@@ -40,7 +40,7 @@
@@ -55,26 +55,8 @@
-
-
+
@@ -106,9 +88,9 @@
diff --git a/docs/articles/TroubleshootingApiCalls.html b/docs/articles/TroubleshootingApiCalls.html index b1ee5f83..c286a245 100644 --- a/docs/articles/TroubleshootingApiCalls.html +++ b/docs/articles/TroubleshootingApiCalls.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - - - + + - +- @@ -470,7 +358,7 @@-
Security Database
+Security Database
-2020-02-18
+2020-04-19
Source:vignettes/SecurityDatabase.Rmd@@ -281,161 +263,78 @@SecurityDatabase.Rmd- Combine & groom the credentials.
- Upload to SQL Server (called
-auxiliary_securityhere).+rm(list=ls(all=TRUE)) #Clear the memory for any variables set from any previous runs. - -# ---- load-sources ------------------------------------------------------------ - -# ---- load-packages ----------------------------------------------------------- -if( !require(OuhscMunge) ) - stop('The `OuhscMunge` package needs to be installed with `devtools::install_github("OuhscBbmc/OuhscMunge")`.') - -testit::assert( - "The `OuhscMunge` package should meet a minimal version.", - compareVersion( as.character(packageVersion("OuhscMunge")), "0.1.9.9009") >= 0L -) - -library(magrittr) -requireNamespace("DBI") -requireNamespace("odbc") -requireNamespace("dplyr") -requireNamespace("readr") -requireNamespace("tibble") -requireNamespace("testit") -requireNamespace("checkmate") -requireNamespace("OuhscMunge") # devtools::install_github("OuhscBbmc/OuhscMunge") - - -# ---- declare-globals --------------------------------------------------------- -# This file assume your campus has two REDCap instances. -# Modify each (a) database name, (b) REDCap URL, and (c) DSN name. - -name_production <- "production" -name_dev <- "dev" - -uri_production <- "https://redcap-production.ouhsc.edu/redcap/api/", -uri_dev <- "https://redcap-dev.ouhsc.edu/redcap/api/" - -dsn_production <- "redcap-production" -dsn_dev <- "redcap-dev" -dsn_source <- "auxiliary_security" # The DSN of the token server. - -# The Activity Directory name that should precede each username. -# This should correspond with the result of SQL Server's `SYSTEM_USER` function -# (https://msdn.microsoft.com/en-us/library/ms179930.aspx) -ldap_prefix <- "OUHSC\\" - -#### -# Nothing below this line should need to change, assuming: -# 1. the vignette was followed exactly (https://ouhscbbmc.github.io/REDCapR/articles/SecurityDatabase.html), -# 2. your campus has exactly two REDCap instances. - -# SQL sent to the MySQL database underneath each REDCap instance. -sql <- " - SELECT username, project_id, api_token - FROM redcap_user_rights - WHERE api_token IS NOT NULL -" - -# Update this ad-hoc CSV. Each row should represent one REDCap instance. -ds_url <- tibble::tribble( - ~instance , ~redcap_uri, - name_production , uri_production, - name_dev , uri_dev -) - -# Remove variables that aren't used below. -rm(uri_production, uri_dev) - - -# ---- load-data --------------------------------------------------------------- - -# Load the credentials from the first/production REDCap instance. -cnn_production <- DBI::dbConnect(odbc::odbc(), dsn=dsn_production) -ds_production <- DBI::dbGetQuery(cnn_production, sql) -DBI::dbDisconnect(cnn_production); rm(cnn_production, dsn_production) - -# Load the credentials from the second/dev REDCap instance. -cnn_dev <- DBI::dbConnect(odbc::odbc(), dsn=dsn_dev) -ds_dev <- DBI::dbGetQuery(cnn_dev, sql) -DBI::dbDisconnect(cnn_dev); rm(cnn_dev, dsn_dev) - -rm(sql) - -# Assert these are valid datasets and contain at least 5 rows. -# Adjust '5' to smaller value if necessary. It's just to catch blatant retrieval problems. -checkmate::assert_data_frame(ds_production, min.rows=5) -checkmate::assert_data_frame(ds_dev , min.rows=5) - - -# ---- tweak-data -------------------------------------------------------------- - -# Label each instance, so they're distinguishable later. -ds_production$instance <- name_production -ds_dev$instance <- name_dev - -# Stack the token collection from each instance. Then prefix the username and include the URL of each instance. -ds <- - ds_production %>% - dplyr::union(ds_dev) %>% # Remove union if the dev instance isn't included. - tibble::as_tibble() %>% - dplyr::select( - username = username, - project_id = project_id, - instance = instance, - token = api_token - ) %>% - dplyr::mutate( - username = paste0(ldap_prefix, username), # Qualify for the Active Directory. - ) %>% - dplyr::left_join( ds_url, by="instance") %>% # Include the instance URL. - dplyr::arrange(instance, project_id, username) %>% - tibble::rowid_to_column("id") # For the sake of a clustered primary key. - -rm(ds_production, ds_dev, ds_url) -rm(name_production, name_dev) -rm(ldap_prefix) - - -# ---- verify-values ----------------------------------------------------------- - -# Assert that the dataset is well-behaved. -# OuhscMunge::verify_value_headstart(ds) -checkmate::assert_integer( ds$id , any.missing=FALSE, lower=1, upper=.Machine$integer.max, unique=TRUE) -checkmate::assert_character(ds$username , any.missing=FALSE, pattern="^.{1,255}$" ) -checkmate::assert_integer( ds$project_id , any.missing=FALSE, lower=1, upper=.Machine$integer.max ) -checkmate::assert_character(ds$token , any.missing=FALSE, pattern="^[A-Z0-9]{32}$" , unique=TRUE) -checkmate::assert_character(ds$instance , any.missing=FALSE, pattern="^.{1,255}$" ) -checkmate::assert_character(ds$redcap_uri , any.missing=FALSE, pattern="^.{1,255}$" ) - -testit::assert( - "The `username` x `project_id` x `instance` must be unique.", - sum(duplicated(paste0(ds$username, "-", ds$project_id, "-", ds$instance))) == 0L -) - -testit::assert("At least 10 tokens should be ready to write." , 10L <= nrow(ds)) - - -# ---- specify-columns-to-upload ----------------------------------------------- - -# Dictate the exact columns and order that will be uploaded. -columns_to_write <- c("id", "username", "project_id", "instance", "token", "redcap_uri") -ds_slim <- ds[, columns_to_write] -rm(columns_to_write) - - -# ---- upload-to-db ------------------------------------------------------------------ - -OuhscMunge::upload_sqls_odbc( - d = ds_slim, - schema_name = "redcap_private", - table_name = "tbl_credential", - dsn_name = dsn_source, - create_table = FALSE, - clear_table = TRUE, - transaction = TRUE, - verbose = TRUE -) -# Uploading 252 tokens takes 0.004 minutes.rm(list=ls(all=TRUE)) #Clear the memory for any variables set from any previous runs. + +# ---- load-sources ------------------------------------------------------------ + +# ---- load-packages ----------------------------------------------------------- +if (!require(OuhscMunge)) + stop('The `OuhscMunge` package needs to be installed with `remotes::install_github("OuhscBbmc/OuhscMunge")`.') + +testit::assert( + "The `OuhscMunge` package should meet a minimal version.", + compareVersion( as.character(packageVersion("OuhscMunge")), "0.1.9.9009") >= 0L +) + +library(magrittr) +requireNamespace("DBI") +requireNamespace("odbc") +requireNamespace("dplyr") +requireNamespace("readr") +requireNamespace("tibble") +requireNamespace("testit") +requireNamespace("checkmate") +requireNamespace("OuhscMunge") # remotes::install_github("OuhscBbmc/OuhscMunge") + + +# ---- declare-globals --------------------------------------------------------- +# This file assume your campus has two REDCap instances. +# Modify each (a) database name, (b) REDCap URL, and (c) DSN name. + +name_production % + dplyr::union(ds_dev) %>% # Remove union if the dev instance isn't included. + tibble::as_tibble() %>% + dplyr::select( + username = username, + project_id = project_id, + instance = instance, + token = api_token + ) %>% + dplyr::mutate( + username = paste0(ldap_prefix, username), # Qualify for the Active Directory. + ) %>% + dplyr::left_join( ds_url, by="instance") %>% # Include the instance URL. + dplyr::arrange(instance, project_id, username) %>% + tibble::rowid_to_column("id") # For the sake of a clustered primary key. + +rm(ds_production, ds_dev, ds_url) +rm(name_production, name_dev) +rm(ldap_prefix) + + +# ---- verify-values ----------------------------------------------------------- + +# Assert that the dataset is well-behaved. +# OuhscMunge::verify_value_headstart(ds) +checkmate::assert_integer( ds$id , any.missing=FALSE, lower=1, upper=.Machine$integer.max, unique=TRUE) +checkmate::assert_character(ds$username , any.missing=FALSE, pattern="^.{1,255}$" ) +checkmate::assert_integer( ds$project_id , any.missing=FALSE, lower=1, upper=.Machine$integer.max ) +checkmate::assert_character(ds$token , any.missing=FALSE, pattern="^[A-Z0-9]{32}$" , unique=TRUE) +checkmate::assert_character(ds$instance , any.missing=FALSE, pattern="^.{1,255}$" ) +checkmate::assert_character(ds$redcap_uri , any.missing=FALSE, pattern="^.{1,255}$" ) + +testit::assert( + "The `username` x `project_id` x `instance` must be unique.", + sum(duplicated(paste0(ds$username, "-", ds$project_id, "-", ds$instance))) == 0L +) + +testit::assert("At least 10 tokens should be ready to write." , 10L <= nrow(ds)) + + +# ---- specify-columns-to-upload ----------------------------------------------- + +# Dictate the exact columns and order that will be uploaded. +columns_to_write@@ -444,22 +343,11 @@
diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 00000000..5a859415 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 00000000..1cdd573b --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $(''); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('diff --git a/docs/authors.html b/docs/authors.html index 3364d87c..32ba9174 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - + @@ -202,7 +191,7 @@@@ -97,26 +100,8 @@ - Reference
-- - - Articles - - - - +
- + Articles
- Changelog @@ -124,7 +109,7 @@
-
-
+
@@ -153,7 +138,7 @@
Authors
Authors
');
+ $li.append($a);
+ return $li;
+ },
+
+ generateNavItem: function(headingEl) {
+ var anchor = this.generateAnchor(headingEl);
+ var $heading = $(headingEl);
+ var text = $heading.data('toc-text') || $heading.text();
+ return this.generateNavEl(anchor, text);
+ },
+
+ // Find the first heading level (` - Reference -
- - - Articles - - - - + Articles
-
Changelog
@@ -87,7 +69,7 @@
-
-
+
@@ -114,47 +96,47 @@
-
We’ve been using R with REDCap’s API since 2012 and have developed
-REDCapR. Before encapsulating these functions in a package, we were replicating 50+ lines of code to contact REDCap and robustly transform the returned csv into an Rdata.frame; it took twice that much to implement batching. All this can be done in one call toredcap_read():+ds <- redcap_read(redcap_uri=uri, token=token)$dataWeâve been using R with REDCapâs API since 2012 and have developed
+REDCapR. Before encapsulating these functions in a package, we were replicating 50+ lines of code to contact REDCap and robustly transform the returned csv into an Rdata.frame; it took twice that much to implement batching. All this can be done in one call toredcap_read():ds <- redcap_read(redcap_uri=uri, token=token)$data
The
-redcap_read()function also accepts values for subsetting/filtering the records and fields. Here are two examples; the first selects only a portion of the rows, while the second selects only a portion of the columns. Documentation for the additional 20+ functions are found at ouhscbbmc.github.io/REDCapR/reference.-# Return only records with IDs of 1 and 4 -desired_records <- c(1, 4) -ds_some_rows <- redcap_read( - redcap_uri = uri, - token = token, - records = desired_records -)$data - -# Return only the fields record_id, name_first, and age -desired_fields <- c("record_id", "name_first", "age") -ds_some_fields <- redcap_read( - redcap_uri = uri, - token = token, - fields = desired_fields -)$dataThe
-REDCapRpackage includes the SSL certificate retrieved byhttr::find_cert_bundle(). Your REDCap server’s identity is always verified, unless the setting is overridden (alternative certificates can also be provided).To keep our maintenance efforts manageable, the package implements only the REDCap API functions that have been requested. If there’s a feature that would help your projects, please tell us in a new issue in REDCapR’s GitHub repository. A troubleshooting document helps diagnose issues with the API.
++# Return only records with IDs of 1 and 4 +desired_records <- c(1, 4) +ds_some_rows <- redcap_read( + redcap_uri = uri, + token = token, + records = desired_records +)$data + +# Return only the fields record_id, name_first, and age +desired_fields <- c("record_id", "name_first", "age") +ds_some_fields <- redcap_read( + redcap_uri = uri, + token = token, + fields = desired_fields +)$data
The
+REDCapRpackage includes the SSL certificate retrieved byhttr::find_cert_bundle(). Your REDCap serverâs identity is always verified, unless the setting is overridden (alternative certificates can also be provided).To keep our maintenance efforts manageable, the package implements only the REDCap API functions that have been requested. If thereâs a feature that would help your projects, please tell us in a new issue in REDCapRâs GitHub repository. A troubleshooting document helps diagnose issues with the API.
Installation and Documentation
The release version can be installed from CRAN.
-+install.packages("REDCapR")install.packages("REDCapR")
The development version can be installed from GitHub after installing the
-remotespackage.+install.packages("remotes") # Run this line if the 'remotes' package isn't installed already. -remotes::install_github(repo="OuhscBbmc/REDCapR")install.packages("remotes") # Run this line if the 'remotes' package isn't installed already. +remotes::install_github(repo="OuhscBbmc/REDCapR")
The ouhscbbmc.github.io/REDCapR site describes the package functions, and includes documents involving basic operations, advanced operations, token security, and troubleshooting.
Also checkout the other packages that exist for communicating with REDCap, which are listed in the REDCap Tools directory.
Collaborative Development
-We encourage input and collaboration. If you’re familiar with GitHub and R packages, feel free to submit a pull request. If you’d like to report a bug or make a suggestion, please create a GitHub issue; issues are a usually a good place to ask public questions too. However, feel free to email Will (wibeasley@hotmail.com). Please note that this project is released with a Contributor Code of Conduct; by participating in this project you agree to abide by its terms. We have some starting material described in the
-./documentation-for-developers/directory.We’d like to thank the following developers for their advice and code contributions: Benjamin Nutter, Rollie Parrish, Scott Burns, John Aponte, Andrew Peters, and Hao Zhu.
+We encourage input and collaboration. If youâre familiar with GitHub and R packages, feel free to submit a pull request. If youâd like to report a bug or make a suggestion, please create a GitHub issue; issues are a usually a good place to ask public questions too. However, feel free to email Will (wibeasley@hotmail.com). Please note that this project is released with a Contributor Code of Conduct; by participating in this project you agree to abide by its terms. We have some starting material described in the
+./documentation-for-developers/directory.Weâd like to thank the following developers for their advice and code contributions: Benjamin Nutter, Rollie Parrish, Scott Burns, John Aponte, Andrew Peters, and Hao Zhu.
Funders
-Much of this package has been developed to support the needs of the following projects. We appreciate the support. (So far) the primary developers of REDCapR are the external evaluators for Oklahoma’s MIECHV program. See the preliminary CQI reports (many of which use REDCapR) at http://ouhscbbmc.github.io/MReportingPublic/.
+Much of this package has been developed to support the needs of the following projects. We appreciate the support. (So far) the primary developers of REDCapR are the external evaluators for Oklahomaâs MIECHV program. See the preliminary CQI reports (many of which use REDCapR) at http://ouhscbbmc.github.io/MReportingPublic/.
- OUHSC CCAN Independent Evaluation of the State of Oklahoma Competitive Maternal, Infant, and Early Childhood Home Visiting (MIECHV) Project. HRSA/ACF D89MC23154. David Bard, PI, OUHSC; 2011-2015. @@ -243,13 +225,13 @@
-
-
+
@@ -114,47 +96,47 @@
-
- Reference -
- - - Articles - - - - +
- + Articles
- Changelog @@ -125,7 +110,7 @@
- Reference -
- - - Articles - - - - +
- + Articles
- Changelog @@ -131,7 +116,7 @@
- Reference -
- - - Articles - - - - +
- + Articles
- Changelog @@ -124,7 +109,7 @@
`, then ``, etc.) that has more than one element. Defaults to 1 (for ``).
+ getTopLevel: function($scope) {
+ for (var i = 1; i <= 6; i++) {
+ var $headings = this.findOrFilter($scope, 'h' + i);
+ if ($headings.length > 1) {
+ return i;
+ }
+ }
+
+ return 1;
+ },
+
+ // returns the elements for the top level, and the next below it
+ getHeadings: function($scope, topLevel) {
+ var topSelector = 'h' + topLevel;
+
+ var secondaryLevel = topLevel + 1;
+ var secondarySelector = 'h' + secondaryLevel;
+
+ return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+ },
+
+ getNavLevel: function(el) {
+ return parseInt(el.tagName.charAt(1), 10);
+ },
+
+ populateNav: function($topContext, topLevel, $headings) {
+ var $context = $topContext;
+ var $prevNav;
+
+ var helpers = this;
+ $headings.each(function(i, el) {
+ var $newNav = helpers.generateNavItem(el);
+ var navLevel = helpers.getNavLevel(el);
+
+ // determine the proper $context
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+ } else if ($prevNav && $context === $topContext) {
+ // create a new level of the tree and switch to it
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+ } // else use the current $context
+
+ $context.append($newNav);
+
+ $prevNav = $newNav;
+ });
+ },
+
+ parseOps: function(arg) {
+ var opts;
+ if (arg.jquery) {
+ opts = {
+ $nav: arg
+ };
+ } else {
+ opts = arg;
+ }
+ opts.$scope = opts.$scope || $(document.body);
+ return opts;
+ }
+ },
+
+ // accepts a jQuery object, or an options object
+ init: function(opts) {
+ opts = this.helpers.parseOps(opts);
+
+ // ensure that the data attribute is in place for styling
+ opts.$nav.attr('data-toggle', 'toc');
+
+ var $topContext = this.helpers.createChildNavList(opts.$nav);
+ var topLevel = this.helpers.getTopLevel(opts.$scope);
+ var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+ this.helpers.populateNav($topContext, topLevel, $headings);
+ }
+ };
+
+ $(function() {
+ $('nav[data-toggle="toc"]').each(function(i, el) {
+ var $nav = $(el);
+ Toc.init($nav);
+ });
+ });
+})();
diff --git a/docs/docsearch.json b/docs/docsearch.json
index 3df6fce9..cdc94736 100644
--- a/docs/docsearch.json
+++ b/docs/docsearch.json
@@ -74,7 +74,7 @@
"selector": ".contents h2, .contents h3",
"default_value": "Context"
},
- "text": ".contents p, .contents li, .tempate-article .contents .pre"
+ "text": ".contents p, .contents li"
}
},
"selectors_exclude": [
diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png
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index a170181f..ed2b7a9b 100644
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multiple, smaller REDCap calls. The goal is to (1) reduce the chance of
time-outs, and (2) introduce little breaks between batches so that the
server isn't continually tied up." />
-
-
+
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+
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 95576147..b561a209 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
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+
@@ -42,15 +46,14 @@
-
+
-
-
+
@@ -68,7 +71,7 @@
-
+
@@ -97,26 +100,8 @@
`).
+ getTopLevel: function($scope) {
+ for (var i = 1; i <= 6; i++) {
+ var $headings = this.findOrFilter($scope, 'h' + i);
+ if ($headings.length > 1) {
+ return i;
+ }
+ }
+
+ return 1;
+ },
+
+ // returns the elements for the top level, and the next below it
+ getHeadings: function($scope, topLevel) {
+ var topSelector = 'h' + topLevel;
+
+ var secondaryLevel = topLevel + 1;
+ var secondarySelector = 'h' + secondaryLevel;
+
+ return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+ },
+
+ getNavLevel: function(el) {
+ return parseInt(el.tagName.charAt(1), 10);
+ },
+
+ populateNav: function($topContext, topLevel, $headings) {
+ var $context = $topContext;
+ var $prevNav;
+
+ var helpers = this;
+ $headings.each(function(i, el) {
+ var $newNav = helpers.generateNavItem(el);
+ var navLevel = helpers.getNavLevel(el);
+
+ // determine the proper $context
+ if (navLevel === topLevel) {
+ // use top level
+ $context = $topContext;
+ } else if ($prevNav && $context === $topContext) {
+ // create a new level of the tree and switch to it
+ $context = helpers.createChildNavList($prevNav);
+ } // else use the current $context
+
+ $context.append($newNav);
+
+ $prevNav = $newNav;
+ });
+ },
+
+ parseOps: function(arg) {
+ var opts;
+ if (arg.jquery) {
+ opts = {
+ $nav: arg
+ };
+ } else {
+ opts = arg;
+ }
+ opts.$scope = opts.$scope || $(document.body);
+ return opts;
+ }
+ },
+
+ // accepts a jQuery object, or an options object
+ init: function(opts) {
+ opts = this.helpers.parseOps(opts);
+
+ // ensure that the data attribute is in place for styling
+ opts.$nav.attr('data-toggle', 'toc');
+
+ var $topContext = this.helpers.createChildNavList(opts.$nav);
+ var topLevel = this.helpers.getTopLevel(opts.$scope);
+ var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+ this.helpers.populateNav($topContext, topLevel, $headings);
+ }
+ };
+
+ $(function() {
+ $('nav[data-toggle="toc"]').each(function(i, el) {
+ var $nav = $(el);
+ Toc.init($nav);
+ });
+ });
+})();
diff --git a/docs/docsearch.json b/docs/docsearch.json
index 3df6fce9..cdc94736 100644
--- a/docs/docsearch.json
+++ b/docs/docsearch.json
@@ -74,7 +74,7 @@
"selector": ".contents h2, .contents h3",
"default_value": "Context"
},
- "text": ".contents p, .contents li, .tempate-article .contents .pre"
+ "text": ".contents p, .contents li"
}
},
"selectors_exclude": [
diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png
new file mode 100644
index 00000000..20d59577
Binary files /dev/null and b/docs/favicon-16x16.png differ
diff --git a/docs/favicon-32x32.png b/docs/favicon-32x32.png
new file mode 100644
index 00000000..02f147c0
Binary files /dev/null and b/docs/favicon-32x32.png differ
diff --git a/docs/favicon.ico b/docs/favicon.ico
new file mode 100644
index 00000000..d334a299
Binary files /dev/null and b/docs/favicon.ico differ
diff --git a/docs/index.html b/docs/index.html
index 5eddc9a1..28ed8634 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -12,11 +12,12 @@
-
-
-
-
-
+
+
+
+
+
+
-
-
+
-
+
@@ -45,7 +45,7 @@
@@ -60,26 +60,8 @@
-
diff --git a/docs/reference/constant.html b/docs/reference/constant.html
index 9cb46b71..4682ba7d 100644
--- a/docs/reference/constant.html
+++ b/docs/reference/constant.html
@@ -17,23 +17,27 @@
-
+
-
+
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -42,7 +46,7 @@
-
+
@@ -50,8 +54,7 @@
-
-
+
@@ -69,7 +72,7 @@
-
+
@@ -98,26 +101,8 @@
diff --git a/docs/reference/create_batch_glossary.html b/docs/reference/create_batch_glossary.html
index a170181f..ed2b7a9b 100644
--- a/docs/reference/create_batch_glossary.html
+++ b/docs/reference/create_batch_glossary.html
@@ -18,23 +18,27 @@
-
+
-
+
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -43,7 +47,7 @@
-
+
@@ -56,8 +60,7 @@
multiple, smaller REDCap calls. The goal is to (1) reduce the chance of
time-outs, and (2) introduce little breaks between batches so that the
server isn't continually tied up." />
-
-
+
@@ -75,7 +78,7 @@
-
+
@@ -104,26 +107,8 @@
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 95576147..b561a209 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,23 +17,27 @@
-
+
-
+
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -42,15 +46,14 @@
-
+
-
-
+
@@ -68,7 +71,7 @@
-
+
@@ -97,26 +100,8 @@
@@ -45,7 +45,7 @@
@@ -60,26 +60,8 @@
