1+ # ==============================================================================#
2+ # NOTE: This script is written such that it is run from 'top' to 'bottom'
3+ # or programmatically via the Terminal.
4+ # ('R CMD BATCH --vanilla <script.R>'.)
5+ # Please do not jump around when running this script.
6+ # ==============================================================================#
7+ # NOTE: You MUST temporarily update tcplQuery() by adding a line at the top of the
8+ # function: print(query).
9+ # This is because the queries will be captured from output and saved as
10+ # part of the mocking data.
11+ # ==============================================================================#
12+ # # r packages
13+ devtools :: load_all()
14+
15+ library(here )
16+ library(dplyr )
17+ library(stringr )
18+ # ---------------------------#
19+ # # code to prepare `mc_test` dataset goes here
20+ # source the user ID, password, host, and database information for connection
21+ # - NOTE: To replicate one will need to save their own 'db_cred.R', including
22+ # the 'userid', 'userpwd', 'host', and DB collection via 'ivtdb'.
23+ source(file = here :: here(" data-raw/db_cred.R" verbose = FALSE )
24+ # connect to the DB
25+ tcplConf(user = userid ,
26+ pass = userpwd ,
27+ host = host ,
28+ db = ivtdb ,
29+ drvr = " MySQL"
30+
31+ # pick endpoints and ids
32+ # load the number of rows and max hitc per aeid
33+ mc5_counts <- tcplQuery(" SELECT DISTINCT aeid,
34+ COUNT( aeid ) as n,
35+ max(hitc) as max_hitc
36+ FROM invitrodb.mc5 GROUP BY aeid" )
37+ # filter to only include where at least one sample is active and n < 10
38+ mc5_counts <- mc5_counts %> % filter(max_hitc > 0.9 & n == 2 )
39+ # pick one aeid
40+ aeid <- selected <- mc5_counts [sample(1 : nrow(mc5_counts ),size = 1 ,replace = FALSE ),aeid ]
41+ # obtain the acid for the example dataset
42+ acid <- tcplLoadAcid(fld = ' aeid' val = aeid )$ acid
43+ # pick one sample/row from each level (lvl 3 contains ids back to lvl 0 and lvl 6 does back to lvl 4)
44+ l3 <- tcplLoadData(lvl = 3 , fld = " acid" val = acid )
45+ l3_sample1 <- l3 [sample(1 : nrow(l3 ),size = 1 ,replace = FALSE )]
46+ l3_sample2 <- l3 [sample(1 : nrow(l3 ),size = 2 ,replace = FALSE )]
47+ l5 <- tcplLoadData(lvl = 5 , fld = " aeid" val = aeid , add.fld = FALSE )
48+ l5_sample1 <- l5 [sample(1 : nrow(l5 ),size = 1 ,replace = FALSE )]
49+ l5_sample2 <- l5 [sample(1 : nrow(l5 ),size = 2 ,replace = FALSE )]
50+ l6 <- tcplLoadData(lvl = 6 , fld = " aeid" val = aeid , add.fld = FALSE )
51+ l6_sample1 <- l6 [sample(1 : nrow(l6 ),size = 1 ,replace = FALSE )]
52+ l6_sample2 <- l6 [sample(1 : nrow(l6 ),size = 2 ,replace = FALSE )]
53+ l7 <- tcplLoadData(lvl = 7 , fld = " aeid" val = aeid , add.fld = FALSE )
54+ l7_sample1 <- l7 [sample(1 : nrow(l7 ),size = 1 ,replace = FALSE )]
55+ l7_sample2 <- l7 [sample(1 : nrow(l7 ),size = 2 ,replace = FALSE )]
56+ # pick compare.val endpoints and ids
57+ # be sure to only allow to choose from endpoints with the same number of samples
58+ mc5_counts <- filter(mc5_counts , n == mc5_counts [aeid == selected ]$ n & aeid != selected )
59+ compare.aeid <- mc5_counts [sample(1 : nrow(mc5_counts ),size = 1 ,replace = FALSE ),aeid ]
60+ compare.l5 <- tcplLoadData(lvl = 5 , fld = " aeid" val = compare.aeid )
61+ compare.l5_sample1 <- compare.l5 [sample(1 : nrow(compare.l5 ),size = 1 ,replace = FALSE )]
62+ compare.l5_sample2 <- compare.l5 [sample(1 : nrow(compare.l5 ),size = 2 ,replace = FALSE )]
63+
64+
65+ get_query_data <- function (lvl , fld , val , compare.val = NULL , add.fld = TRUE , func = " tcplLoadData"
66+ message(compare.val )
67+ if (func == " tcplLoadData"
68+ # IMPORTANT || MUST ADD TEMPORARY LINE TO TCPLQUERY --------------------------
69+ # add temporary line to top of tcplQuery to get the query string: print(query)
70+ query_strings <- capture.output(result <- tcplLoadData(lvl = lvl , fld = fld , val = val , add.fld = add.fld ))
71+ } else if (func == " tcplPlot"
72+ query_strings <- capture.output(result <- tcplPlot(type = " mc" fld = fld ,
73+ val = val , compare.val = compare.val ,
74+ output = " pdf" multi = TRUE , flags = TRUE ,
75+ fileprefix = " temp_tcplPlot"
76+ file.remove(stringr :: str_subset(list.files(), " ^temp_tcplPlot" # clean up
77+ }
78+
79+ query_strings <- unique(gsub(" \\\\ " " \\\" " " \" " " " " \\\\ n" " \\\n " " \\ [1\\ ] " " " query_strings )))))
80+
81+ # use queries to save data
82+ dat <- lapply(query_strings , function (query_string ) {
83+ return (tcplQuery(query_string ))
84+ })
85+ names(dat ) <- query_strings
86+
87+ # also store fld and val in list object for use in test case
88+ dat [fld ] <- val
89+ if (! is.null(compare.val )) dat [sprintf(" compare.%s" fld )] <- compare.val
90+ return (dat )
91+
92+ }
93+
94+
95+ # to add more tests with new/different data to test-tcplLoadData.R, add lines below and run script
96+ mc_test <- list (
97+ tcplConfQuery = tcplQuery(" SHOW VARIABLES LIKE 'max_allowed_packet'"
98+ mc0_by_m0id = get_query_data(lvl = 0 , fld = " m0id" val = l3_sample1 $ m0id ),
99+ mc0_by_acid = get_query_data(lvl = 0 , fld = " acid" val = acid ),
100+ mc1_by_m1id = get_query_data(lvl = 1 , fld = " m1id" val = l3_sample1 $ m1id ),
101+ mc1_by_acid = get_query_data(lvl = 1 , fld = " acid" val = acid ),
102+ mc2_by_m2id = get_query_data(lvl = 2 , fld = " m2id" val = l3_sample1 $ m2id ),
103+ mc2_by_acid = get_query_data(lvl = 2 , fld = " acid" val = acid ),
104+ mc3_by_m3id = get_query_data(lvl = 3 , fld = " m3id" val = l3_sample1 $ m3id ),
105+ mc3_by_aeid = get_query_data(lvl = 3 , fld = " aeid" val = aeid ),
106+ mc4_by_m4id = get_query_data(lvl = 4 , fld = " m4id" val = l5_sample1 $ m4id ),
107+ mc4_by_aeid = get_query_data(lvl = 4 , fld = " aeid" val = aeid , add.fld = FALSE ),
108+ mc5_by_m5id = get_query_data(lvl = 5 , fld = " m5id" val = l5_sample1 $ m5id ),
109+ mc5_by_aeid = get_query_data(lvl = 5 , fld = " aeid" val = aeid , add.fld = FALSE ),
110+ mc6_by_m6id = get_query_data(lvl = 6 , fld = " m6id" val = l6_sample1 $ m6id ),
111+ mc6_by_aeid = get_query_data(lvl = 6 , fld = " aeid" val = aeid ),
112+ mc7_by_m7id = get_query_data(lvl = 7 , fld = " m7id" val = l7_sample1 $ m7id ),
113+ mc7_by_aeid = get_query_data(lvl = 7 , fld = " aeid" val = aeid ),
114+ mcagg_by_aeid = get_query_data(lvl = " agg" fld = " aeid" val = aeid ),
115+ plot_single_m4id = get_query_data(fld = " m4id"
116+ val = l5_sample1 $ m4id ,
117+ func = " tcplPlot"
118+ plot_multiple_m4id = get_query_data(fld = " m4id"
119+ val = list (l5_sample2 $ m4id ),
120+ func = " tcplPlot"
121+ plot_single_aeid = get_query_data(fld = " aeid"
122+ val = aeid ,
123+ func = " tcplPlot"
124+ plot_multiple_aeid = get_query_data(fld = " aeid"
125+ val = list (c(aeid , compare.aeid )),
126+ func = " tcplPlot"
127+ plot_single_spid = get_query_data(fld = c(" spid" " aeid"
128+ val = list (l5_sample1 $ spid , aeid ),
129+ func = " tcplPlot"
130+ plot_multiple_spid = get_query_data(fld = c(" spid" " aeid"
131+ val = list (l5_sample2 $ spid , aeid ),
132+ func = " tcplPlot"
133+ plot_single_m4id_compare = get_query_data(fld = " m4id"
134+ val = l5_sample1 $ m4id ,
135+ compare.val = compare.l5_sample1 $ m4id ,
136+ func = " tcplPlot"
137+ plot_multiple_m4id_compare = get_query_data(fld = " m4id"
138+ val = list (l5_sample2 $ m4id ),
139+ compare.val = list (compare.l5_sample2 $ m4id ),
140+ func = " tcplPlot"
141+ plot_single_aeid_compare = get_query_data(fld = " aeid"
142+ val = aeid ,
143+ compare.val = compare.aeid ,
144+ func = " tcplPlot"
145+ plot_multiple_aeid_compare = get_query_data(fld = " aeid"
146+ val = list (c(aeid , compare.aeid )),
147+ compare.val = list (c(compare.aeid , aeid )),
148+ func = " tcplPlot"
149+ plot_single_spid_compare = get_query_data(fld = c(" spid" " aeid"
150+ val = list (l5_sample1 $ spid , aeid ),
151+ compare.val = list (compare.l5_sample1 $ spid , compare.aeid ),
152+ func = " tcplPlot"
153+ plot_multiple_spid_compare = get_query_data(fld = c(" spid" " aeid"
154+ val = list (l5_sample2 $ spid , aeid ),
155+ compare.val = list (compare.l5_sample2 $ spid , compare.aeid ),
156+ func = " tcplPlot"
157+ )
158+ # ---------------------------#
159+ # # save the data
160+ usethis :: use_data(mc_test , overwrite = TRUE )
161+ # ---------------------------#
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