Merge pull request #129 from solvebio/import-examples

import shortcut examples

examples/README.md

@@ -1,10 +1,25 @@
 SolveBio Python Examples
 ======================
 
-Please start with the [basic Python tutorial](https://docs.solvebio.com/docs/tutorial).
+Complete beginner? Please start with the [basic Python tutorial](https://docs.solvebio.com/docs/tutorial).
 
-Advanced Examples
------------------
+## Importing data
+
+There are many ways to import data into SolveBio.
+
+**Web**:
+You can import VCF & JSON files directly via the [SolveBio web interface](https://my.solvebio.com/files) ([web import documentation](https://support.solvebio.com/hc/en-us/articles/218889718-Importing-VCF-and-JSON-Data
+)).
+
+**SolveBio Python client shortcut**:
+[Handy dandy command line shortcut](https://github.com/solvebio/solvebio-python/blob/master/examples/import/README.md) built into the SolveBio Python client.
+
+**Python script**:
+Or use an
+[example simple Python script](https://github.com/solvebio/solvebio-python/blob/master/examples/import_data.py).
+
+
+## Advanced Examples
 
 IPython/Jupyter notebooks do not load embedded graphs in the GitHub viewer.
 For optimal experience, please use these links:

examples/import/README.md

@@ -0,0 +1,25 @@
+SolveBio Import Shortcut Example
+======================
+
+Make sure you're using the newest version of SolveBio with `pip install solvebio --upgrade`
+
+The SolveBio Python client provides a simple command line shortcut to import data.
+
+Your DOMAIN is the subdomain of your SolveBio account. You can find your domain by going to [SolveBio](https://my.solvebio.com/organization/people) - your organization name is your domain.
+
+To run the example commands, download the [example_input.json](https://github.com/solvebio/solvebio-python/blob/master/examples/import/example_input.json) and [example_template.json](https://github.com/solvebio/solvebio-python/blob/master/examples/import/example_template.json) files.
+
+In your command line:
+```bash
+solvebio import DOMAIN:ExampleDepo/1.0.0/ExampleDataset example_input.json --create-dataset --auto-approve
+```
+
+If you want to add SolveBio entities to your data, you can with a template file (you can also do it later on the SolveBio web interface).
+```
+solvebio import DOMAIN:ExampleDepo/1.0.0/ExampleEntityDataset example_input.json --create-dataset --auto-approve --template-file example_template.json
+```
+
+To get a full list of the arguments options available, try
+```
+solvebio import -h
+```

examples/import/example_input.json

@@ -0,0 +1,3 @@
+{"aa": "p.T235M", "classification": "missense", "solvebio_variant_id": "GRCh37-1-155932911-155932911-A", "transcript": "ENST00000313695", "genomic_coordinates": {"start": 155932911, "stop": 155932911, "build": "GRCh37", "chromosome": "1"}, "gene_id": "ARHGEF2", "cosmic_id": "998184", "cdna": "c.704C>T","hgvs_g": "NC_000001.10:g.155932911G>A", "hgvs_c": "ENST00000313695:c.704C>T"}
+{"aa": "p.A185T", "classification": "missense", "solvebio_variant_id": "GRCh37-1-155934866-155934866-T", "transcript": "ENST00000313695", "genomic_coordinates": {"start": 155934866, "stop": 155934866, "build": "GRCh37", "chromosome": "1"}, "gene_id": "ARHGEF2", "cosmic_id": "998184", "cdna": "c.553G>A","hgvs_g": "NC_000001.10:g.155934866C>T", "hgvs_c": "ENST00000313695:c.553G>A"}
+{"aa": "p.A77T", "classification": "missense", "solvebio_variant_id": "GRCh37-1-155936237-155936237-T", "transcript": "ENST00000313695", "genomic_coordinates": {"start": 155936237, "stop": 155936237, "build": "GRCh37", "chromosome": "1"}, "gene_id": "ARHGEF2", "cosmic_id": "998184", "cdna": "c.229G>A","hgvs_g": "NC_000001.10:g.155936237C>T", "hgvs_c": "ENST00000313695:c.229G>A"}

examples/import/example_template.json

@@ -0,0 +1,13 @@
+{
+  "name": "Example SolveBio import template",
+  "fields": [
+    {
+      "name": "gene_id",
+      "entity_type": "gene"
+    },
+    {
+      "name": "solvebio_variant_id",
+      "entity_type": "variant"
+    }
+  ]
+}

examples/import_data.py

@@ -1,7 +1,12 @@
 import solvebio
 
+# find your solvebio domain
+solvebio.login()
+user = solvebio.User.retrieve()
+my_domain = user['account']['domain']
+
 # create a dataset
-dataset_name = '{0}:SampleImport/1.0.0/SampleImport'.format('your-domain')
+dataset_name = '{0}:SampleImport/1.0.0/SampleImport'.format(my_domain)
 dataset = solvebio.Dataset.get_or_create_by_full_name(dataset_name)
 
 # create a manifest object and a file to it