From fdf8c777519685f2b832de8b83d103f5f74b2369 Mon Sep 17 00:00:00 2001
From: David Arndt <arndtd@gmail.com>
Date: Wed, 27 Mar 2019 21:39:48 -0600
Subject: [PATCH] README: Add query examples and put query info first.

---
 README.md | 99 ++++++++++++++++++++++++++++++++++---------------------
 1 file changed, 62 insertions(+), 37 deletions(-)

diff --git a/README.md b/README.md
index f3445b0..24cc6fa 100644
--- a/README.md
+++ b/README.md
@@ -1,44 +1,16 @@
 [**ClassyFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. This is the repository for the ClassyFire API, which allows you to send requests to and pull information from the ClassyFire web server.
 
+This ClassyFire API currently requires a version of the `rest-client` gem prior to v2. In order to use the commands below in a Ruby console, first run e.g.
+
+    irb
+    > gem 'rest-client', '=1.8.0'
+    > require 'rest-client'
+    > require 'path/to/classyfire_api.rb'
+
+
 # **Endpoints** #
 
-##1. Entity##
-
-Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification.
-
-###GET###
-
-**/entities/{entityInchikey}**
-
-A chemical compound's classification can be retrieved in the JSON or XML format. The compound's information is accessed via the InChIkey as show in the following examples. In this example, the entity has the InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.
-
-    ClassyFireAPI.get_entity_classification("BDAGIHXWWSANSR-UHFFFAOYSA-N","json")
-
-Where:
-
-* The entity's InChIKey is "BDAGIHXWWSANSR-UHFFFAOYSA-N",
-* The output format is "json" (JSON).
-
-##2. Sequence##
-
-Sequences are represented by the Sequence model, through which one can access the compound's structure-based classification.
-
-###GET###
-
-**/sequence/{fingerprint}**
-
-A (FASTA) sequence's classification can be retrieved in the JSON. In this example, the sequence has the fingerprint = "8bf70c23ac100cd2c3955081d8613325"
-
-    ClassyFireAPI.get_sequence_classification("8bf70c23ac100cd2c3955081d8613325","json")
-
- Where:
-
-* The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325",
-* The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS"
-* The output format is "json" (JSON).
-
-
-##3. Query##
+##1. Query##
 
 The Query model represents the chemical structure to be classified. Its attributes are the query label and the query input.
 The query label is an identifier
@@ -58,6 +30,24 @@ where the parameters are:
 * The entity's structure represented in the SMILES format: CCCOCC and COCC=CCCC.
 * The query is of type 'STRUCTURE'
 
+To submit multiple structures from a file, use e.g.
+
+    ClassyFireAPI.submit_query_input_in_chunks("input.tsv")
+
+where `input.tsv` is a tab-separated file, and each line must contain either
+
+* Only a structural representation: SMILES, InChI, or
+* A tab-separated pair of an ID and the corresponding structure representation: SMILES, InChI
+
+To  submit multiple IUPAC name from a file, use e.g.
+
+    ClassyFireAPI.submit_query_input_in_chunks("input.tsv", type="IUPAC NAME")
+
+where `input.tsv` is a tab-separated file, and each line must contain either
+
+* Only an IUPAC name, or
+* A tab-separated pair of an ID and the corresponding IUPAC name
+
 ###GET###
 
 **/queries/{queryId}**
@@ -71,6 +61,41 @@ where:
 * The query id is 443431,
 * The output format is "json" (JSON)
 
+##2. Entity##
+
+Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification.
+
+###GET###
+
+**/entities/{entityInchikey}**
+
+A chemical compound's classification can be retrieved in the JSON or XML format. The compound's information is accessed via the InChIkey as show in the following examples. In this example, the entity has the InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.
+
+    ClassyFireAPI.get_entity_classification("BDAGIHXWWSANSR-UHFFFAOYSA-N","json")
+
+Where:
+
+* The entity's InChIKey is "BDAGIHXWWSANSR-UHFFFAOYSA-N",
+* The output format is "json" (JSON).
+
+##3. Sequence##
+
+Sequences are represented by the Sequence model, through which one can access the compound's structure-based classification.
+
+###GET###
+
+**/sequence/{fingerprint}**
+
+A (FASTA) sequence's classification can be retrieved in the JSON. In this example, the sequence has the fingerprint = "8bf70c23ac100cd2c3955081d8613325"
+
+    ClassyFireAPI.get_sequence_classification("8bf70c23ac100cd2c3955081d8613325","json")
+
+ Where:
+
+* The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325",
+* The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS"
+* The output format is "json" (JSON).
+
 
 # **Help and Feedback** #