Add URL data locators to launch sub-command (#920)

* initial commit of URL support for launch

* lint

* modify tests to use new data locator

* add locator unit tests

* fix typo in faq

* more lint

* update faq per PR review
This commit is contained in:
Bruce Martin
2019-09-15 09:01:53 -07:00
committed by GitHub
parent 0f520f2fd4
commit 20317fd08f
12 changed files with 196 additions and 26 deletions
+16
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@@ -94,3 +94,19 @@ This may happen, especially as we work out bugs in our installation process! Ple
#### I'm following the developer instructions and get an error about "missing files and directories” when trying to build the client
This is likely because you do not have node and npm installed, we recommend using [nvm](https://github.com/creationix/nvm) if you're new to using these tools.
# Data access
#### Can I use a _s3:_ or _gs:_ URL with `cellxgene launch`?
Yes. Support for S3 and GCS is not enabled by default. If you wish to directly access S3 or GFS, install one or both of the following packages using `pip`:
- [s3fs](https://s3fs.readthedocs.io/en/latest/) for S3 support
- [gcsfs](https://gcsfs.readthedocs.io/en/latest/) for GCS support
For example:
```
pip install s3fs
cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad
```
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@@ -21,6 +21,12 @@ If you want an example dataset download [this file](https://github.com/chanzucke
cellxgene launch pbmc3k.h5ad --open
```
You can also directly specify URLs as a data source, and the data will be downloaded during launch
```
cellxgene launch https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad
```
On Mac OS and Ubuntu, you should see your web browser open with the following
<img width="450" src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-opening-screenshot.png" pad="50px">