From 7b8751d684da8b3243d641d9fac7add42471110f Mon Sep 17 00:00:00 2001
From: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>
Date: Mon, 5 Nov 2018 13:58:46 -0800
Subject: [PATCH 01/12] fixed link to agronomic metadata tutorial

---
 traits/01-web-access.Rmd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/traits/01-web-access.Rmd b/traits/01-web-access.Rmd
index e0b4872..f3dc7cb 100644
--- a/traits/01-web-access.Rmd
+++ b/traits/01-web-access.Rmd
@@ -1,4 +1,4 @@
----
+6---
 title: "Accessing Trait Data Via the BETYdb Web Interface"
 author: "David LeBauer"
 date: "`r Sys.Date()`"
@@ -32,4 +32,4 @@ On the Welcome page there is a search option for trait and yield data. This tool
   * if you want all of the data, including data that has not gone through QA/QC, make sure to check the 'include unchecked records' option
 * in the upper right, you will see a button that will allow you to download the search results as a CSV file. Click it. Open the file in a text editor or spreadsheet program and review its contents.
 
-Note that the web interface only provides a core set of data and limited meta-data. To access all of the data within BETYdb, it is necessary to search and merge multiple tables. More complex queries, such as those in the [Agronomic metadata](../traits/04-agronomic-metadata.Rmd).
+Note that the web interface only provides a core set of data and limited meta-data. To access all of the data within BETYdb, it is necessary to search and merge multiple tables. More complex queries, such as those in the [Agronomic metadata](../traits/06-agronomic-metadata.Rmd).

From 6872cc78fb04b0f043187a1222345a4a5995face Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Tue, 6 Nov 2018 13:34:50 -0800
Subject: [PATCH 02/12] Updated tutorial. Added a summary showing the 3 ways to
 access API data.

---
 traits/02-betydb-api-access.Rmd | 219 ++++++++++++++++----------------
 1 file changed, 112 insertions(+), 107 deletions(-)

diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index 8d90266..c579098 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -1,107 +1,112 @@
----
-title: "Accessing Trait Data Via the BETYdb API"
-author: "David LeBauer"
-date: "11/7/2017"
-output: html_document
----
-
-
-## Using URLs to construct Queries
-
-The first step toward reproducible pipelines is to automate the process of searching the database and returning results. This is one of the key roles of an Application programming interface, or 'API'. You can learn to use the API in less than 20 minutes, starting now. 
-
-### What is an API?
-
-An API is an 'Application Programming Interface'. An API is a way that you and your software can connect to and access data. 
-
-All of our databases have web interfaces for humans to browse as well as APIs that are constructed as URLs. 
-
-
-### Using Your API key to Connect
-
-An API key is like a password. It allows you to access data, and should be kept private. 
-Therefore, we are not going to put it in code that we share. The one exception is the key 9999999999999999999999999999999999999999 that will allow you to access metadata tables (all tables except _traits_ and _yields_). It will also allow you to access all of the simulated data in the terraref.ncsa.illinois.edu/bety-test database.
-
-A common way of handling private API keys is to place it in a text file in your home directory. 
-Don't put it in a project directory where it might be inadvertently shared.
-
-Here is how to find and save your API key:
-
-* click file --> new --> text file
-* copy the api key that was sent when you registered into the file
-* file --> save as '~/.betykey'
-
-For the public key, you can call this file `~/.betykey_public`. 
-
-### Components of a URL query
-
-
-* base url: `terraref.ncsa.illinois.edu/bety`
-* path to the api: `/api/beta`
-* api endpoint: `/search` or `traits` or `sites`. For BETYdb, these are the names of database tables. 
-* Query parameters: `genus=Sorghum`
-* Authentication: `key=9999999999999999999999999999999999999999` is the public key for the TERRA REF traits database. 
-
-
-### Constructing a URL query
-
-First, lets construct a query by putting together a URL.
-
-1. start with the database url: `terraref.ncsa.illinois.edu/bety`
-  * this url brings you to the home page
-2. Add the path to the API, `/api/beta`
-  * now we have terraref.ncsa.illinois.edu/bety/api/beta, which points to the API documentation
-3. Add the name of the table you want to query. Lets start with `variables`
-  * terraref.ncsa.illinois.edu/bety/api/beta/variables
-4. add query terms by appending a `?` and combining with `&`, for example:
-  * `key=9999999999999999999999999999999999999999`
-  * `type=trait` where the variable type is 'trait'
-  * `name=~height` where the variable name contains 'height'
-5. This is your complete query:
-  * `terraref.ncsa.illinois.edu/bety/api/beta/variables?type=trait&name=~height&key=9999999999999999999999999999999999999999`
-  * it will query all variables that are type trait and have 'height' in the name
-  * Does it return the expected values?
-  
-
-#### Your Turn
-
-> What will the URL https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999 return?
-
-> write a URL that will query the database for sites with "Field Scanner" in the name field. Hint: combine two terms with a `+` as in `Field+Scanner`
-
-What do you see? Do you think that this is all of the records? What happens if you add `&limit=none`? 
-
-### Our first Query 
-
-#### Shell
-
-```sh
-wget -O sorghum.json \\ # -O names the output file 
-   "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=999999999999999999999999999999999999
-9999"
-```
-
-If you want to write the query without exposing the key in plain text, you can construct it thus:
-
-```sh
-wget -O sorghum.json \\
-    "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=`cat ~/.betykey_public`"
-```
-
-> What does `cat ~/.betykey_public` do?
-
-> How can you look at the files?
-
-
-#### R - using the jsonlite package
-
-```{r text-api}
-sorghum.json <- readLines(
-  paste0("https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=", 
-         readLines('~/.betykey')))
-
-## print(sorghum.json) 
-## not a particularly useful format
-## lets convert to a data frame
-sorghum <- jsonlite::fromJSON(sorghum.json)
-```
+---
+title: "Accessing Trait Data Via the BETYdb API"
+author: "David LeBauer"
+date: "11/7/2017"
+output: html_document
+---
+
+
+## Using URLs to construct Queries
+
+The first step toward reproducible pipelines is to automate the process of searching the database and returning results. This is one of the key roles of an Application programming interface, or 'API'. You can learn to use the API in less than 20 minutes, starting now. 
+
+### What is an API?
+
+An API is an 'Application Programming Interface'. An API is a way that you and your software can connect to and access data. 
+
+All of our databases have web interfaces for humans to browse as well as APIs that are constructed as URLs. 
+
+
+### Using Your API key to Connect
+
+An API key is like a password. It allows you to access data, and should be kept private. 
+Therefore, we are not going to put it in code that we share. The one exception is the key 9999999999999999999999999999999999999999 that will allow you to access metadata tables (all tables except _traits_ and _yields_). It will also allow you to access all of the simulated data in the terraref.ncsa.illinois.edu/bety-test database.
+
+A common way of handling private API keys is to place it in a text file in your home directory. 
+Don't put it in a project directory where it might be inadvertently shared.
+
+Here is how to find and save your API key:
+
+* click file --> new --> text file
+* copy the api key that was sent when you registered into the file
+* file --> save as '~/.betykey'
+
+For the public key, you can call this file `~/.betykey_public`. 
+
+### URL query
+
+## Components of a URL query
+
+* base url: `terraref.ncsa.illinois.edu/bety`
+* path to the api: `/api/beta`
+* api endpoint: `/search` or `traits` or `sites`. For BETYdb, these are the names of database tables. 
+* Query parameters: `genus=Sorghum`
+* Authentication: `key=9999999999999999999999999999999999999999` is the public key for the TERRA REF traits database. 
+
+### Ways to access API data
+
+1. Through a URL query
+2. Using the bash shell
+3. Using the R jsonlite package
+
+
+## Constructing a URL query
+
+First, lets construct a query by putting together a URL.
+
+1. start with the database url: `terraref.ncsa.illinois.edu/bety`
+  * this url brings you to the home page
+2. Add the path to the API, `/api/beta`
+  * now we have terraref.ncsa.illinois.edu/bety/api/beta, which points to the API documentation
+3. Add the name of the table you want to query. Lets start with `variables`
+  * terraref.ncsa.illinois.edu/bety/api/beta/variables
+4. add query terms by appending a `?` and combining with `&`, for example:
+  * `key=9999999999999999999999999999999999999999`
+  * `type=trait` where the variable type is 'trait'
+  * `name=~height` where the variable name contains 'height'
+5. This is your complete query:
+  * `terraref.ncsa.illinois.edu/bety/api/beta/variables?type=trait&name=~height&key=9999999999999999999999999999999999999999`
+  * it will query all variables that are type trait and have 'height' in the name
+  * Does it return the expected values?
+  
+
+#### Your Turn
+
+> What will the URL https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999 return?
+
+> Write a URL that will query the database for sites with "Field Scanner" in the name field. Hint: combine two terms with a `+` as in `Field+Scanner`
+
+What do you see? Do you think that this is all of the records? What happens if you add `&limit=none`? 
+
+ 
+#### Shell
+
+```sh
+wget -O sorghum.json \\ # -O names the output file 
+   "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999"
+```
+
+If you want to write the query without exposing the key in plain text, you can construct it thus:
+
+```sh
+wget -O sorghum.json \\
+    "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=`cat ~/.betykey_public`"
+```
+
+> What does `cat ~/.betykey_public` do?
+
+> How can you look at the files?
+
+
+#### R - using the jsonlite package
+
+```{r text-api}
+sorghum.json <- readLines(
+  paste0("https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=", 
+         readLines('~/.betykey')))
+
+## print(sorghum.json) 
+## not a particularly useful format
+## lets convert to a data frame
+sorghum <- jsonlite::fromJSON(sorghum.json)
+```

From 2c80e2e05b400f01c8fb9b2b2c5c92b92d790ddd Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Tue, 6 Nov 2018 14:30:41 -0800
Subject: [PATCH 03/12] Further updated the tutorial on how to access API using
 URL query and bash shell.

---
 traits/02-betydb-api-access.Rmd | 34 +++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index c579098..d564018 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -33,7 +33,14 @@ Here is how to find and save your API key:
 
 For the public key, you can call this file `~/.betykey_public`. 
 
-### URL query
+### Ways to access API data
+
+1. Through a URL query
+2. Using the bash shell
+3. Using the R jsonlite package
+
+
+### Accessing data using a URL query
 
 ## Components of a URL query
 
@@ -43,13 +50,6 @@ For the public key, you can call this file `~/.betykey_public`.
 * Query parameters: `genus=Sorghum`
 * Authentication: `key=9999999999999999999999999999999999999999` is the public key for the TERRA REF traits database. 
 
-### Ways to access API data
-
-1. Through a URL query
-2. Using the bash shell
-3. Using the R jsonlite package
-
-
 ## Constructing a URL query
 
 First, lets construct a query by putting together a URL.
@@ -69,8 +69,7 @@ First, lets construct a query by putting together a URL.
   * it will query all variables that are type trait and have 'height' in the name
   * Does it return the expected values?
   
-
-#### Your Turn
+## Your Turn
 
 > What will the URL https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999 return?
 
@@ -78,25 +77,28 @@ First, lets construct a query by putting together a URL.
 
 What do you see? Do you think that this is all of the records? What happens if you add `&limit=none`? 
 
- 
-#### Shell
+
+#### Accessing data using the Shell
+
+Type the following command into a bash shell (the -O option names the output file): 
 
 ```sh
-wget -O sorghum.json \\ # -O names the output file 
+wget -O sorghum.json
    "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999"
 ```
 
-If you want to write the query without exposing the key in plain text, you can construct it thus:
+If you want to write the query without exposing the key in plain text, you can construct it like this:
 
 ```sh
-wget -O sorghum.json \\
+wget -O sorghum.json
     "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=`cat ~/.betykey_public`"
 ```
 
-> What does `cat ~/.betykey_public` do?
+> Do you know what `cat ~/.betykey_public`. Run the command and see what it outputs in your shell.
 
 > How can you look at the files?
 
+Hint: search what a json file is
 
 #### R - using the jsonlite package
 

From 67665616699a6fc5a8f75e0890c4e7bd667a3d42 Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Tue, 6 Nov 2018 14:54:30 -0800
Subject: [PATCH 04/12] Further updated tutorial. Added short comment on the
 use of the fromJSON function.

---
 traits/02-betydb-api-access.Rmd | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index d564018..87db5fa 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -100,7 +100,9 @@ wget -O sorghum.json
 
 Hint: search what a json file is
 
-#### R - using the jsonlite package
+### Accessing API data using the R jsonlite package
+
+JSON content can be converted into a R data frame using the fromJSON function.
 
 ```{r text-api}
 sorghum.json <- readLines(

From b017aa2219493314f07984f445cc631ab6818664 Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Tue, 6 Nov 2018 15:49:41 -0800
Subject: [PATCH 05/12] Further updated R jsonlite portion of tutorial

---
 traits/02-betydb-api-access.Rmd | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index 87db5fa..e828afe 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -102,7 +102,8 @@ Hint: search what a json file is
 
 ### Accessing API data using the R jsonlite package
 
-JSON content can be converted into a R data frame using the fromJSON function.
+JSON content can be converted into a R object using the fromJSON function.
+Access the 'data' element of the R object to get the data frame.
 
 ```{r text-api}
 sorghum.json <- readLines(
@@ -113,4 +114,5 @@ sorghum.json <- readLines(
 ## not a particularly useful format
 ## lets convert to a data frame
 sorghum <- jsonlite::fromJSON(sorghum.json)
+sorghum.dataframe <- sorghum$data
 ```

From bd4c8f426d4f49dc7975cf86b2bd705d63293a06 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@email.arizona.edu>
Date: Wed, 7 Nov 2018 10:01:45 -0800
Subject: [PATCH 06/12] Update traits/01-web-access.Rmd

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>
---
 traits/01-web-access.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/traits/01-web-access.Rmd b/traits/01-web-access.Rmd
index f3dc7cb..fb7d2dd 100644
--- a/traits/01-web-access.Rmd
+++ b/traits/01-web-access.Rmd
@@ -1,4 +1,4 @@
-6---
+---
 title: "Accessing Trait Data Via the BETYdb Web Interface"
 author: "David LeBauer"
 date: "`r Sys.Date()`"

From d24928c12e3dfdda6b8a2f707d6495307610447a Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Wed, 7 Nov 2018 11:56:36 -0800
Subject: [PATCH 07/12] added comment. link to traitvis webapp not working.

---
 traits/00-BETYdb-getting-started.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/traits/00-BETYdb-getting-started.Rmd b/traits/00-BETYdb-getting-started.Rmd
index fb5d3c4..63e2d18 100644
--- a/traits/00-BETYdb-getting-started.Rmd
+++ b/traits/00-BETYdb-getting-started.Rmd
@@ -40,5 +40,5 @@ The traitvis webapp provides an interface for exploring available data that is u
 * website: https://traitvis.workbench.terraref.org
 
 ```{r}
-knitr::include_app("https://traitvis.workbench.terraref.org/", height = "1400px")
+knitr::include_app("https://traitvis.workbench.terraref.org/", height = "1400px") #fix link? no screenshot is displayed in html output
 ```

From 169ab1a8208d53fd05cf39a90317c4dcf7ca99ec Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Wed, 7 Nov 2018 12:27:23 -0800
Subject: [PATCH 08/12] fixed links to terraref and pecan sites, betydb
 schemas, and doi reference. also updated comment on embedded shiny app (link
 to traitvis app does work).

---
 traits/00-BETYdb-getting-started.Rmd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/traits/00-BETYdb-getting-started.Rmd b/traits/00-BETYdb-getting-started.Rmd
index 63e2d18..a8e5f13 100644
--- a/traits/00-BETYdb-getting-started.Rmd
+++ b/traits/00-BETYdb-getting-started.Rmd
@@ -14,15 +14,15 @@ It contains trait (phenotype) data at the plot or plant level as well as meta da
 ### Introduction to BETYdb 
 
 The TERRA REF trait database (terraref.ncsa.illinois.edu/bety) uses the BETYdb data schema (structure) and web application.
-The BETYdb software is actively used and developed by the [TERRA Reference](terraref.org) program as well as by the [PEcAn project](pecanproject.org).
+The BETYdb software is actively used and developed by the [TERRA Reference](http://terraref.org) program as well as by the [PEcAn project](http://pecanproject.org).
 
 For more information about BETYdb, see the following:
 
 * BETYdb documentation (available via the web application under 'Docs')
   * _Data Access_: how to access data
   * _Data Entry Workflow:_ how to add data to the database
-  * _BETYdb Technical Documentation_ is written for advanced users and website and database administrators who may also be interested in the [full database schema](betydb.org/schemas)
-* BETYdb: A Yield, Trait and Ecosystem Service Database Applied to Second Generation Bioenergy Feedstocks. ([LeBauer et al, 2017](dx.doi.org/10.1111/gcbb.12420))
+  * _BETYdb Technical Documentation_ is written for advanced users and website and database administrators who may also be interested in the [full database schema](https://www.betydb.org/schemas)
+* BETYdb: A Yield, Trait and Ecosystem Service Database Applied to Second Generation Bioenergy Feedstocks. ([LeBauer et al, 2017](https://onlinelibrary.wiley.com/doi/abs/10.1111/gcbb.12420))
 
 Other than the TERRA REF trait database, there are a handful of other projects that use the BETYdb software, mostly with the PEcAn and TERRA programs. The content presented here is focused on the TERRA REF instance of BETYdb. Most of the information presented here is relevant to other databases, but the TERRA program has more emphasis on trait diversity among cultivars or genotypes within a crop whereas PEcAn focuses on the diversity of traits within ecosystems and plant functional types. In addition, the TERRA program is more focused on high throughput phenotyping - intensive monitoring of agricultural breeding trials whereas PEcAn focuses on assimilating heterogeneous data to forecast ecosystem functioning. Fortunately, both uses can use the shared ecosystem of software used for these tasks. For example, the PEcAn crop modeling infrastructure can be directly used to infer additional targets of breeding, and the diversity of traits observed in breeding trials can be a first step toward predicting the impacts of crop traits on productivity and ecosystem functioning.
 
@@ -40,5 +40,5 @@ The traitvis webapp provides an interface for exploring available data that is u
 * website: https://traitvis.workbench.terraref.org
 
 ```{r}
-knitr::include_app("https://traitvis.workbench.terraref.org/", height = "1400px") #fix link? no screenshot is displayed in html output
+knitr::include_app("https://traitvis.workbench.terraref.org", height = "1400px") #not working; shiny app is not being displayed in html output
 ```

From 8d903a45f366faf8be0148345c10a2c538ea811f Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Wed, 7 Nov 2018 12:41:34 -0800
Subject: [PATCH 09/12] updated beta user program link, and fixed links to
 agronomic metadata tutorial and terraref bety home page

---
 traits/01-web-access.Rmd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/traits/01-web-access.Rmd b/traits/01-web-access.Rmd
index f3dc7cb..a6a5ec8 100644
--- a/traits/01-web-access.Rmd
+++ b/traits/01-web-access.Rmd
@@ -1,4 +1,4 @@
-6---
+---
 title: "Accessing Trait Data Via the BETYdb Web Interface"
 author: "David LeBauer"
 date: "`r Sys.Date()`"
@@ -12,7 +12,7 @@ output: html_document
 ### Web interface
 
 * Sign up for an account at https://terraref.ncsa.illinois.edu/bety
-* Sign up for the TERRA REF [beta user program](https://docs.google.com/forms/d/e/1FAIpQLScBsD042RrRok70BCGCRwARTcm9etvVHqvQaz1c5X7c5y0H3w/viewform?c=0&w=1)
+* Sign up for the TERRA REF [beta user program](https://docs.google.com/forms/d/e/1FAIpQLScIUJL_OSL9BvBOdlczErds3aOg5Lwz4NIdNQnUiXdsLsYdhw/viewform)
 * Wait for database access to be granted
 * Your API key will be sent in the email. It can also be found - and regenerated - by navigating to the Users page (data --> [users](https://terraref.ncsa.illinois.edu/bety/users)) in the web interface.
 
@@ -25,11 +25,11 @@ On the Welcome page there is a search option for trait and yield data. This tool
 
 ### Download search results as as csv file from the web interface
 
-* Point your browser to terraref.ncsa.illinois.edu/bety
+* Point your browser to https://terraref.ncsa.illinois.edu/bety/
 * login 
 * enter "NDVI" in the search box
 * on the next page you will see the results of this search 
   * if you want all of the data, including data that has not gone through QA/QC, make sure to check the 'include unchecked records' option
 * in the upper right, you will see a button that will allow you to download the search results as a CSV file. Click it. Open the file in a text editor or spreadsheet program and review its contents.
 
-Note that the web interface only provides a core set of data and limited meta-data. To access all of the data within BETYdb, it is necessary to search and merge multiple tables. More complex queries, such as those in the [Agronomic metadata](../traits/06-agronomic-metadata.Rmd).
+Note that the web interface only provides a core set of data and limited meta-data. To access all of the data within BETYdb, it is necessary to search and merge multiple tables. More complex queries, such as those in the [Agronomic metadata](06-agronomic-metadata.Rmd).

From dd392788318419eeadb436fc422dc8a33fa44592 Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Wed, 7 Nov 2018 13:56:10 -0800
Subject: [PATCH 10/12] made changes according to previous comments

---
 traits/02-betydb-api-access.Rmd | 46 ++++++++++++++++-----------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index e828afe..d835965 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -20,18 +20,18 @@ All of our databases have web interfaces for humans to browse as well as APIs th
 ### Using Your API key to Connect
 
 An API key is like a password. It allows you to access data, and should be kept private. 
-Therefore, we are not going to put it in code that we share. The one exception is the key 9999999999999999999999999999999999999999 that will allow you to access metadata tables (all tables except _traits_ and _yields_). It will also allow you to access all of the simulated data in the terraref.ncsa.illinois.edu/bety-test database.
+Therefore, we are not going to put it in code that we share. The one exception is the key 9999999999999999999999999999999999999999 that will allow you to access metadata tables (all tables except _traits_ and _yields_). It will also allow you to access all of the simulated data in the https://terraref.ncsa.illinois.edu/bety-test database.
 
-A common way of handling private API keys is to place it in a text file in your home directory. 
+A common way of handling private API keys is to place it in a text file in your current directory. 
 Don't put it in a project directory where it might be inadvertently shared.
 
 Here is how to find and save your API key:
 
 * click file --> new --> text file
 * copy the api key that was sent when you registered into the file
-* file --> save as '~/.betykey'
+* file --> save as '.betykey'
 
-For the public key, you can call this file `~/.betykey_public`. 
+For the public key, you can call this file `.betykey_public`. 
 
 ### Ways to access API data
 
@@ -42,10 +42,11 @@ For the public key, you can call this file `~/.betykey_public`.
 
 ### Accessing data using a URL query
 
+
 ## Components of a URL query
 
 * base url: `terraref.ncsa.illinois.edu/bety`
-* path to the api: `/api/beta`
+* path to the api: `/api/v1`
 * api endpoint: `/search` or `traits` or `sites`. For BETYdb, these are the names of database tables. 
 * Query parameters: `genus=Sorghum`
 * Authentication: `key=9999999999999999999999999999999999999999` is the public key for the TERRA REF traits database. 
@@ -56,63 +57,60 @@ First, lets construct a query by putting together a URL.
 
 1. start with the database url: `terraref.ncsa.illinois.edu/bety`
   * this url brings you to the home page
-2. Add the path to the API, `/api/beta`
-  * now we have terraref.ncsa.illinois.edu/bety/api/beta, which points to the API documentation
+2. Add the path to the API, `/api/v1`
+  * now we have terraref.ncsa.illinois.edu/bety/api/v1, which points to the API documentation
 3. Add the name of the table you want to query. Lets start with `variables`
-  * terraref.ncsa.illinois.edu/bety/api/beta/variables
+  * terraref.ncsa.illinois.edu/bety/api/v1/variables
 4. add query terms by appending a `?` and combining with `&`, for example:
   * `key=9999999999999999999999999999999999999999`
   * `type=trait` where the variable type is 'trait'
   * `name=~height` where the variable name contains 'height'
 5. This is your complete query:
-  * `terraref.ncsa.illinois.edu/bety/api/beta/variables?type=trait&name=~height&key=9999999999999999999999999999999999999999`
+  * `terraref.ncsa.illinois.edu/bety/api/v1/variables?type=trait&name=~height&key=9999999999999999999999999999999999999999`
   * it will query all variables that are type trait and have 'height' in the name
   * Does it return the expected values?
   
 ## Your Turn
 
-> What will the URL https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999 return?
+> What will the URL https://terraref.ncsa.illinois.edu/bety/api/v1/species?genus=Sorghum&key=9999999999999999999999999999999999999999 return?
 
 > Write a URL that will query the database for sites with "Field Scanner" in the name field. Hint: combine two terms with a `+` as in `Field+Scanner`
 
 What do you see? Do you think that this is all of the records? What happens if you add `&limit=none`? 
 
 
+
 #### Accessing data using the Shell
 
-Type the following command into a bash shell (the -O option names the output file): 
+Type the following command into a bash shell (the `-o` option names the output file): 
 
 ```sh
-wget -O sorghum.json
-   "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=9999999999999999999999999999999999999999"
+curl -o sorghum.json \
+   "https://terraref.ncsa.illinois.edu/bety/api/v1/species?genus=Sorghum&key=9999999999999999999999999999999999999999"
 ```
 
 If you want to write the query without exposing the key in plain text, you can construct it like this:
 
 ```sh
-wget -O sorghum.json
-    "https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=`cat ~/.betykey_public`"
+curl -o sorghum.json \
+    "https://terraref.ncsa.illinois.edu/bety/api/v1/species?genus=Sorghum&key=`cat .betykey_public`"
 ```
 
-> Do you know what `cat ~/.betykey_public`. Run the command and see what it outputs in your shell.
+> What does `cat .betykey_public` do? 
 
 > How can you look at the files?
 
-Hint: search what a json file is
-
 ### Accessing API data using the R jsonlite package
 
-JSON content can be converted into a R object using the fromJSON function.
-Access the 'data' element of the R object to get the data frame.
-
 ```{r text-api}
 sorghum.json <- readLines(
-  paste0("https://terraref.ncsa.illinois.edu/bety/api/beta/species?genus=Sorghum&key=", 
-         readLines('~/.betykey')))
+  paste0("https://terraref.ncsa.illinois.edu/bety/api/v1/species?genus=Sorghum&key=", 
+         readLines('.betykey')))
 
 ## print(sorghum.json) 
 ## not a particularly useful format
 ## lets convert to a data frame
 sorghum <- jsonlite::fromJSON(sorghum.json)
-sorghum.dataframe <- sorghum$data
 ```
+
+More on how to use the rOpenSci traits package coming up in the [next tutorial](03-access-r-traits.Rmd)

From 63616dcc873f5766894b9e42f9b42a814395ab36 Mon Sep 17 00:00:00 2001
From: Kimberly Huynh <kimberlyh9888@gmail.com>
Date: Wed, 7 Nov 2018 15:24:54 -0800
Subject: [PATCH 11/12] made minor edits - assuming betykey in traits directory
 since ~ does not work on Windows

---
 index.Rmd                                          | 4 +++-
 traits/02-betydb-api-access.Rmd                    | 4 ----
 traits/03-access-r-traits.Rmd                      | 8 ++++----
 traits/04-danforth-indoor-phenotyping-facility.Rmd | 5 +++--
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/index.Rmd b/index.Rmd
index dba5486..26484cc 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -13,4 +13,6 @@ output:
 
 ```{r}
 knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
-```
\ No newline at end of file
+options(warn = -1)
+```
+
diff --git a/traits/02-betydb-api-access.Rmd b/traits/02-betydb-api-access.Rmd
index d835965..b1cd1b5 100644
--- a/traits/02-betydb-api-access.Rmd
+++ b/traits/02-betydb-api-access.Rmd
@@ -96,10 +96,6 @@ curl -o sorghum.json \
     "https://terraref.ncsa.illinois.edu/bety/api/v1/species?genus=Sorghum&key=`cat .betykey_public`"
 ```
 
-> What does `cat .betykey_public` do? 
-
-> How can you look at the files?
-
 ### Accessing API data using the R jsonlite package
 
 ```{r text-api}
diff --git a/traits/03-access-r-traits.Rmd b/traits/03-access-r-traits.Rmd
index 77adde3..f0eab25 100644
--- a/traits/03-access-r-traits.Rmd
+++ b/traits/03-access-r-traits.Rmd
@@ -33,11 +33,11 @@ library(dplyr)
 ```{r writing-key}
 # This should be done once with the key sent to you in your email
 # writeLines('abcdefg_rest_of_key_sent_in_email', 
-#            con = '~/.betykey')
+#            con = '.betykey')
 
 # Example with the public key:
 writeLines('9999999999999999999999999999999999999999', 
-           con = '~/.betykey_public')
+           con = '.betykey_public')
 ```
 
 #### R - using the traits package
@@ -55,7 +55,7 @@ sorghum_info <- betydb_query(table = 'species',
                             api_version = 'beta',
                             limit = 'none',
                             betyurl = "https://terraref.ncsa.illinois.edu/bety/", 
-                            key = readLines('~/.betykey', warn = FALSE))
+                            key = readLines('.betykey', warn = FALSE))
 
 ```
 
@@ -65,7 +65,7 @@ Notice all of the arguments that the `betydb_query` function requires? We can ch
 
 
 ```{r}
-options(betydb_key = readLines('~/.betykey', warn = FALSE),
+options(betydb_key = readLines('.betykey', warn = FALSE),
         betydb_url = "https://terraref.ncsa.illinois.edu/bety/",
         betydb_api_version = 'beta')
 ```
diff --git a/traits/04-danforth-indoor-phenotyping-facility.Rmd b/traits/04-danforth-indoor-phenotyping-facility.Rmd
index 394c162..96104ef 100644
--- a/traits/04-danforth-indoor-phenotyping-facility.Rmd
+++ b/traits/04-danforth-indoor-phenotyping-facility.Rmd
@@ -2,7 +2,8 @@
 title: "Phenotype Analysis"
 author: "David LeBauer, Craig Willis"
 date: "`r Sys.Date()`"
-output: md_document
+output:
+  html_document: default
 ---
 
 ```{r 02-setup, include=FALSE}
@@ -26,7 +27,7 @@ library(traits)
 Unlike the first two tutorials, now we will be querying real data from the public TERRA REF database. So we will use a new URL, https://terraref.ncsa.illinois.edu/bety/, and we will need to use our own private key.
 
 ```{r terraref-connect-options}
-options(betydb_key = readLines('~/.betykey', warn = FALSE),
+options(betydb_key = readLines('.betykey', warn = FALSE),
         betydb_url = "https://terraref.ncsa.illinois.edu/bety/",
         betydb_api_version = 'beta')
 ```

From 83f357505f1d903839f6ce2540b8db21922ec408 Mon Sep 17 00:00:00 2001
From: David LeBauer <dlebauer@email.arizona.edu>
Date: Wed, 7 Nov 2018 14:31:45 -0800
Subject: [PATCH 12/12] Update
 traits/04-danforth-indoor-phenotyping-facility.Rmd

Co-Authored-By: kimberlyh66 <44081116+kimberlyh66@users.noreply.github.com>
---
 traits/04-danforth-indoor-phenotyping-facility.Rmd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/traits/04-danforth-indoor-phenotyping-facility.Rmd b/traits/04-danforth-indoor-phenotyping-facility.Rmd
index 96104ef..19937ed 100644
--- a/traits/04-danforth-indoor-phenotyping-facility.Rmd
+++ b/traits/04-danforth-indoor-phenotyping-facility.Rmd
@@ -27,7 +27,7 @@ library(traits)
 Unlike the first two tutorials, now we will be querying real data from the public TERRA REF database. So we will use a new URL, https://terraref.ncsa.illinois.edu/bety/, and we will need to use our own private key.
 
 ```{r terraref-connect-options}
-options(betydb_key = readLines('.betykey', warn = FALSE),
+options(betydb_key = readLines('.betykey'),
         betydb_url = "https://terraref.ncsa.illinois.edu/bety/",
         betydb_api_version = 'beta')
 ```
@@ -115,4 +115,4 @@ ggplot(data = danforth_sorghum, aes(x = date, y = mean, color = cultivar)) +
 2. An 'entity' is a replicate. 
    * How many entities are there? 
    * How many entities per cultivar? 
-   * Did they all make it through the entire growing season?
\ No newline at end of file
+   * Did they all make it through the entire growing season?