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Changelog

Source: NEWS.md

dbparser 2.0.3

CRAN release: 2024-04-20

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

CRAN release: 2024-02-16

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

CRAN release: 2023-03-27

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

CRAN release: 2023-03-17

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

CRAN release: 2020-08-26

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

CRAN release: 2020-06-08

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

CRAN release: 2020-05-10

  • 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

CRAN release: 2020-02-21

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

CRAN release: 2019-08-28

  • 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

CRAN release: 2019-07-11

  • Fix CRAN errors and notes

dbparser 1.0.2

CRAN release: 2019-07-08

  • 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

CRAN release: 2019-04-16

  • 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

CRAN release: 2018-12-17

  • Initial release that contains core functionalities