Merge pull request #724 from OHDSI/develop

develop merge for release 1.7.2

1.7 release description bump

Cleaned up .gitignore

Brought back missing analyses, bugfixes for PG/Oracle, Redshift (#321)

* Fix for #317 (more Oracle cast issues), #313 (allow vocabDatabaseSchema parameter in achillesHeel), #312 (convert cdmVersion to character). Also, some strange encoding in the exportToJson.R script. Removed redundant concept_hierarchy.sql file (this was supposed to be removed for 1.6).

* Added analyses 822, 823, 1822, 1823 back. Fixed missing null cast in Heel RD 25. Adjusted analysis_details CSV to match new analyses. Added drop index statements.

* Fixes to analysis_details CSV, analysis 1822 had the wrong field name, added drop if not null statements in dropAllScratchTables

* Removed usage of DatabaseConnector::getTableNames() due to inconsistent effectiveness in Redshift

* Updated version number to 1.6.1

v1.6.0 Release Candidate (#297)

* Multi-threading redesign, CTAS usage, logging, cost support

* Update notes.md

tiny change to make formatting correct

* Update rule_3.sql

30 changed to 60 per existing proposal in issues

* Added OhdsiRTools installation step if package not present

* Update .travis.yml

fix for travis error

* Fixed missing is_installed function call, remove cohort-based analyses if no cohort table available. Removed old tests, which are replaced with parameterized tests.

* Added logMultiThreadPerformance conditional check

* smallCellCount is now the precise case of the small cell count variable

* Altered serial temp table drop statement to conform to SqlRender replacement pattern

* Translation of rendered drop temp table SQLs was missing

* Missing period in is_installed function call

* Fixed join issue in GlobalRowCnt Heel queries

* Fixed wrong name of outputPath variable in compressIntoOneFile portion

* Added concept_hierarchy tables to dropAllScratchTables. Added distinct to merge_heel_results to remove duplicates.

* Removed allReports.rda, using a CSV instead

* Updated instructions on allReports.csv usage

* Re-org of CSV files. Added README-developers.md reference guide. Changed @heelPrefix to @tempHeelPrefix. Added warnOnMissingParameters = TRUE to all renderSql / loadRenderTranslateSql calls.

* Delete .~lock.heel_results_derived_details.csv#

* Simplification of CSVs and SQL files for Heels, and updated achillesHeel function to align. Updated Developer README.

* Removed Heel rules 15 and 16 as they are for CDMv4

* Updating Heels to include most recent commits in Master (casts for impala, cross joins, docker)

* Fixed createIndices return path for redshift and netezza

* Changed serial Heels to explicit temp tables rather than parameterized temp tables

* rule27 cross join bugs, deprecated results_database_schema mention in rule31

* Updated developer readme's serial heel SQL file conventions. Fixed compressIntoOneFile feature in exportToJson to clean up junk paths in the zip file.

* Fixes #299

* Remove unused tests. See #299.

* Solve docker run error possibly resulting from CRLF vs LF issue

* Fixes #301

* Removed redundant merge_concept_hierarchy.sql file, as this was moved out of the concept_hierarchies folder

* latest release wording in readme

* Update heel_rules_all.csv

columns were shifted and information confused - this file fixes it

* Update README.md

links added to correct new files

* Fix for #305, the zip file not containing all folders and files.

* Updates to readme per Vojtech's request

Fixes for queries 691, 791, 891, 1891 for Impala. (#223)

Update AchillesHeel_v5.sql

new derived measure for death data
new derived measure for Data Quality study (size of Achilles metadata; informative non sensitive dataset info)

Merge pull request #127 from OHDSI/devH5

new rules 32,33 and 34 and updates and one new analysis

Fixed closing brace on sqlRender IF block.

Use concept_class_id when looking up condition concept type report.

Fixes #107.

Note: this commit regenerates roxygen2 documentation using the latest build which removes the specific version number from the comments.  Please update your local roxygen package before builds.