[WIP] Add python examples for met and traits

.gitignore

@@ -2,5 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
-_bookdown_files
+_bookdown_files/
 *.tif

.travis.yml

@@ -2,6 +2,10 @@ language: R
 sudo: false
 cache: packages
 
+branches: 
+  except: 
+  - develop
+
 before_install: 
   - sudo apt-get install libudunits2-dev
   - sudo apt-get install libgdal-dev

README.md

@@ -5,28 +5,27 @@
 
 ## An introduction to the use of TERRA REF data and software
 
-This repository provides a set of tutorials that are divided by data types and use cases. 
+This repository provides a set of tutorials that are divided by data types and use cases.
 
-In the repository, you will find three folders that contain examples of how to access data:
+In the repository, you will find folders that contain examples of how to access data. 
+Within each folder there are both R markdown and Jupyter notebooks.
 
-* traits
-* sensors
-* plantCV
+_If you are **interested in learning how to use the TERRA REF data**_, please find these tutorials published in book form at [terraref.org/tutorials](https://terraref.org/tutorials).
 
-Within each folder there are both R markdown and Jupyter notebooks. These describe different approaches to accessing data. These are intended to cover diverse use cases, and you will find information about accessing data from web interfaces but the primary focus is on accessing data using R, Python, SQL, and REST APIs. These are intended to provide quick-start introductions to access data along with computing environments required for further exploration. They are not intended to teach analyses, although some illustrative visualizations and statistical models are provided.
+If you want to **fix, improve, or contribute new tutorials**, please continue reading here!
 
 This is a work in progress, and an open source community that welcomes contributions in many forms. Please feel welcome to ask questions, provide suggestions or share analyses that may be of interest to others.
 
 
-## Getting Started
+## Contributing
 
-### Requirements
+While you can run many of these tutorials locally, many require access to the TERRA REF filesystem and databases. These are available on a web-based cloud development environment that provides Rstudio, Jupyter Notebooks, and other interfaces. Therefore, the _only technical requirements_ are:
 
-All of the tutorials have been designed to work in the cloud and can be accessed using a web browser. Therefore, the _only technical requirements_ are:
 * Web browser
 * Internet connection
 
 In addition, you will need to:
+
 * Sign up as as a TERRA REF [Beta User by filling out this application](http://terraref.org/beta).
 * Sign up for an account on the [TERRA REF Workbench](https://www.workbench.terraref.org), and wait for approval.
 
@@ -38,4 +37,4 @@ Although we provide a few pre-configured computing environments, Workbench is de
 
 **To get started**, follow the [Workbench Quick Start](https://htmlpreview.github.io/?https://github.com/terraref/tutorials/blob/master/workbench/ndslabs_workbench_intro.html).
 
-This will walk you through the process of getting started with the first tutorials on how to access data.
+This will walk you through the process of getting started with the first tutorials on how to access data.

_bookdown.yml

@@ -10,6 +10,10 @@ rmd_files: ["index.Rmd",
 "vignettes/02-get-weather-data-R.Rmd",
 "vignettes/03-get-images-python.Rmd", 
 "vignettes/04-synthesis-data.Rmd", 
+"traits/00-BETYdb-getting-started.Rmd",
 "traits/03-access-r-traits.Rmd",
+"traits/08-access-traits-python.Rmd",
 "sensors/01-meteorological-data.Rmd",
-"sensors/06-list-datasets-by-plot.Rmd"]
+"sensors/06-list-datasets-by-plot.Rmd",
+"sensors/10-meteorological-data-python.Rmd",
+"data_use_policy.Rmd"]

data_use_policy.Rmd

@@ -0,0 +1,38 @@
+# Data Use Policy {#data_use_policy}
+
+## Release with Attribution
+
+We plan to make data from the Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform (TERRA-REF) project available for use with attribution. Each type of data will include or point to the appropriate attribution policy.
+
+## Timing and Control of Release
+
+We plan to release the data in stages or tiers. For pre-release access please complete the [beta tester application](https://terraref.org/beta).
+
+1. The **first tier** will be an internal release to the TERRA-REF team and the standards committee. This first tier release will be to quality check and calibrate the data and will take place as data sets are produced and compiled. 
+2. The **second tier** will enable the release of the data generated solely by the TERRA-REF team to other TERRA teams as well as non-TERRA entities. Release of the data to the second tier may occur prior to publication and that access is granted with the understanding that the contributions and interests of the TERRA-REF team should be recognized and respected by the users of the data. The TERRA-REF team reserves the right to analyze and published its own data. Resource users should appropriately cite the source of the data and acknowledge the resource produces. The publication of the data, as suggested in the TERRA-REF Authorship Guidelines, should specify the collaborative nature of the project, and authorship is expected to include all those TERRA-REF team members contributing significantly to the work. 
+3. The **third tier** will provide the public with access to curated datasets from the TERRA REF program. It is an objective of the TERRA-REF team to release of the data to the public by November 2019. These will be released under the conditions described below. 
+
+## Genomic Data
+
+### Restrictions on dataset usage
+
+Genomic data for the _Sorghum bicolor_ Bioenergy Association Panel (BAP) from the TERRA-REF project is available pre-publication to maximize the community benefit of these resources. Use of the raw and processed data that is available should follow the principles of the [Fort Lauderdale Agreement](https://www.genome.gov/pages/research/wellcomereport0303.pdf) and the [Department of Energy's Joint Genome Institute (JGI) early release policies](http://genome.jgi.doe.gov/pages/data-usage-policy.jsf).
+
+By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by TERRA-REF and/or its collaborators of a comprehensive genome analysis ("Reserved Analyses"). "Reserved analyses" include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome-scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the TERRA-REF project is expected to extend until the publication of the results of the sequencing project is accepted. Scientific users are free to publish papers dealing with specific genes or small sets of genes using the sequence data. If these data are used for publication, the following acknowledgment should be included: 'These sequence data were produced by the US Department of Energy Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform (TERRA-REF) Project'. These data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. The assembly and sequence data should not be redistributed or repackaged without permission from TERRA-REF. Any redistribution of the data during the embargo period should carry this notice: "The TERRA-REF project provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. Once the sequence is moved to unreserved status, the data will be freely available for any subsequent use."
+
+We prefer that potential users of these sequence data contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered Reserved Analyses.
+
+## Software and Algorithms
+
+For algorithms, we intend to release via BSD 3 clause or MIT / BSD compatible license. Algorithms are available on GitHub in the terraref organization: github.com/terraref.
+
+## Images, Phenotypes, and Other Raw Data
+
+For other raw data, such as phenotypic data and associated metadata, we intend to release data under [CC0: Creative Commons with No Rights Reserved - Public Domain)](https://creativecommons.org/share-your-work/public-domain/cc0/). This is to enable reuse of these data, but **Scientists are expected cite our data and research publications.** For more information, see related discussion and links in https://github.com/terraref/reference-data/issues/216.
+
+## Contacts
+
+* Todd Mockler, Project/Genomics Lead (email: [email protected])
+* David LeBauer, Computing Pipeline Lead (email: [email protected])
+* Nadia Shakoor, Project Director (email: [email protected])
+