From 3a11ba2918795821600b7113d0758415718d263a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 11 Jun 2018 12:46:06 +0200
Subject: combine gui with rest

---
 lib/substance.rb | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 lib/substance.rb

(limited to 'lib/substance.rb')

diff --git a/lib/substance.rb b/lib/substance.rb
new file mode 100644
index 0000000..fef1b7e
--- /dev/null
+++ b/lib/substance.rb
@@ -0,0 +1,30 @@
+# Get all substances
+get "/substance/?" do
+  substances = Substance.all
+  case @accept
+  when "text/uri-list"
+    uri_list = substances.collect{|substance| uri("/substance/#{substance.id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    substances = JSON.parse substances.to_json
+    substances.each_index do |idx|
+      substances[idx][:URI] = uri("/substance/#{substances[idx]["_id"]["$oid"]}")
+    end
+    return substances.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+# Get a substance
+get "/substance/:id/?" do
+  case @accept
+  when "application/json"
+    substance = Substance.find :id => params[:id]
+    not_found_error "Substance with id: #{params[:id]} not found." unless substance
+    substance[:URI] = uri("/substance/#{substance.id}")
+    return substance.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
-- 
cgit v1.2.3


From 9750e0309500259e9a56e267ce87984fb5bb5e53 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 26 Nov 2018 15:29:26 +0000
Subject: clean out; better response codes; prepare for batch

---
 lib/substance.rb | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

(limited to 'lib/substance.rb')

diff --git a/lib/substance.rb b/lib/substance.rb
index fef1b7e..f493714 100644
--- a/lib/substance.rb
+++ b/lib/substance.rb
@@ -6,24 +6,28 @@ get "/substance/?" do
     uri_list = substances.collect{|substance| uri("/substance/#{substance.id}")}
     return uri_list.join("\n") + "\n"
   when "application/json"
-    substances = JSON.parse substances.to_json
-    substances.each_index do |idx|
-      substances[idx][:URI] = uri("/substance/#{substances[idx]["_id"]["$oid"]}")
-    end
-    return substances.to_json
+    list = substances.collect{|substance| uri("/substance/#{substance.id}")}
+    substances = JSON.parse list.to_json
+    return JSON.pretty_generate substances
   else
     bad_request_error "Mime type #{@accept} is not supported."
   end
 end
 
-# Get a substance
+# Get a substance by ID
 get "/substance/:id/?" do
   case @accept
   when "application/json"
-    substance = Substance.find :id => params[:id]
-    not_found_error "Substance with id: #{params[:id]} not found." unless substance
-    substance[:URI] = uri("/substance/#{substance.id}")
-    return substance.to_json
+    mongoid = /^[a-f\d]{24}$/i
+    halt 400, "Input #{params[:id]} is no valid ID.".to_json unless params[:id].match(mongoid)
+    substance = Substance.find params[:id]
+    if substance
+      out = {"compound": {"id": substance.id, "inchi": substance.inchi, "smiles": substance.smiles, "warnings": substance.warnings}}
+      response['Content-Type'] = @accept
+      return JSON.pretty_generate JSON.parse(out.to_json)
+    else
+      halt 400, "Substance with ID #{input} not found."
+    end
   else
     bad_request_error "Mime type #{@accept} is not supported."
   end
-- 
cgit v1.2.3


From 741701df8ff0861b3607a30e9aaf8b8a0c303cdf Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 13 Jun 2019 15:28:59 +0000
Subject: update with API

---
 lib/substance.rb | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

(limited to 'lib/substance.rb')

diff --git a/lib/substance.rb b/lib/substance.rb
index f493714..5d57505 100644
--- a/lib/substance.rb
+++ b/lib/substance.rb
@@ -1,5 +1,5 @@
 # Get all substances
-get "/substance/?" do
+get "/api/substance/?" do
   substances = Substance.all
   case @accept
   when "text/uri-list"
@@ -10,25 +10,25 @@ get "/substance/?" do
     substances = JSON.parse list.to_json
     return JSON.pretty_generate substances
   else
-    bad_request_error "Mime type #{@accept} is not supported."
+    halt 400, "Mime type #{@accept} is not supported."
   end
 end
 
 # Get a substance by ID
-get "/substance/:id/?" do
+get "/api/substance/:id/?" do
   case @accept
   when "application/json"
-    mongoid = /^[a-f\d]{24}$/i
-    halt 400, "Input #{params[:id]} is no valid ID.".to_json unless params[:id].match(mongoid)
     substance = Substance.find params[:id]
     if substance
-      out = {"compound": {"id": substance.id, "inchi": substance.inchi, "smiles": substance.smiles, "warnings": substance.warnings}}
-      response['Content-Type'] = @accept
+      out = {"compound": {"id": substance.id, 
+                          "inchi": substance.inchi, 
+                          "smiles": substance.smiles 
+      }}
       return JSON.pretty_generate JSON.parse(out.to_json)
     else
-      halt 400, "Substance with ID #{input} not found."
+      halt 400, "Substance with ID #{params[:id]} not found."
     end
   else
-    bad_request_error "Mime type #{@accept} is not supported."
+    halt 400, "Mime type #{@accept} is not supported."
   end
 end
-- 
cgit v1.2.3