From 8b2debc8032fcd95c0a0b4c0dff16495f241f208 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 21:41:04 +0000 Subject: [PATCH 01/26] README.md edited online with Bitbucket --- README.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..3c80c81 --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +# README # + +[**ClassFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. The ClassyFire API allows you to send requests to and pull information from the ClassyFire server. + +### What is this repository for? ### + +* Quick summary +* Version +* [Learn Markdown](https://bitbucket.org/tutorials/markdowndemo) + +### How do I get set up? ### + +* Summary of set up +* Configuration +* Dependencies +* Database configuration +* How to run tests +* Deployment instructions + +### Contribution guidelines ### + +* Writing tests +* Code review +* Other guidelines + +### Who do I talk to? ### + +* Repo owner or admin +* Other community or team contact \ No newline at end of file From 99a12342f6fd9357a4cf54464606a2fae36952be Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 21:43:37 +0000 Subject: [PATCH 02/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3c80c81..fcf7ec8 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # README # -[**ClassFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. The ClassyFire API allows you to send requests to and pull information from the ClassyFire server. +[**ClassyFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. The ClassyFire API allows you to send requests to and pull information from the ClassyFire server. ### What is this repository for? ### From d4f950595db82ec8456452bb6fb4dde645b76a94 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:02:34 +0000 Subject: [PATCH 03/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fcf7ec8..190cfd6 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # README # -[**ClassyFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. The ClassyFire API allows you to send requests to and pull information from the ClassyFire server. +[**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 allows you to send requests to and pull information from the ClassyFire web server. ### What is this repository for? ### From 927ef38cd1b56b0e824ca01bbe04cbf348ba059d Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:32:43 +0000 Subject: [PATCH 04/26] README.md edited online with Bitbucket --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 190cfd6..e240c77 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,9 @@ * Writing tests * Code review * Other guidelines +* Endpoints + +### Directory Structure ### ### Who do I talk to? ### From e65a2632a3e1944609e7393d5cf48c6e10a1b58c Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:35:05 +0000 Subject: [PATCH 05/26] README.md edited online with Bitbucket --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index e240c77..065fdc8 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,9 @@ ### Directory Structure ### +* [lib](ClassyFire_API / lib / ) + + ### Who do I talk to? ### * Repo owner or admin From 7488db16ff9c9cb2f019929cd82a451d536ae4f6 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:35:35 +0000 Subject: [PATCH 06/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 065fdc8..9609864 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ ### Directory Structure ### -* [lib](ClassyFire_API / lib / ) +* [lib](ClassyFire_API/lib/) ### Who do I talk to? ### From d6028f25033f98897a64bce85ffe843165355c3c Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:39:28 +0000 Subject: [PATCH 07/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9609864..5c129a6 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ ### Directory Structure ### -* [lib](ClassyFire_API/lib/) +* lib ### Who do I talk to? ### From 61385e5db0dbef9cff547a56b28ee4c986b31aa7 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:42:11 +0000 Subject: [PATCH 08/26] README.md edited online with Bitbucket --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 5c129a6..3c98936 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,13 @@ -# README # [**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 allows you to send requests to and pull information from the ClassyFire web server. -### What is this repository for? ### +# What is this repository for? # * Quick summary * Version * [Learn Markdown](https://bitbucket.org/tutorials/markdowndemo) -### How do I get set up? ### +# How do I get set up? # * Summary of set up * Configuration @@ -17,19 +16,20 @@ * How to run tests * Deployment instructions -### Contribution guidelines ### +# Contribution guidelines # * Writing tests * Code review * Other guidelines -* Endpoints -### Directory Structure ### +# **Endpoints** # + +# Directory Structure # * lib -### Who do I talk to? ### +# Who do I talk to? # * Repo owner or admin * Other community or team contact \ No newline at end of file From b1565725f394fa8a37917a50b3c399f403499a74 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 22:43:34 +0000 Subject: [PATCH 09/26] README.md edited online with Bitbucket --- README.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 3c98936..cb71833 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,12 @@ - [**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 allows you to send requests to and pull information from the ClassyFire web server. -# What is this repository for? # +# **What is this repository for?** # * Quick summary * Version * [Learn Markdown](https://bitbucket.org/tutorials/markdowndemo) -# How do I get set up? # +# **How do I get set up?** # * Summary of set up * Configuration @@ -16,7 +15,7 @@ * How to run tests * Deployment instructions -# Contribution guidelines # +# **Contribution guidelines** # * Writing tests * Code review @@ -24,12 +23,12 @@ # **Endpoints** # -# Directory Structure # +# **Directory Structure** # * lib -# Who do I talk to? # +# **Who do I talk to?** # * Repo owner or admin * Other community or team contact \ No newline at end of file From dd5e917e9113cf8e74948e10539c35d66c985904 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:07:39 +0000 Subject: [PATCH 10/26] README.md edited online with Bitbucket --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index cb71833..b0ae02b 100644 --- a/README.md +++ b/README.md @@ -23,6 +23,16 @@ # **Endpoints** # +> ## Entities +> /entities +> > GET +> > > You can retrieve a chemical compound's classification 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. +> > > +> > > curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://localhost:3000/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json +> > > +> > > curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://localhost:3000/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json + + # **Directory Structure** # * lib From 4a36cc2262765f292a0c9d914765a191d8b49c43 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:08:59 +0000 Subject: [PATCH 11/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b0ae02b..574979b 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ # **Endpoints** # -> ## Entities +## Entities > /entities > > GET > > > You can retrieve a chemical compound's classification 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. From 2eb00b6244bd9736b087a17419aa15e2f6a0b786 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:10:30 +0000 Subject: [PATCH 12/26] README.md edited online with Bitbucket --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 574979b..ab64066 100644 --- a/README.md +++ b/README.md @@ -24,8 +24,8 @@ # **Endpoints** # ## Entities -> /entities -> > GET + /entities +> GET > > > You can retrieve a chemical compound's classification 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. > > > > > > curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://localhost:3000/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json From 7bc4ac41130f8c88d166b4a2c656ff4146b160fc Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:11:08 +0000 Subject: [PATCH 13/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ab64066..2956a79 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ # **Endpoints** # ## Entities - /entities +> /entities > GET > > > You can retrieve a chemical compound's classification 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. > > > From 99298065f942587eb75d9856686754b2f243ada7 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:11:32 +0000 Subject: [PATCH 14/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2956a79..8d69e51 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ # **Endpoints** # -## Entities +> ## Entities > /entities > GET > > > You can retrieve a chemical compound's classification 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. From 10a2155de9b3ae924b42ea8508c1f0d299b3426a Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:16:26 +0000 Subject: [PATCH 15/26] README.md edited online with Bitbucket --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8d69e51..37b1a74 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,9 @@ # **Endpoints** # -> ## Entities -> /entities +> ##1. Entities +> +> ###/entities > GET > > > You can retrieve a chemical compound's classification 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. > > > From 90d3acb84a08645cbccf583dc0fbd4757cc96794 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Jul 2014 23:18:57 +0000 Subject: [PATCH 16/26] README.md edited online with Bitbucket --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 37b1a74..ec8972d 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ > ##1. Entities > -> ###/entities +> ###GET/entities > GET > > > You can retrieve a chemical compound's classification 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. > > > From 0b3726be7e77fceda3864863ec3c88a3b3a99679 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 02:21:44 +0000 Subject: [PATCH 17/26] README.md edited online with Bitbucket --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index ec8972d..49dd977 100644 --- a/README.md +++ b/README.md @@ -26,12 +26,12 @@ > ##1. Entities > > ###GET/entities -> GET -> > > You can retrieve a chemical compound's classification 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. + +> >You can retrieve a chemical compound's classification 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. > > > -> > > curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://localhost:3000/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json +> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json > > > -> > > curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://localhost:3000/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json +> > >curl -H "Accept: application/xml" -H "Content-Type: application/xml" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.xml # **Directory Structure** # From ce41e7a45e5c4bfa0effbb0c21efebfa3101d8ec Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 02:47:02 +0000 Subject: [PATCH 18/26] README.md edited online with Bitbucket --- README.md | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 49dd977..3aca2b4 100644 --- a/README.md +++ b/README.md @@ -23,9 +23,10 @@ # **Endpoints** # -> ##1. Entities -> -> ###GET/entities +> ##1. Entities## +> >Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification. + +> >###GET /entities### > >You can retrieve a chemical compound's classification 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. > > > @@ -34,6 +35,14 @@ > > >curl -H "Accept: application/xml" -H "Content-Type: application/xml" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.xml +> ##1. Queries## +> >The Query model represents a list of chemical structures to be classified. The query object can be submitted via a POST request. The classification results can be retrieved via a GET request. + +> >###POST /Queries### +> > +> > + + # **Directory Structure** # * lib From 47bb44caa5f61df26dcea684e84166815af55c23 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 03:10:33 +0000 Subject: [PATCH 19/26] README.md edited online with Bitbucket --- README.md | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 3aca2b4..17c3592 100644 --- a/README.md +++ b/README.md @@ -23,24 +23,33 @@ # **Endpoints** # -> ##1. Entities## +> ##1. Entity## +> > > >Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification. - -> >###GET /entities### - -> >You can retrieve a chemical compound's classification 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. +> > +> >###GET### +> > +> >**/entities/{entity_inchikey}** +> > +> >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. > > > > > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json > > > > > >curl -H "Accept: application/xml" -H "Content-Type: application/xml" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.xml -> ##1. Queries## -> >The Query model represents a list of chemical structures to be classified. The query object can be submitted via a POST request. The classification results can be retrieved via a GET request. +> ##2. Query## +> >The Query model represents a list of chemical structures to be classified. Its attributes are the query label and the query input. +> >*The query label is an identifier +> >* The query input contains a list of structures represented in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Each line contains a structure representation preceded by a compound identifier(optionally), if available. + -> >###POST /Queries### -> > -> > +> >###POST### +> >A query can be submitted using the POST method as demonstrated in the following example. +> > > + +> >###GET### +> > The classification results can be retrieved via a GET method. # **Directory Structure** # From 1c92eb5279018e8ae6c59897ec67089ebccd1592 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 04:01:56 +0000 Subject: [PATCH 20/26] README.md edited online with Bitbucket --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 17c3592..604f76e 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ # **Endpoints** # > ##1. Entity## -> > +> > >Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification. > > > >###GET### @@ -39,15 +39,15 @@ > ##2. Query## -> >The Query model represents a list of chemical structures to be classified. Its attributes are the query label and the query input. +> +> >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 -> >* The query input contains a list of structures represented in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Each line contains a structure representation preceded by a compound identifier(optionally), if available. - - +> >* The query input contains the compound's identifier (optional) and its structural representation, separated by a comma. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. +> > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. -> > > - +> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" http://classyfire.wishartlab.com/queries/ +> > > >###GET### > > The classification results can be retrieved via a GET method. From 288cf6386d5d5c1b89ac1791a013c8ffa38eb795 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 04:12:01 +0000 Subject: [PATCH 21/26] README.md edited online with Bitbucket --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 604f76e..a994535 100644 --- a/README.md +++ b/README.md @@ -46,10 +46,18 @@ > > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. -> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" http://classyfire.wishartlab.com/queries/ +> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" "http://classyfire.wishartlab.com/queries/" +> >where the parameters are: +> >*The query label: curl_test +> >*The entity identifier: ID1 +> >*The entity's structure represented in the SMILES format: C(=O)O > > > >###GET### +> > +> >**/queries/{query_id}** +> > > > The classification results can be retrieved via a GET method. +> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET "http://localhost:3000/queries/88.json" # **Directory Structure** # From 480afaab1f63845308d823358126b6831c200069 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 04:18:09 +0000 Subject: [PATCH 22/26] README.md edited online with Bitbucket --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index a994535..057ec3a 100644 --- a/README.md +++ b/README.md @@ -33,9 +33,9 @@ > > > >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. > > > -> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.json +> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/entities/BDAGIHXWWSANSR-UHFFFAOYSA-N.json > > > -> > >curl -H "Accept: application/xml" -H "Content-Type: application/xml" -X GET http://classyfire.wishartlab.com/entities/LABTWGUMFABVFG-ONEGZZNKSA-N.xml +> > >curl -H "Accept: application/xml" -H "Content-Type: application/xml" -X GET http://classyfire.wishartlab.com/entities/BDAGIHXWWSANSR-UHFFFAOYSA-N.xml > ##2. Query## @@ -46,7 +46,7 @@ > > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. -> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" "http://classyfire.wishartlab.com/queries/" +> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" http://classyfire.wishartlab.com/queries/ > >where the parameters are: > >*The query label: curl_test > >*The entity identifier: ID1 @@ -56,8 +56,11 @@ > > > >**/queries/{query_id}** > > -> > The classification results can be retrieved via a GET method. -> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET "http://localhost:3000/queries/88.json" +> >The classification results can be retrieved via a GET method. +> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.json +> >where the query id is 88 and the result is encoded in the JSON format. +> >The result can also be returned in the XML format. +> > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.xml # **Directory Structure** # From 45c25de39aa7a63a0e98037c9eb3e85e82c49ae1 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 04:43:15 +0000 Subject: [PATCH 23/26] README.md edited online with Bitbucket --- README.md | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 057ec3a..da18a52 100644 --- a/README.md +++ b/README.md @@ -40,17 +40,22 @@ > ##2. 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 -> >* The query input contains the compound's identifier (optional) and its structural representation, separated by a comma. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. +> >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 +> > > +> > > The query input contains the compound's identifier (optional) and its structural representation, separated by a comma. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. > > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. > > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" http://classyfire.wishartlab.com/queries/ +> > > >where the parameters are: -> >*The query label: curl_test -> >*The entity identifier: ID1 -> >*The entity's structure represented in the SMILES format: C(=O)O +> > +> > >The query label: curl_test +> > > +> > >The entity identifier: ID1 +> > +> > >The entity's structure represented in the SMILES format: C(=O)O > > > >###GET### > > @@ -58,8 +63,11 @@ > > > >The classification results can be retrieved via a GET method. > > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.json +> > > >where the query id is 88 and the result is encoded in the JSON format. +> > > >The result can also be returned in the XML format. +> > > > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.xml From 064362f488f59314be2cd20a0e851566e6166038 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 04:44:17 +0000 Subject: [PATCH 24/26] README.md edited online with Bitbucket --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index da18a52..b31017a 100644 --- a/README.md +++ b/README.md @@ -51,11 +51,11 @@ > > > >where the parameters are: > > -> > >The query label: curl_test +> > >The query label: curl_test, > > > -> > >The entity identifier: ID1 +> > >The entity identifier: ID1, > > -> > >The entity's structure represented in the SMILES format: C(=O)O +> > >The entity's structure represented in the SMILES format: C(=O)O. > > > >###GET### > > From 9ee6f39e7ce682f7a4878b0eebecf8db690a390e Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 19:20:05 +0000 Subject: [PATCH 25/26] README.md edited online with Bitbucket --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b31017a..30aa3d7 100644 --- a/README.md +++ b/README.md @@ -61,14 +61,13 @@ > > > >**/queries/{query_id}** > > -> >The classification results can be retrieved via a GET method. +> >The classification results can be retrieved via a GET method in the JSON or XML format. +> > > > > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.json > > -> >where the query id is 88 and the result is encoded in the JSON format. -> > -> >The result can also be returned in the XML format. -> > > > >curl -H "Accept: application/json" -H "Content-Type: application/json" -X GET http://classyfire.wishartlab.com/queries/88.xml +> > +> >where the query id is 88. # **Directory Structure** # From a2e0d221bf5a2bd3456be2b83de01e6a801b4220 Mon Sep 17 00:00:00 2001 From: djoumbou Date: Thu, 10 Jul 2014 22:56:22 +0000 Subject: [PATCH 26/26] README.md edited online with Bitbucket --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 30aa3d7..25bc9ee 100644 --- a/README.md +++ b/README.md @@ -47,15 +47,15 @@ > > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. -> > >curl -d "query[label]=curl_test&query[query_input]=ID1,C(=O)O&submit=Submit query" http://classyfire.wishartlab.com/queries/ +> > >curl -is http://localhost:3000/queries.json -X POST -d '{"label":"curl_test","query_input":"MOL1,CCCOCC\nMOL2,COCC=CCCC"}' -H "Content-Type: application/json" > > > >where the parameters are: > > > > >The query label: curl_test, > > > -> > >The entity identifier: ID1, +> > >The entity identifiers: ID1,ID2 > > -> > >The entity's structure represented in the SMILES format: C(=O)O. +> > >The entity's structure represented in the SMILES format: CCCOCC and COCC=CCCC. > > > >###GET### > >