)
• Fix CRAN Notes (#93)
• Fix package documentation and site references

dbparser 1.1.0

Major Changes

• Functions have been splitted into 6 categories DrugBank Database Loading, Carriers, Targets, Transporters, Drug and common parsers. All function names are changed to reflect the function family. The related documentation is also updated (#66, #75).
• dbparser now can cite the package by calling citation("dbparser") (#71).
• Adding more user friendly error messages (#76, #81).
• User can now pass DBI database connection to parser functions as an argument beside SQLite and MariaDB (#87).

DEFUNCT

• open_db, open_mdb and close_db functions are no longer supported. Creating and maintaining database is completely user responsibility and the database connection can be passed to parser functions (#87).

DOCUMENTATION FIXES

• New tutorials for how to use dbparser have been created (#78, #79).
• Contribution guide has been added.
• Code of conduct has been added (#70).
• Enhance function reference documentation to include section for each type (#68).

dbparser 1.0.4

• Fix save drugs tibbles as csv several issues.
• Update SQL database tibbles saver functions.
• Update SQL database saver functions documentations.
• Support MariaDB and introduce related functionalities.

dbparser 1.0.3

• Fix CRAN errors and notes

dbparser 1.0.2

• Fix zip file location issue
• Replace Secondary and third keys columns from drug framework with other_keys column that contains any other keys that might exist in addition to the primary key
• Add average-mass, monoisotopic-mass and calculated-properties parsers.
• Support saving parsed drugs related parsed database as csv

dbparser 1.0.1

• Fix CRAN Note
• Improve documentation
• Refactor unused functions
• Remove Count features from drug data set
• Fix several typos in documentation and code
• Fix consistency issue of CLASS of tibbles Returned by dbparser
• Check if DrugBank database exist before parsing
• Add support for international_brands and salts elements
• Properly rename some features to have clear names
• Reduce datasets size by getting unique rows only
• Support reading zip file containing DrugBank xml database

dbparser 1.0.0

• Initial release that contains core functionalities

Dainanahan/dbparser documentation built on April 20, 2024, 5:21 p.m.