Update doc

3 files changed, 79 insertions, 53 deletions

diff --git a/README.md b/README.md
index 344f747..ea25a8f 100644
--- a/README.md
+++ b/README.md
@@ -3,60 +3,81 @@ OpenTox Algorithm
 
 - An [OpenTox](http://www.opentox.org) REST Webservice
 - Implements the OpenTox algorithm API for
-    - fminer
     - lazar
+    - subgraph descriptor calculation (fminer)
+    - physico-chemical descriptor calculation (pc) for more than 300 descriptors
+    - feature selection (fs) using recursive feature elimination (rfe)
 
 REST operations
 ---------------
 
-    Get a list of all algorithms  GET   /                       -  URIs of algorithms                    200
-    Get a representation of the   GET   /fminer/                -  fminer representation                 200,404
-     fminer algorithms
-    Get a representation of the   GET   /fminer/bbrc            -  bbrc representation                   200,404
-    bbrc algorithm
-    Get a representation of the   GET   /fminer/last            -  last representation                   200,404
-     last algorithm
-    Get a representation of the   GET   /lazar                  -  lazar representation                  200,404
-     lazar algorithm
-    Get a representation of the   GET   /feature_selection      -  feature selection representation      200,404
-     feature selection algorithms
-    Get a representation of the   GET   /feature_selection/rfe  -  rfe representation                    200,404
-     rfe algorithm
-
-
-    Create bbrc features          POST  /fminer/bbrc            dataset_uri,                URI for feature dataset   200,400,404,500
-                                                                feature_uri,
-                                                                [min_frequency=5 per-mil],
-                                                                [feature_type=trees],
-                                                                [backbone=true],
-                                                                [min_chisq_significance=0.95],
-                                                                [nr_hits=false]
-    Create last features          POST  /fminer/last            dataset_uri,                URI for feature dataset   200,400,404,500
-                                                                feature_uri,
-                                                                [min_frequency=8 %],
-                                                                [feature_type=trees],
-                                                                [nr_hits=false]
-    Create lazar model            POST  /lazar                  dataset_uri,                URI for lazar model       200,400,404,500
-                                                                [prediction_feature],
-                                                                [feature_generation_uri],
-                                                                [prediction_algorithm],
-                                                                [feature_dataset_uri],
-                                                                [pc_type=null],
-                                                                [nr_hits=false (class. using wt. maj. vote), true (else)],
-                                                                [min_sim=0.3 (nominal), 0.4 (numeric features)]
-                                                                [min_train_performance=0.1]
-
-    Create selected features      POST /feature_selection/rfe   dataset_uri,                URI for dataset 200,400,404,500
-                                                                prediction_feature,
-                                                                feature_dataset_uri,
-                                                                [del_missing=false]
-
-
+DESCRIPTION                  REST  ADDRESS           ARGUMENTS                      RETURN                    CODES
+
+Get a representation of the  GET   /lazar            -                              lazar representation      200,404
+lazar algorithm
+
+Get a list of all algorithms GET   /                 -                              URIs of algorithms        200
+Get a representation of the  GET   /fminer/          -                              fminer representation     200,404
+fminer algorithms
+Get a representation of the  GET   /fminer/bbrc      -                              bbrc representation       200,404
+bbrc algorithm
+Get a representation of the  GET   /fminer/last      -                              last representation       200,404
+last algorithm
+
+Get a representation of the  GET   /pc               -                              URIs of algorithms        200,404
+pc algorithms
+Get a representation of the  GET   /pc/<name>        -                              descriptor representation 200,404
+pc algorithm <name>
+
+Get a representation of the  GET   /fs               -                              fs representation         200,404
+fs algorithms
+Get a representation of the  GET   /fs/rfe           -                              rfe representation        200,404
+rfe algorithm
+
+Create lazar model           POST  /lazar            dataset_uri,                   URI for lazar model       200,400,404,500
+                                                     [prediction_feature],
+                                                     [feature_generation_uri],
+                                                     [feature_dataset_uri],
+                                                     [prediction_algorithm],
+                                                     [pc_type=null],
+                                                     [lib=null],
+                                                     [nr_hits=false (cl.wmv), 
+                                                       true (else)],
+                                                     [min_sim=0.3 (nominal), 0.4 
+                                                       (numeric features)],
+                                                     [min_train_performance=0.1]
+
+Create bbrc features         POST  /fminer/bbrc      dataset_uri,                   URI for feature dataset   200,400,404,500
+                                                     prediction_feature,
+                                                     [min_frequency=5 per-mil],
+                                                     [feature_type=trees],
+                                                     [backbone=true],
+                                                     [min_chisq_significance=0.95],
+                                                     [nr_hits=false]
+Create last features         POST  /fminer/last      dataset_uri,                   URI for feature dataset   200,400,404,500
+                                                     prediction_feature,
+                                                     [min_frequency=8 %],
+                                                     [feature_type=trees],
+                                                     [nr_hits=false]
+
+Create features              POST /pc/AllDescriptors dataset_uri,                   URI for dataset           200,400,404,500
+                                                     [pc_type=constitutional,
+                                                     topological,geometrical,
+                                                     electronic,cpsa,hybrid],
+                                                     [lib=cdk,joelib,openbabel]
+
+Create feature               POST /pc/<name>         dataset_uri                    URI for dataset           200,400,404,500
+
+Select features              POST /fs/rfe            dataset_uri,                   URI for dataset           200,400,404,500
+                                                     prediction_feature,
+                                                     feature_dataset_uri,
+                                                     [del_missing=false]
 Synopsis
 --------
 
 - prediction\_algorithm: One of "weighted\_majority\_vote" (default for classification),  "local\_svm\_classification", "local\_svm\_regression" (default for regression). "weighted\_majority\_vote"  is not applicable for regression.
-- pc_type: Mandatory for feature dataset, one of [geometrical, topological, electronic, constitutional, hybrid, cpsa].
+- pc_type: Mandatory for feature datasets that do not contain appropriate feature metadata, one of [geometrical, topological, electronic, constitutional, hybrid, cpsa].
+- lib: Mandatory for feature datasets that do not contain appropriate feature metadata, one of [cdk, openbabel, joelib].
 - nr_hits: Whether nominal features should be instantiated with their occurrence counts in the instances. One of "true", "false". 
 - min_sim: The minimum similarity threshold for neighbors. Numeric value in [0,1].
 - min_train_performance. The minimum training performance for "local\_svm\_classification" (Accuracy) and "local\_svm\_regression" (R-squared). Numeric value in [0,1].
@@ -124,7 +145,13 @@ Creates a standard Lazar model.
 
 * * *
 
-### Create a feature dataset of selected features
-    curl -X POST -d dataset_uri={dataset_uri} -d prediction_feature_uri={prediction_feature_uri} -d feature_dataset_uri={feature_dataset_uri} -d del_missing=true http://webservices.in-silico.ch/test/algorithm/feature_selection/rfe
+### Create a feature dataset of physico-chemical descriptors with CDK
+    curl -X POST -d dataset_uri={dataset_uri} -d lib=cdk http://webservices.in-silico.ch/test/algorithm/pc/AllDescriptors
+
+* * *
+
+### Select features from a feature dataset
+    curl -X POST -d dataset_uri={dataset_uri} -d prediction_feature_uri={prediction_feature_uri} -d feature_dataset_uri={feature_dataset_uri} http://webservices.in-silico.ch/test/algorithm/fs/rfe
+
 
 Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
diff --git a/fminer.rb b/fminer.rb
index ee504fc..da06fc8 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -39,6 +39,7 @@ get "/fminer/bbrc/?" do
       { DC.description => "Feature type, can be 'paths' or 'trees'", OT.paramScope => "optional", DC.title => "feature_type" },
       { DC.description => "BBRC classes, pass 'false' to switch off mining for BBRC representatives.", OT.paramScope => "optional", DC.title => "backbone" },
       { DC.description => "Significance threshold (between 0 and 1)", OT.paramScope => "optional", DC.title => "min_chisq_significance" },
+      { DC.description => "Whether subgraphs should be weighted with their occurrence counts in the instances (frequency)", OT.paramScope => "optional", DC.title => "nr_hits" },
   ]
   }
   case request.env['HTTP_ACCEPT']
@@ -69,7 +70,7 @@ get "/fminer/last/?" do
       { DC.description => "Feature URI for dependent variable", OT.paramScope => "mandatory", DC.title => "prediction_feature" },
       { DC.description => "Minimum frequency", OT.paramScope => "optional", DC.title => "min_frequency" },
       { DC.description => "Feature type, can be 'paths' or 'trees'", OT.paramScope => "optional", DC.title => "feature_type" },
-      { DC.description => "Maximum number of hops", OT.paramScope => "optional", DC.title => "hops" },
+      { DC.description => "Whether subgraphs should be weighted with their occurrence counts in the instances (frequency)", OT.paramScope => "optional", DC.title => "nr_hits" },
   ]
   }
   case request.env['HTTP_ACCEPT']
@@ -253,7 +254,6 @@ end
 # @param [optional] parameters LAST parameters, accepted parameters are
 #   - min_frequency freq  Minimum frequency (default 5)
 #   - feature_type Feature type, can be 'paths' or 'trees' (default "trees")
-#   - hops Maximum number of hops
 #   - nr_hits Set to "true" to get hit count instead of presence
 # @return [text/uri-list] Task URI
 post '/fminer/last/?' do
@@ -272,7 +272,6 @@ post '/fminer/last/?' do
     end
     @@last.SetMinfreq(fminer.minfreq)
     @@last.SetType(1) if params[:feature_type] == "paths"
-    @@last.SetMaxHops(params[:hops]) if params[:hops]
     @@last.SetConsoleOut(false)
 
 
diff --git a/fs.rb b/fs.rb
index 1c8ac67..490e34e 100644
--- a/fs.rb
+++ b/fs.rb
@@ -29,7 +29,7 @@ get "/fs/rfe/?" do
     RDF.type => [OT.Algorithm,OTA.PatternMiningSupervised],
     OT.parameters => [
       { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" },
-      { DC.description => "Prediction Feature URI", OT.paramScope => "mandatory", DC.title => "prediction_feature_uri" },
+      { DC.description => "Prediction Feature URI", OT.paramScope => "mandatory", DC.title => "prediction_feature" },
       { DC.description => "Feature Dataset URI", OT.paramScope => "mandatory", DC.title => "feature_dataset_uri" },
       { DC.description => "Delete Instances with missing values", OT.paramScope => "optional", DC.title => "del_missing" }
   ]
@@ -55,7 +55,7 @@ end
 post '/feature_selection/rfe/?' do 
 
   raise OpenTox::NotFoundError.new "Please submit a dataset_uri." unless params[:dataset_uri]
-  raise OpenTox::NotFoundError.new "Please submit a prediction_feature_uri." unless params[:prediction_feature_uri]
+  raise OpenTox::NotFoundError.new "Please submit a prediction_feature_uri." unless params[:prediction_feature]
   raise OpenTox::NotFoundError.new "Please submit a feature_dataset_uri." unless params[:feature_dataset_uri]
 
   ds_csv=OpenTox::RestClientWrapper.get( params[:dataset_uri], {:accept => "text/csv"} )
@@ -63,7 +63,7 @@ post '/feature_selection/rfe/?' do
   ds.puts(ds_csv)
   ds.flush()
 
-  prediction_feature = URI.escape(params[:prediction_feature_uri].split('/').last) # get col name
+  prediction_feature = URI.escape(params[:prediction_feature].split('/').last) # get col name
   
   fds_features = OpenTox::Dataset.new(params[:feature_dataset_uri]).load_features
   fds_csv=OpenTox::RestClientWrapper.get( params[:feature_dataset_uri], {:accept => "text/csv"})