Merge pull request #33 from Sage-Bionetworks/develop

Develop

Author: Kenneth Daily

DESCRIPTION

@@ -1,12 +1,14 @@
 Package: synapseusagereports
 Title: Generate a Reports of Synapse Project Usage
-Version: 0.3-alpha
+Version: 0.3
 Authors@R: person("Kenneth", "Daily", email = "[email protected]", role = c("aut", "cre"))
 Description: Generate a RMarkdown report of Synapse Project usage, including users, page views and downloads.
 Depends: R (>= 3.3.1)
 License: MIT
 Encoding: UTF-8
 LazyData: true
+URL: https://github.com/Sage-Bionetworks/synapseusagereports
+BugReports: https://github.com/Sage-Bionetworks/synapseusagereports/issues
 RoxygenNote: 6.1.0
 Imports:
   dplyr,
@@ -18,6 +20,6 @@ Imports:
   optparse,
   readr,
   testthat,
-  synapseClient
-Remotes:
-  Sage-Bionetworks/rSynapseClient
+  synapser
+Additional_repositories:
+  https://sage-bionetworks.github.io/ran

R/lib.R

@@ -136,36 +136,25 @@ getData <- function(con, qTemplate, projectId, timestampBreaksDf) {
 #' @export
 getTeamMemberDF <- function(teamId) {
 
-  totalNumberOfResults <- 1000
-  offset <- 0
-  limit <- 50
-  userListREST <- list()
+  foo <- synapser::synGetTeamMembers(teamId)
+  foo <- foo$asList()
 
-  while(offset<totalNumberOfResults) {
-    result <- synapseClient::synRestGET(sprintf("/teamMembers/%s?limit=%s&offset=%s", teamId, limit, offset))
-
-    totalNumberOfResults <- result$totalNumberOfResults
-
-    userListREST <- c(userListREST, result$results)
-
-    offset <- offset + limit
-  }
+  foo %>% {
+      tibble(teamId=purrr::map_chr(., 'teamId'),
+             userId=purrr::map_chr(., c("member", "ownerId")))
+    }
 
-  userList <- plyr::ldply(userListREST,
-                          function(x) data.frame(userId=as.character(x$member$ownerId),
-                                                 teamId=as.character(x$teamId)))
-  userList
 }
 
 #' @export
 aclToMemberList <- function(acl) {
-  aclMemberList <- plyr::ldply(acl@resourceAccess@content,
-                               function(x) data.frame(principalId=as.character(x@principalId),
-                                                      teamId=acl@id))
+  aclMemberList <- plyr::ldply(acl$resourceAccess,
+                               function(x) data.frame(principalId=as.character(x$principalId),
+                                                      teamId=acl$id))
 
   accessUsers <- plyr::llply(chunk(aclMemberList$principalId, 50),
-                             function(x) synapseClient::synRestGET(sprintf("/userGroupHeaders/batch?ids=%s",
-                                                                           paste(x, collapse=",")))$children)
+                             function(x) synapser::synRestGET(sprintf("/userGroupHeaders/batch?ids=%s",
+                                                                      paste(x, collapse=",")))$children)
 
   userGroupHeaders <- do.call(c, accessUsers)
 
@@ -174,11 +163,9 @@ aclToMemberList <- function(acl) {
 }
 
 #' @export
-aclToUserList <- function(synId) {
-  acl <- synapseClient::synGetEntityACL(synId)
-
+aclToUserList <- function(acl) {
   aclMemberList <- aclToMemberList(acl)
-  aclMemberList$teamId <- synId
+  aclMemberList$teamId <- acl$id
 
   userList <- plyr::ldply(aclMemberList$ownerId, getTeamMemberDF)
 
@@ -194,7 +181,8 @@ aclToUserList <- function(synId) {
 processAclUserList <- function(projectId, aclTeamOrder) {
   # Get users at project level and select the team
   # they are on dependent on the ordering in aclTeamOrder
-  aclUserList <- aclToUserList(paste0("syn", projectId))
+  acl <- synapser::synRestGET(sprintf('/entity/%s/acl', paste0("syn", projectId)))
+  aclUserList <- aclToUserList(acl)
   aclUserList$teamId <- factor(aclUserList$teamId,
                                levels=aclTeamOrder,
                                ordered=TRUE)
@@ -235,8 +223,8 @@ getQueryUserProfiles <- function(queryData, useTeamGrouping, aclUserList) {
 
 
   accessUsers <- plyr::llply(chunk(unique(queryData$userId), 50),
-                             function(x) synapseClient::synRestGET(sprintf("/userGroupHeaders/batch?ids=%s",
-                                                                           paste(x, collapse=",")))$children)
+                             function(x) synapser::synRestGET(sprintf("/userGroupHeaders/batch?ids=%s",
+                                                                      paste(x, collapse=",")))$children)
 
   accessUsersChildren <- do.call(c, accessUsers)
 
@@ -258,18 +246,18 @@ getQueryUserProfiles <- function(queryData, useTeamGrouping, aclUserList) {
   allUsers$teamId[allUsers$userId == "273950"] <- "Anonymous"
 
   if (useTeamGrouping) {
-    teamInfo <- plyr::ddply(allUsers %>%
-                              dplyr::filter(teamId != "Registered Synapse User",
-                                            teamId != "Anonymous",
-                                            !startsWith(as.character(allUsers$teamId),
-                                                        "syn")) %>%
-                              dplyr::select(teamId) %>% dplyr::distinct(),
-                      plyr::.(teamId),
-                      function(x) {
-                        tmp <- synapseClient::synRestGET(sprintf("/team/%s", x$teamId));
-                        data.frame(teamId=x$teamId, teamName=tmp$name)
-                      }
-    )
+    tmp_all_users <- allUsers %>%
+      dplyr::filter(teamId != "Registered Synapse User",
+                    teamId != "Anonymous") %>%
+      dplyr::select(teamId) %>% dplyr::distinct(.keep_all=TRUE)
+
+    teamInfo <- lapply(as.list(as.character(tmp_all_users$teamId)),
+                       function (x) synapser::synGetTeam(x)) %>%
+                       {
+                         tibble(teamId=tmp_all_users$teamId,
+                                teamName=purrr::map_chr(., 'name'))
+                       }
+
     if (nrow(teamInfo) > 0) {
       allUsers <- dplyr::left_join(allUsers, teamInfo, by="teamId")
     } else {

inst/scripts/render_report.R

@@ -1,6 +1,6 @@
 #!/usr/bin/env Rscript
 
-suppressPackageStartupMessages(library(synapseClient))
+suppressPackageStartupMessages(library(synapser))
 suppressPackageStartupMessages(library(optparse))
 suppressPackageStartupMessages(library(synapseusagereports))
 
@@ -12,7 +12,11 @@ option_list <- list(
   make_option(c("--acl_team_order"), type = "character",
               help = "comma separated list of teams in ACL.",
               dest = "acl_team_order",
-              default = '')
+              default = ''),
+  make_option(c("--synapse_config"), type = "character",
+              help = "Synapse configuration file.",
+              dest = "synapse_config",
+              default="~/.synapseConfig")
 )
 
 arguments <- parse_args(OptionParser(usage = "%prog [options] file",
@@ -22,7 +26,7 @@ arguments <- parse_args(OptionParser(usage = "%prog [options] file",
 opts <- arguments$options
 data_file <- arguments$args
 
-synapseLogin()
+login <- capture.output(synLogin())
 
 render_report(project_id = opts$project_id,
               acl_team_order = opts$acl_team_order,

inst/scripts/report_data_query.R

@@ -2,7 +2,6 @@
 
 suppressPackageStartupMessages(library(dplyr))
 suppressPackageStartupMessages(library(readr))
-suppressPackageStartupMessages(library(synapseClient))
 suppressPackageStartupMessages(library(RMySQL))
 suppressPackageStartupMessages(library(yaml))
 suppressPackageStartupMessages(library(testthat))
@@ -37,8 +36,6 @@ if (n_months_from_today > 6) {
   message("Your start date is more than 6 months ago. The results of your queries may be incorrect.")
 }
 
-foo <- suppressMessages(synapseLogin())
-
 config <- yaml.load_file(opts$config_file)
 
 con <- dbConnect(MySQL(),

inst/templates/report.Rmd

@@ -10,13 +10,13 @@ params:
 
 ```{r libs, echo=FALSE, warning=FALSE, message=FALSE}
 library(dplyr)
-library(synapseClient)
+library(synapser)
 library(RMySQL)
 library(yaml)
 library(lubridate)
 library(synapseusagereports)
 
-synapseLogin()
+foo <- capture.output(synLogin())
 
 options(xtable.type="html")
 
@@ -34,21 +34,21 @@ knitr::opts_chunk$set(
 int_project_id <- gsub("syn", "", params$projectId)
 proj <- synGet(params$projectId)
 
-if (is.na(params$aclTeamOrder)) {
+if (is.na(params$aclTeamOrder) | params$aclTeamOrder == '') {
   useTeamGrouping <- FALSE
 } else {
   useTeamGrouping <- TRUE
   aclTeamOrder <- stringr::str_split(params$aclTeamOrder, 
-                                   pattern=',', 
-                                   simplify = FALSE)[[1]]
+                                     pattern=',', 
+                                     simplify = FALSE)[[1]]
 }
 
 
 queryData <- readr::read_csv(params$queryDataFile) %>% 
   mutate(userId=as.character(userId))
 ```
 
-### Activity on Synapse project `r proj@properties$name` (`r params$projectId`) from `r min(queryData$date)` to `r max(queryData$date)`.
+### Activity on Synapse project `r proj$properties$name` (`r params$projectId`) from `r min(queryData$date)` to `r max(queryData$date)`.
 
 ```{r users}
 if (useTeamGrouping) {

synapseProjectUsageStatistics.Rproj synapseusagereports.RprojsynapseProjectUsageStatistics.Rproj renamed to synapseusagereports.Rproj

@@ -0,0 +1,4 @@
+library(testthat)
+library(synapseusagereports)
+
+test_check("synapseusagereports")

tests/testthat.R

@@ -0,0 +1,8 @@
+context("test-lib")
+
+test_acl_json <- '{"id":"syn12509922","resourceAccess":[{"principalId":3323072,"accessType":["DELETE","DOWNLOAD","READ","CHANGE_SETTINGS","UPDATE","MODERATE","CREATE","CHANGE_PERMISSIONS"]}],"etag":"19a13eb7-8d24-4d26-b9d7-b8fa97b8ce92","creationDate":"2018-06-11T18:41:45.244Z","uri":"/entity/syn12509922/acl"}'
+test_acl <- jsonlite::fromJSON(test_acl_json, simplifyVector = FALSE)
+
+test_that("acl to user list", {
+  expect_equal(aclToMemberList(test_acl), )
+})