New to Jupyter? Learn more about the popular tool for data scientists on Jupyter.org (disclaimer: CTDS is not responsible for the content).- - + +
@@ -1055,12 +1052,12 @@
+ 
+ 
+ 
+ Start a new notebook by clicking the tiles in the launcher and choose between Python 3 or R Studio as the base programmatic language. 
Further reading: read more about how to download data files into the Workspaces - here. + here.
@@ -1164,9 +1161,9 @@Users can upload data files or Notebooks from the local machine to the home directory by clicking on “Upload” and access them in the Notebook (see below).
-
+ 
@@ -1180,15 +1177,15 @@ Upload, save, and download Fil
Users can save the notebook by clicking "File" - "Save as", as shown below.
- 
+ 
- Save the notebook under “File” - "Save as".
+ Save the notebook under “File” - "Save Notebook as".
- Users can download notebooks by clicking "File" - "Download as", as shown below.
+ Users can download notebooks by clicking "File" - "Download", as shown below.
- 
+ 
Download the notebook for example as ".ipynb".
@@ -1223,9 +1220,9 @@ Environments, Languages,
-
Python 3 (read more)
- -
+
@@ -1241,17 +1238,17 @@
Environments, Languages,
Python 3 and RStudio in Jupyter
- Both Python 3 and RStudio are available in Jupyter Notebooks.
Users can expect to be able to use typical Python or RStudio packages, such as PyPI or CRAN. For Python and RStudio, users can start a new notebook under
- "New", as shown below.
+ Both Python 3 and R are available in Jupyter Notebooks.
Users can expect to be able to use typical Python or R packages, such as PyPI or CRAN. For Python and R, users can start a new notebook with a tile under
+ "Notebook", as shown below.
-
+
Find Python 3 or RStudio when starting a new notebook under “New”.
- STATA in Jupyter
+
- leveraging the CTDS-owned python software development kit (SDK) and the tool “Gen3-client” if the file size exceeds 250 MB.
+ leverages CTDS-owned python software development kit (SDK) as well as a cloud based computing platform. Data used for local work must be downloaded via a manifest and then Gen3-client.
-
+ -
+ Download and configure the Gen3-client
a. Follow the download instructions of the Gen3-client here. The client can be downloaded
+ here.
b. In your terminal, configure your profile using the following command:
+
+ gen3-client configure --profile=<profile_name> --cred=<credentials.json> --apiendpoint=<api_endpoint_url>
+
+ #Mac/Linux:
+ gen3-client configure --profile=demo
+ --cred=~/Downloads/demo-credentials.json --apiendpoint=https://brh.data-commons.org/
+
+ #Windows:
+ gen3-client configure --profile=demo
+ --cred=C:\Users\demo\Downloads\demo-credentials.json --apiendpoint=https://brh.data-commons.org/
+
+ #Output:
+ 10:08:20 Profile 'demo' has been configured successfully.
+
If successfully executed, a configuration file will be stored under the directory the user specified under “cred”. For troubleshooting, refer to the instructions found
+ here.
+
c. Download files by using the following command, which references the manifest file name and its location:
+
+ gen3-client download-multiple --profile=<profile_name> --manifest=<manifest_file> --download-path=<path_for_files>
+
+ gen3-client download-multiple --profile=demo --manifest=manifest.json --download-path=downloads
+
+ #Output:
+
+ 2021/06/03 16:48:46 Reading manifest...
+ 200 B / 200 B [===================] 100.00% 0s
+ WARNING: flag "rename" was set to false in "original" mode, duplicated files under "downloads/" will be overwritten
+ Proceed? [y/n]: y
+ 2021/06/03 16:48:47 Total number of GUIDs: 1
+ 2021/06/03 16:48:47 Preparing file info for each file, please wait...
+ 1 / 1 [============================================] 100.00% 0s
+ 2021/06/03 16:48:47 File info prepared successfully
+ arcos_all_washpost.tsv.gz 6.41 GiB / 6.41 GiB [=======================================================] 100.00% 0s
+
+
-
+
-
a) Download Data Files using the Gen3-client
In order to download data files above 250 MB, users will need to utilize the Gen3-client command line tool developed by the University of Chicago’s Center for Translational Data Science.
-
+
Find below a guide to download data files using the Gen3-client:
-
Log in to BRH on https://brh.data-commons.org/login.
-
+ Link your accounts to FAIR repositories as described here.
-
@@ -1717,22 +1800,22 @@
a) Download Data Files usi
-
Select a study and click on the button “Download".
-
+
+ 
- Need help? Please contact our help + Need help? Please contact our help desk.
@@ -2114,4 +2197,4 @@