From 1c3f21477f536d413e3e13bced6af1878deba0ee Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 27 Jan 2021 11:42:30 +0000
Subject: Uploader

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 api/README.md |  5 ++++
 api/upload.md | 92 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 create mode 100644 api/README.md
 create mode 100644 api/upload.md

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+# GENENETWORK API
+
+This document is an index to the GeneNetwork API information.
+
+- [Upload API](./upload.md)
diff --git a/api/upload.md b/api/upload.md
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+# GeneNetwork upload API
+
+## API
+
+The REST API will accept gzipped tar ball which contains multiple
+files:
+
+1. A metadata file (JSON)
+2. A phenotype file
+
+On upload to the API the data gets unpacked into files in a temporary
+directory. Next we compute an MD5SUM over the directory and it gets
+renamed to the hash value. So, after unpacking, first we have
+
+```
+GENENETWORK_UPLOAD_DIR/tempdir/metadata.json
+                              /phenotypes.tsv
+```
+
+The upload directory is set in the GN2
+[config](https://github.com/genenetwork/genenetwork2/blob/testing/etc/default_settings.py). After
+computing the HASH we rename it to
+
+```
+GENENETWORK_UPLOAD_DIR/e524ee7ea9b1f452c58abe560960a60f/metadata.json
+                                                       /phenotypes.tsv
+```
+
+On success the upload REST API returns this HASH to the invoker:
+
+```
+{
+  "status": 0,
+  "token": "e524ee7ea9b1f452c58abe560960a60f"
+}
+```
+
+On error the result should include the error output
+
+```
+{
+  "status": 128
+  "error": "gzip failed to unpack file"
+}
+```
+
+### Metadata
+
+The metadata file is a simple JSON file containing
+
+```js
+{
+  "title": "This is my dataset for testing the REST API",
+  "description": "Longer description"
+  "date": "20210127",
+  "authors": [
+    "R.W. Williams"
+  ],
+  "cross": "BXD"
+}
+```
+
+### Phenotype file
+
+The phenotype file is a tab delimited 'spreadsheet' where the columns
+contain phenotypes and the rows contain individuals. Example
+
+```
+      pheno
+BXD01 5.060
+BXD02 307.866
+BXD03 185.400
+BXD04 380.729
+BXD05 150.066
+BXD06 94.483
+BXD07 438.700
+BXD08 NA
+BXD09 130.457
+BXD10 184.900
+BXD11 223.400
+BXD12 167.250
+BXD13 313.950
+BXD14 219.383
+BXD15 277.800
+BXD16 6.467
+BXD17 364.967
+BXD18 132.016
+BXD19 468.133
+BXD20 309.500
+```
+
+Missing data are 'NA'. Multiple pheno columns are possible.
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