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

.travis.yml

@@ -9,6 +9,7 @@ r_packages:
 
 r_github_packages:
   - OHDSI/DatabaseConnector
+  - OHDSI/OhdsiRTools
 
 before_install:
   - Rscript -e 'update.packages(ask = FALSE)'

Achilles.Rproj

@@ -1,18 +1,18 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-BuildType: Package
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --no-multiarch
-PackageRoxygenize: rd,namespace
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --no-multiarch
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -1,20 +1,23 @@
-Package: Achilles
-Type: Package
-Title: Creates descriptive statistics summary for an entire OMOP CDM instance
-Version: 1.5
-Date: 2016-10-20
-Author: Patrick Ryan, Martijn Schuemie, Vojtech Huser, Chris Knoll
-Maintainer: Patrick Ryan <[email protected]>
-LazyData: true
-Description: creates descriptive statistics summary for an entire OMOP CDM
-    instance. Since Aug 2016 only CDM v5 is actively being extended. Achilles
-    Heel component does data quality assesment.
-Depends:
-    SqlRender,
-    DatabaseConnector (>= 1.11.4),
-    rjson
-Suggests:
-    testthat
-License: Apache License
-Roxygen: list(wrap = FALSE)
-RoxygenNote: 6.0.1
+Package: Achilles
+Type: Package
+Title: Creates descriptive statistics summary for an entire OMOP CDM instance
+Version: 1.6
+Date: 2018-04-09
+Author: Patrick Ryan, Martijn Schuemie, Vojtech Huser, Chris Knoll, Ajit Londhe
+Maintainer: Patrick Ryan <[email protected]>
+LazyData: true
+Description: creates descriptive statistics summary for an entire OMOP CDM
+    instance. Since Aug 2016 only CDM v5 is actively being extended. Achilles
+    Heel component does data quality assesment.
+Depends:
+    SqlRender,
+    DatabaseConnector (>= 2.0.0),
+    rjson,
+    OhdsiRTools
+Suggests:
+    testthat,
+    dplyr,
+    R.utils
+License: Apache License
+Roxygen: list(wrap = FALSE)
+RoxygenNote: 6.0.1

Dockerfile

@@ -19,6 +19,7 @@ RUN echo deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main >> /et
       r-cran-dbi \
       r-cran-ffbase \
       r-cran-urltools \
+      libxml2-dev \
       littler \
       openjdk-7-jdk \
     && rm -rf /var/lib/apt/lists/* \
@@ -32,14 +33,32 @@ RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
 ENV LC_ALL en_US.UTF-8
 ENV LANG en_US.UTF-8
 
+# Install OHDSI/OhdsiRTools 
+RUN R -e "install.packages( \
+ c( \
+  'XML', \
+  'RJSONIO' \
+ ), \ 
+ repos='http://cran.rstudio.com/', \
+) "
+
 # Install Achilles requirements that need to be installed from source
 RUN echo 'options(repos=structure(c(CRAN="http://cran.cnr.berkeley.edu/")))' > /root/.Rprofile && \
     /usr/share/doc/littler/examples/install.r remotes && \
     /usr/share/doc/littler/examples/install.r docopt && \
+    /usr/share/doc/littler/examples/install.r openxlsx && \
+    /usr/share/doc/littler/examples/install.r httr && \
+    /usr/share/doc/littler/examples/install.r rjson && \
+    /usr/share/doc/littler/examples/install.r R.oo && \
+    /usr/share/doc/littler/examples/install.r formatR && \
+    /usr/share/doc/littler/examples/install.r R.utils && \
+    /usr/share/doc/littler/examples/install.r snow && \
+    /usr/share/doc/littler/examples/install.r mailR && \
     /usr/share/doc/littler/examples/installGithub.r \
       OHDSI/SqlRender \
       OHDSI/DatabaseConnectorJars \
       OHDSI/DatabaseConnector \
+      OHDSI/OhdsiRTools \
     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
 # Configure workspace

NAMESPACE

@@ -3,8 +3,9 @@
 export(achilles)
 export(achillesHeel)
 export(addDatasource)
-export(conceptHierarchy)
+export(createConceptHierarchy)
 export(createIndices)
+export(dropAllScratchTables)
 export(exportConditionEraToJson)
 export(exportConditionToJson)
 export(exportDashboardToJson)
@@ -25,3 +26,4 @@ export(fetchAchillesAnalysisResults)
 export(fetchAchillesHeelResults)
 export(getAnalysisDetails)
 export(showReportTypes)
+export(validateSchema)