Add sample data

README.md

@@ -10,7 +10,7 @@ This is the simplest configuration for developers to start with.
    **IMPORTANT**: Set both the Username and Email to the same valid email address.
    Admin logins will break if you do not.
 3. Run `docker-compose run --rm django ./manage.py makeclient --username your.email@email.com --uri http://localhost:8081/`
-4. Run `docker-compose run --rm django ./manage.py populate --username your.email@email.com --csv /path/to/your/import.csv`
+4. Run `docker-compose run --rm django ./manage.py populate --csv /srv/samples/scans_to_review-2019-01-23.csv`. This will populate the DB with the sample scans.
 
 ### Run Application
 1. Run `docker-compose up`

development.md

@@ -15,12 +15,11 @@ Otherwise
 
 #### Importing Data
 (Note: it might be prudent to run the previous steps before this, i.e. `reset_db`, `migrate`, and `createsuperuser`)
-1. Place folder containing sample data at root of project.
-   - This folder will be referenced here as `sample_data` but can be arbitrarily named.
-   - *NOTE:* `sample_data` should contain a CSV (referenced here as `file.csv`) with all paths prefixed by `/opt/django-project/`
-2. Run `docker-compose build`
-3. Finally, run `docker-compose run --rm  django python manage.py populate --csv /opt/django-project/sample_data/file.csv`. This will create the corresponding models in the database.
-   - *NOTE:* Ensure that correct filenames/paths are used.
+1. To import the sample data, set the import CSV to `/srv/samples/scans_to_review-2019-01-23.csv` in the GUI and click the Import button.
+   If you have not set up the initial project yet, this can be done with `docker-compose run --rm  django python manage.py populate --csv /srv/samples/scans_to_review-2019-01-23.csv`.
+2. To import other data, set the `SAMPLES_DIR` environment variable in your shell prior to running `docker-compose up`.
+   The `SAMPLES_DIR` should contain your import CSV and all of the data to be imported.
+   docker-compose will mount that directory at the same path (`${SAMPLES_DIR}:${SAMPLES_DIR}`), so your import CSV can use the same paths as on your native file system.
 
 
 ## Frontend

docker-compose.override.yml

@@ -10,6 +10,7 @@ services:
     env_file: ./dev/.env.docker-compose
     volumes:
       - .:/opt/django-project
+      - ${SAMPLES_DIR-./samples}:${SAMPLES_DIR-/srv/samples}
     ports:
       - 8000:8000
     depends_on:
@@ -33,6 +34,7 @@ services:
     env_file: ./dev/.env.docker-compose
     volumes:
       - .:/opt/django-project
+      - ${SAMPLES_DIR-./samples}:${SAMPLES_DIR-/srv/samples}
     depends_on:
       - postgres
       - rabbitmq

samples/datasnap-2019-01-23/fs/storage/XNAT/archive/ohsu_incoming/arc001/D-99999-P-9-2081220/RESOURCES/nifti/nifti_catalog.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cat:Catalog ID="nifti" xmlns:arc="http://nrg.wustl.edu/arc" xmlns:cat="http://nrg.wustl.edu/catalog" xmlns:pipe="http://nrg.wustl.edu/pipe" xmlns:prov="http://www.nbirn.net/prov" xmlns:scr="http://nrg.wustl.edu/scr" xmlns:val="http://nrg.wustl.edu/val" xmlns:wrk="http://nrg.wustl.edu/workflow" xmlns:xdat="http://nrg.wustl.edu/security" xmlns:xnat="http://nrg.wustl.edu/xnat" xmlns:xnat_a="http://nrg.wustl.edu/xnat_assessments" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<cat:metaFields>
+	<cat:metaField name="AUDIT">190176:Tue Jan 22 21:48:59 PST 2019=Added:3</cat:metaField>
+</cat:metaFields>
+<cat:entries>
+	<cat:entry URI="2_ncanda-mprage-v1/dcm2image.log" content="U" createdBy="RestAPI" createdEventId="190176" createdTime="2019-01-22T21:48:59.710" digest="50e8ddec11fde04768ed286aa8a72993" format="U" name="dcm2image.log">
+		<cat:tags>
+			<cat:tag>U</cat:tag>
+		</cat:tags>
+	</cat:entry>
+	<cat:entry URI="2_ncanda-mprage-v1/image.nii.gz" content="U" createdBy="RestAPI" createdEventId="190176" createdTime="2019-01-22T21:48:59.710" digest="25257c86dbe0a4c9528c73ecb0397904" format="U" name="image.nii.gz">
+		<cat:tags>
+			<cat:tag>U</cat:tag>
+		</cat:tags>
+	</cat:entry>
+	<cat:entry URI="2_ncanda-mprage-v1/image.nii.xml" content="U" createdBy="RestAPI" createdEventId="190176" createdTime="2019-01-22T21:48:59.710" digest="6b0da5dda68ade789d581eb612b17fc3" format="U" name="image.nii.xml">
+		<cat:tags>
+			<cat:tag>U</cat:tag>
+		</cat:tags>
+	</cat:entry>
+</cat:entries>
+</cat:Catalog>