ctrdata 1.10.1 (2022-07-24)

• fix documentation issues (https://stat.ethz.ch/pipermail/r-package-devel/2022q3/008240.html)
• fix unit test with unused but missing argument
• fix GitHub actions and tests

ctrdata 1.10.0 (2022-07-01)

• ctrLoadQueryIntoDb new parameter euctrresultsfilespath, deprecating euctrresultspdfpath
• ctrLoadQueryIntoDb now also extracts and saves results files other than PDF files
• ctrFindActiveSubstanceSynonyms() returns NULL for non-existing active substance

ctrdata 1.9.1 (2022-04-24)

• type e811… variables
• bugfix in dbGetFieldsIntoDf
• bugfix annotations mix up for some backends
• editorial update vignettes

ctrdata 1.9.0 (2022-03-13)

• chunked trial batches in ndjson files for accelerated database import
• if package dplyr is loaded, functions return a tibble instead of a data frame
• update and correct documentation
• dbFindFields() returns a vector of fields which now has as names the register in which a field occurs
• accelerated binary checks (cygwin / Windows)
• remove internet proxy mangling in order to use system configuration (e.g., transparent proxies used, or environment variable https_proxy specified by user)
• refactored internal caching
• correct dbGetFieldsIntoDf() for specific nested data structures
• correct dfTrials2Long() for specific fields
• correct dbFindIdsUniqueTrials() when only single trial in any register
• modify field typing to decode HTML entities
• type some fields as difftime, e.g. min_age in CTGOV
• speed up parts of dbGetFieldsIntoDf() and simplify more fields
• dbFindFields() returns names of all leaf and node fields
• improve and update documentation
• changed EU Member State to default to DE for dbFindIdsUniqueTrials()
• corrected installCygwinWindowsDoInstall() to properly update an installation (remove –prune-install)
• test all binaries after installCygwinWindowsDoInstall() and only cache successful binary testing
• correct typing required_header.download_date
• improve numbering in dfTrials2Long, covering nested items

ctrdata 1.8.0.9001 (2021-12-11)

• thorough documentation improvement
• simplified dbFindFields
• cleaned up testing binaries
• cleaned up heper scripts
• removed ctrGetQueryUrlFromBrowser(), long deprecated

ctrdata 1.8.0.9000 (2021-11-22)

• uses nodbi 0.6.0
• can use PostgreSQL as backend
• include PostgreSQL in Github Actions

ctrdata 1.8.0 (2021-11-18)

• changes to match nodbi 0.5.0
• simplifying database operations (user-visible functions: ctrLoadQueryIntoDb, dbFindIdsUniqueTrials, dbGetFieldsIntoDf), without changes to API

ctrdata 1.7.1.9000 (2021-08-23)

• new development version

ctrdata 1.7.1 (2021-08-22)

• fix DBI not needed in Imports anymore (CRAN Note)
• fix potential file name issue in conversion script
• fix dbFindFields() to never return _id (previously depended on database backend)
• changed tests (not on CRAN detection, register availability, additional tests)

ctrdata 1.7.0 (2021-07-24)

• much reduced database backend-specific code, using nodbi 0.4.3 (released 2021-07-23) which also introduces transactions for sqlite using RSQLite >=2.2.4 (released 2021-03-12)
• temporary directory creation only when needed, more automated deletion
• changes in detecting non-functioning register servers
• further streamlined unit testing

ctrdata 1.6.0 (2021-05-09)

• added support for ISRCTN
• refactored checking binaries and caching this info
• updated EUCTR download parameters
• refactored ctrGetQueryUrl and ctrOpenSearchPagesInBrowser
• harmonised error checking
• avoid some errors with external scripts
• refactored url / query mangling, added detailed testing
• refactored storing JSON into database (handle big files, reduce memory)
• improved dbFindIdsUniqueTrials (speed, memory, register coverage)
• factored out conversion to JSON
• accelerated EUCTR results and history download and storage
• external scripts now create multiple chunks of records
• use further identifier fields with dbFindIdsUniqueTrials

ctrdata 1.5.3.9000 (2021-04-29)

• adding user info which field entries could not be typed

ctrdata 1.5.3 (2021-04-19)

• include message how to handle server certificate issues, by propagating user settings for httr to curl operations
• ensure identical return structures when no new trials found
• dfTrials2Long: harmonise identifier level assignment, address cases where field occurs only once in input df
• dfMergeTwoVariablesRelevel: corrected and improved user info
• dfName2Value: remove duplicate rows, e.g. from duplicated criteria

ctrdata 1.5.2 (2021-04-05)

• bugfix of EOL for converting EUCTR files

ctrdata 1.5.1 (2021-03-21)

• bugfix for non-matching euctr protocol and result ids: any trials from EUCTR for which results were downloaded with version 1.5.0 should be downloaded again (ctrLoadQueryIntoDb)
• dfTrials2Long refactored and accelerated
• API change: dfTrials2Long return value (identifier replaces main_id and sub_id)
• new option to save EUCTR results PDF files in user-specified directory

ctrdata 1.5.0 (2021-03-14)

• return values of dbGetFieldsIntoDf are now mostly identical whether using src_mongo or src_sqlite, to best ensure portability of analysis code
• permit dots in queries / URLs
• improved handling of queryterm
• renamed ctrGetQueryUrlFromBrowser to ctrGetQueryUrl
• soft deprecated ctrGetQueryUrlFromBrowser
• ensure parallel retrievals from EUCTR
• speed up routines in dbGetFieldsIntoDf
• make dfTrials2Long handle NA better
• improved documentation, clarified examples
• simplified internals for typing fields, start typing results fields

ctrdata 1.4.1 (2020-11-03)

• reset row names on data frames returned by functions
• update curl parameters when accessing EUCTR

ctrdata 1.4 (2020-10-17)

• new: easy access to variables with dfTrials2Long() + dfName2Value()
• improved dfMergeTwoVariablesRelevel() to maintain type of data
• revised and simplified vignettes
• deprecated: dfListExtractKey()
• refactored parts of euctr retrieval
• notify user when euctr register server does not permit compression and how long retrieval will take

ctrdata 1.3.2.9000 (2020-10-08)

• fixed identifying unique ids

ctrdata 1.3.2 (2020-10-03)

• quote system file paths

ctrdata 1.3.1 (2020-08-01)

• fix error in CI tests

ctrdata 1.3.0 (2020-07-27)

• workaround EUCTR certificate issue
• streamline ctrGetQueryUrlFromBrowser()
• better handling of complex fields
• include further tests for query string handling, checking more parameters and return values
• better clean-up after testing
• ctrLoadQueryIntoDb(querytorerun = …) now looks for the date when the querytorerun was last run, to more often use euctr update options
• switching from travis to github action
• upped coverage of code tested

ctrdata 1.2.1 (2020-05-18)

• tinytest >= 1.2.1 to avoid regression error
• correct testing detail

ctrdata 1.2 (2019-12-07)

• correct cygwin install detail

ctrdata 1.1 (2019-11-12)

• release after nodbi 0.4 is available

ctrdata 1.0.1.9005 (2019-11-09)

• update description for installation from github

ctrdata 1.0.1.9004 (2019-11-04)

• handled mixed arrays and text values in same key of ctgov trial records
• more user information during importing

ctrdata 1.0.1.9003 (2019-11-04)

• further nesting added for euctr trial records
• user verbose information extended for record importing

ctrdata 1.0.1.9002 (2019-11-03)

• improved parsing of euctr trial records
• correct re-opening of sqlite connection

ctrdata 1.0.1 (2019-10-22)

• correction of testing

ctrdata 1.0 (2019-10-16)

• switch to nodbi::scr_{mongo,sqlite}() with re-implementation of most functions
• switch from testthat to tinytest, so that users can check with tinytest::test_package(“ctrdata”)
• improvements to euctr trial import
  
• new function dfListExtractKey

ctrdata 0.18.9005 (2019-05-02)

• speed up testing bash commands under windows

ctrdata 0.18.2 (2019-04-30)

• new release
• extended compatibility with cygwin and Windows

ctrdata 0.18.9004 (2019-04-28)

• find and use any cygw* under windows
• refactored escaping bash command when called under windows

ctrdata 0.18.9002 (2019-04-21)

• corrected typing date fields

ctrdata 0.18.1 (2019-04-14)

• simplified cygwin install
• updated documentation
• corrected inconsistent handling of query terms

ctrdata 0.18.9001 (2019-04-12)

• added automated proxy handling

ctrdata 0.18 (2019-04-11)

• release version
• bug fixes in field typing
• move to use remote mongodb server
• updated vignettes

ctrdata 0.17 (2019-03-27)

• release version

ctrdata 0.16.9002 (2019-03-26)

• improve dbFindFields() formatting
• added parameter to force running a query again

ctrdata 0.16.9001 (2019-03-26

• added further typing (some of the numeric fields)
• improve cygwin install attempts and information

ctrdata 0.16.9000 (2019-03-24)

• removed dependency on local mongodb installation (major rewrite)
• improved support for remote mongodb servers (note changes in host / db / uri parameters)

ctrdata 0.15.9007 (2019-03-15)

• Important: Added no checking of SSL certificates for EUCTR because the EUCTR server is not sending the required intermediate and root certificates, thus failing curl and httr, see https://www.digicert.com/help/?host=www.clinicaltrialsregister.eu

ctrdata 0.15.0 (2019-03-13)

• fixed EUCTR results retrieval (curl return value order not predictable)
• removed second time adding metadata in one function
• streamlined user information and progress feedback

ctrdata 0.14.3 (2019-03-12)

• turned error into message when no new trials are found
• prevent failing tests if no new trials found in rss feed

ctrdata 0.14.2 (2019-03-07)

• harmonise user information

ctrdata 0.14.1 (2019-03-07)

• replaced RCurl (which failed for some register servers) by httr and curl
• create README.md from README.Rmd

ctrdata 0.14 (2019-03-06)

• intention to submit to CRAN, therefore changing several warnings to messages, improve testing of tool chain applications

ctrdata 0.13.3 (2019-03-03)

• prettified dbFindFields() by removing count symbols (XX.) from paths
• improve converting of invalid XML from EUCTR result files to JSON

ctrdata 0.13.2 (2019-02-28)

• made EUCTR retrieval more robust
• added marginal case for url of single trial in EUCTR
• extended timeout for checking online status of EUCTR

ctrdata 0.13.1 (2019-02-24)

• added typing of dates and some logical fields when using dbGetFieldsIntoDf()

ctrdata 0.13 (2019-01-06)

• dbGetVariablesIntoDf() is deprecated, use dbGetFieldsIntoDf() instead
• dbFindVariable() is deprecated, use dbFindFields() instead
• in dbMergeTwoVariablesRelevel() parameter varnames is deprecated, use colnames instead

ctrdata 0.12.1 (2018-12-15)

• added function ctrFindActiveSubstanceSynonyms() to obtain synonyms for an active substance
• added user information on number of trials in CTGOV to be downloaded, and limit this to 5000 per query
• corrected import from EUCTR for details = FALSE

ctrdata 0.12 (2018-05-19)

• added possibility to add user’s annotations to records retrieved with a query (new option annotate.text)

ctrdata 0.11.2 (2018-04-22)

• changed queryterm processing

ctrdata 0.11.1 (2018-04-07)

• improved installFindMongoBinaries(), should now better detect mongo binary locations and use for example in cron scripts, which may not have access to a user’s path information

ctrdata 0.11 (2018-01-28)

• newly retrieved: EUCTR results history, into new fields “firstreceived_results_date” and “version_results_history”
• adding feature as per issue #8

ctrdata 0.10.4 (2017-12-28)

• note on compatibility with mongoDB versions
• fixing issue #8
• simplified license

ctrdata 0.10.3 (2017-11-24)

• changed custom-built “x5_trial_status” to “p_end_of_trial_status” provided by EUCTR

ctrdata 0.10.2 (2017-11-22)

• editorial project updates

ctrdata 0.10.1 (2017-07-30)

• now loading results from euctr where available as xml

ctrdata 0.10.0 (2017-07-25)

• fully load results from ctgov
• prepare loading results from euctr

ctrdata 0.9.14 (2017-06-28)

• refactored system calls
• windows now part of continuous integration

ctrdata 0.9.13 (2017-06-23)

• refactored ctrLoadQueryIntoDb

ctrdata 0.9.12 (2017-06-18)

• Preparing for new CTGOV interface
• Improved documentation
• Corrected ctrGetQueryUrlFromBrowser return value

ctrdata 0.9.11.1 (2017-02-04)

• Improved documentation

ctrdata 0.9.11 (2017-01-15)

• Added functionality: EUCTR fallback import mechanism if large JSON file fails to import into mongoDB (by splitting and importing one JSON file for each trial, tested with several thousand trials)

ctrdata 0.9.10.1 (2017-01-12)

• Fixes issues with conversion of EUCTR records that did not have details.
• Fixes issue that placebo information was converted into IMP fields.

ctrdata 0.9.10.0 (2016-12-28)

• Added metadata attributes to returned objects to indicate database, query, timestamp etc.

ctrdata 0.9.9.5 (2016-12-14)

• Added option ctrLoadQueryIntoDb(querytoupdate = “last”) to re-download last query in collection

ctrdata 0.9.9.4 (2016-11-18)

• Added progress indicator to ctrLoadQueryIntoDb() to indicate network download traffic

ctrdata 0.9.9.3 (2016-11-17)

• deduplication in dbFindIdsUniqueTrials() optimised for speed and memory, added check by ISRCTN

ctrdata 0.9.9.2 (2016-11-13)

• corrected deduplication in dbFindIdsUniqueTrials()

ctrdata 0.9.9.1 (2016-11-12)

• renamed ctrQueryHistoryInDb() to dbQueryHistory()
• note: change in json format of query history, breaking compatibility
• refactored all concerned functions to use mongolite
• rmongodb is no more supported

ctrdata 0.9 (2016-10-17)

• changed implementation of dbFindIdsUniqueTrials()
• editorial changes to examples

ctrdata 0.8.1 (2016-09-07)

• added field to indicate source register
• improved ctrLoadQueryIntoDb() with details = FALSE
• added example for map plotting

ctrdata 0.8 (2016-09-04)

• dbFindIdsUniqueTrials now encapsulates dfFindIdsUniqueEuctrRecord
• dfFindIdsUniqueEuctrRecords removed
• installation instructions updated after recently rmongodb was removed from CRAN

ctrdata 0.7 (2016-05-29)

• dbGetVariablesIntoDf changed to concatenate values in array and objects
• completed test adaptation for travis
• improving perl regex
• checking helper applications

ctrdata 0.6.2 (2016-04-20)

• add / update field “record_last_import” for every imported / updated record

ctrdata 0.6.1 (2016-04-02)

• changed to provide vignettes

ctrdata 0.6 (2016-02-25)

• different update mechanism for EUCTR implemented
• corrected function name from db… to dfFindUniqueEuctrRecord()

ctrdata 0.5.9 (2016-01-23)

• Corrected bugs
• Started preparation of submission to CRAN
• Preparing to include package unit tests

ctrdata 0.5 (2015-11-29)

• Published on github
• Improved documentation

ctrdata 0.4 (2015-10-08)

• Renamed all functions for consistency and ease-of-use

ctrdata 0.3 (2015-10-06)

• Added functionality to download xml data from CTGOV, which includes more data than the csv format

ctrdata 0.2.8

• Changed and extended how history of queries is included in database.
• New function dbCTRQueryHistory()

ctrdata 0.2.7

• Added function for merging variables such as from different registers and optionally to merge values into new values
• Note that function findCTRkey was renamed to dbFindCTRkey because it acts on the database

ctrdata 0.2.5

• Added function for selecting preferred language versions of trials from EUCTR
• Improved use of automatic proxy configuration script

ctrdata 0.2.2

• Added proxy function and improved installation of cygwin under MS Windows

ctrdata 0.2 (2015-09-19)

• Now also working on MS Windows

ctrdata 0.1 (2015-09-15)

• First version with basic functionality
• Limited testing
• Works on Mac OS X (10.10.x)