switching reads to odbc package

checking results are the same
nlsy-links · Jan 4, 2018 · e848104 · e848104
1 parent 5eaf6b6
commit e848104
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diff --git a/analysis/archive-ace/archive-ace.R b/analysis/archive-ace/archive-ace.R
@@ -7,12 +7,14 @@ source("./utility/connectivity.R")
 
 # ---- load-packages -----------------------------------------------------------
 library(NlsyLinks) # devtools::install_github("LiveOak/NlsyLinks")
-library(RODBC)
+# library(RODBC)
 library(ggplot2)
 library(colorspace)
 library(xtable)
 library(plyr)
 
+requireNamespace("odbc")
+
 # ---- declare-globals ---------------------------------------------------------
 #Define CSV of outcomes/phenotypes
 pathInput <- "./ForDistribution/Outcomes/ExtraOutcomes79.csv"
@@ -97,17 +99,16 @@ sql <- paste("
 #   WHERE Process.tblRelatedStructure.RelationshipPath = ", relationshipPath, "
 #       AND (Process.tblRelatedValuesArchive.AlgorithmVersion IN (73, 75))")
 
-sqlDescription <- "SELECT * FROM Archive.tblArchiveDescription" #AlgorithmVersion, Description
+# sqlDescription <- "SELECT AlgorithmVersion, Description, Date2 FROM Archive.tblArchiveDescription where AlgorithmVersion=72" #AlgorithmVersion, Description
+sqlDescription <- "SELECT AlgorithmVersion, Description FROM Archive.tblArchiveDescription" #AlgorithmVersion, Description
 
 # ---- load-data ---------------------------------------------------------------
-channel            <- open_dsn_channel()
-
 startTime <- Sys.time()
+channel            <- open_dsn_channel_odbc()
 # odbcGetInfo(channel)
-
-dsRaw <- sqlQuery(channel, sql, stringsAsFactors=F)
-dsDescription <- sqlQuery(channel, sqlDescription, stringsAsFactors=F)
-odbcClose(channel)
+dsRaw           <- DBI::dbGetQuery(channel, sql)
+dsDescription   <- DBI::dbGetQuery(channel, sqlDescription)
+DBI::dbDisconnect(channel, sql, sqlDescription)
 elapsedTime <- Sys.time() - startTime
 # print(elapsedTime)
 # nrow(dsRaw)

diff --git a/analysis/archive-comparison/archive-comparison.R b/analysis/archive-comparison/archive-comparison.R
@@ -70,32 +70,18 @@ sql <- paste("
 
 
 # sql <- gsub(pattern="\\n", replacement=" ", sql)
-sqlDescription <- "SELECT * FROM Archive.tblArchiveDescription" #AlgorithmVersion, Description
+# sqlDescription <- "SELECT AlgorithmVersion, Description, Date2 FROM Archive.tblArchiveDescription where AlgorithmVersion=72" #AlgorithmVersion, Description
+sqlDescription <- "SELECT AlgorithmVersion, Description FROM Archive.tblArchiveDescription" #AlgorithmVersion, Description
 startTime <- Sys.time()
 
 # ---- load-data ---------------------------------------------------------------
-# channel <- RODBC::odbcDriverConnect("driver={SQL Server};Server=Bee\\Bass; Database=NlsLinks; Uid=NlsyReadWrite; Pwd=nophi")
-channel <- RODBC::odbcDriverConnect("driver={SQL Server};Server=192.168.1.66\\Express_2016; Database=NlsLinks; Uid=NlsyReadWrite; Pwd=nophi")
-
-channel <- RODBC::odbcDriverConnect("Driver={ODBC Driver 13 for SQL Server};Server=192.168.1.66\\Express_2016; Uid=NlsyReadWrite; Pwd=nophi" )
-
-conn <- DBI::dbConnect(
-  RSQLServer::SQLServer(),
-  # "Server=gimble\\Express_2016",
-  # "Server=192.168.1.66\\Express_2016",
-  "192.168.1.66\\Express_2016",
-  "user=NlsyReadWrite; Password=nophi",
-  database = "NlsLinks"
-)
-
-
-channel            <- open_dsn_channel()
-odbcGetInfo(channel)
-
-dsRaw <- sqlQuery(channel, sql, stringsAsFactors=F)
-dsDescription <- sqlQuery(channel, sqlDescription, stringsAsFactors=F)
-
-RODBC::odbcClose(channel); rm(channel, sql, sqlDescription)
+startTime <- Sys.time()
+channel            <- open_dsn_channel_odbc()
+# DBI::dbGetInfo(channel)
+dsRaw           <- DBI::dbGetQuery(channel, sql)
+dsDescription   <- DBI::dbGetQuery(channel, sqlDescription)
+DBI::dbDisconnect(channel, sql, sqlDescription)
+elapsedTime <- Sys.time() - startTime
 (Sys.time() - startTime);  rm(startTime)
 nrow(dsRaw)
 

diff --git a/analysis/archive-comparison/archive-comparison.pdf b/analysis/archive-comparison/archive-comparison.pdf
diff --git a/analysis/archive-comparison/archive-comparison.tex b/analysis/archive-comparison/archive-comparison.tex
@@ -86,11 +86,7 @@
 \begin{knitrout}
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{verbatim}
-##              DBMS_Name               DBMS_Ver        Driver_ODBC_Ver       Data_Source_Name 
-## "Microsoft SQL Server"           "13.00.4206"                "03.80"     "local-nlsy-links" 
-##            Driver_Name             Driver_Ver               ODBC_Ver            Server_Name 
-##      "msodbcsql13.dll"           "14.00.0500"           "03.80.0000" "GIMBLE\\EXPRESS_2016"
-## Time difference of 0.8384829 secs
+## Time difference of 0.4893291 secs
 ## [1] 22176
 \end{verbatim}
 \end{kframe}
@@ -125,8 +121,8 @@
 \caption{ROC for Gen1Housemates (left) and Gen2Siblings (right)}
 \end{figure}
 
-% latex table generated in R 3.4.1 by xtable 1.8-2 package
-% Thu Sep 14 17:11:54 2017
+% latex table generated in R 3.4.3 by xtable 1.8-2 package
+% Thu Jan 04 10:42:50 2018
 \begin{table}[ht]
 \centering
 \begingroup\large
@@ -140,8 +136,8 @@
 \endgroup
 \caption{Counts for Gen1Housemates} 
 \end{table}
-% latex table generated in R 3.4.1 by xtable 1.8-2 package
-% Thu Sep 14 17:11:54 2017
+% latex table generated in R 3.4.3 by xtable 1.8-2 package
+% Thu Jan 04 10:42:51 2018
 \begin{table}[ht]
 \centering
 \begingroup\large
@@ -155,8 +151,8 @@
 \endgroup
 \caption{Counts for Gen1Housemates (Previous version of links)} 
 \end{table}
-% latex table generated in R 3.4.1 by xtable 1.8-2 package
-% Thu Sep 14 17:11:54 2017
+% latex table generated in R 3.4.3 by xtable 1.8-2 package
+% Thu Jan 04 10:42:51 2018
 \begin{table}[ht]
 \centering
 \begingroup\large
@@ -175,8 +171,8 @@
 \endgroup
 \caption{Counts for Gen2Siblings} 
 \end{table}
-% latex table generated in R 3.4.1 by xtable 1.8-2 package
-% Thu Sep 14 17:11:54 2017
+% latex table generated in R 3.4.3 by xtable 1.8-2 package
+% Thu Jan 04 10:42:51 2018
 \begin{table}[ht]
 \centering
 \begingroup\large
@@ -197,11 +193,11 @@
 \end{table}
 
 
-% latex table generated in R 3.4.1 by xtable 1.8-2 package
-% Thu Sep 14 17:11:54 2017
+% latex table generated in R 3.4.3 by xtable 1.8-2 package
+% Thu Jan 04 10:42:51 2018
 \begin{table}[ht]
 \centering
-\begin{tabular}{rrrrlr}
+\begin{tabular}{rrrrrr}
   \hline
 Count & RImplicit2004 & RImplicit & RExplicit & RRoster & Delta \\ 
   \rowcolor{goodColor}  \hline

diff --git a/analysis/archive-comparison/figure/unnamed-chunk-2-1.pdf b/analysis/archive-comparison/figure/unnamed-chunk-2-1.pdf
diff --git a/analysis/archive-comparison/figure/unnamed-chunk-2-2.pdf b/analysis/archive-comparison/figure/unnamed-chunk-2-2.pdf
diff --git a/analysis/eda/counts/counts.R b/analysis/eda/counts/counts.R
@@ -8,7 +8,7 @@ source("./utility/connectivity.R")
 # ---- load-packages -----------------------------------------------------------
 library(magrittr) #Pipes
 # library(ggplot2) #For graphing
-requireNamespace("RODBC")
+requireNamespace("odbc")
 requireNamespace("dplyr")
 requireNamespace("scales") #For formating values in graphs
 requireNamespace("knitr") #For the kable function for tables
@@ -53,10 +53,10 @@ sql_variable <- "
 # ---- load-data ---------------------------------------------------------------
 ds <- database_inventory()
 
-channel            <- open_dsn_channel_rodbc()
-ds_item            <- RODBC::sqlQuery(channel, sql_item    , stringsAsFactors=F)
-ds_variable        <- RODBC::sqlQuery(channel, sql_variable, stringsAsFactors=F)
-RODBC::odbcClose(channel); rm(channel, sql_item, sql_variable)
+channel            <- open_dsn_channel_odbc()
+ds_item            <- DBI::dbGetQuery(channel, sql_item    )
+ds_variable        <- DBI::dbGetQuery(channel, sql_variable)
+DBI::dbDisconnect(channel); rm(channel, sql_item, sql_variable)
 
 # ---- tweak-data --------------------------------------------------------------
 ds_pretty <- ds %>%