From fbfa1f45d93f6b9de111eb95418f4e57a0bb361a Mon Sep 17 00:00:00 2001
From: gebele
Date: Mon, 14 Aug 2017 10:49:50 +0000
Subject: fixed qmrf publications order
---
qmrf_report.rb | 36 ++++++++++++++++++++++--------------
1 file changed, 22 insertions(+), 14 deletions(-)
(limited to 'qmrf_report.rb')
diff --git a/qmrf_report.rb b/qmrf_report.rb
index a23607f..b52e618 100644
--- a/qmrf_report.rb
+++ b/qmrf_report.rb
@@ -7,7 +7,6 @@ def qmrf_report id
qmrfpath = File.dirname qmrfpath
prediction_model = Model::Validation.find id
model = prediction_model.model
- #validation_template = "./views/model_details.haml"
if File.directory?(lazarpath)
lazar_commit = `cd #{lazarpath}; git rev-parse HEAD`.strip
@@ -40,12 +39,14 @@ def qmrf_report id
report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}"
# Reference(s) to main scientific papers and/or software package 2.7
- report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz A., Guetlein M., Rautenberg M., Vorgrimmler D., Gebele D. and Helma C. (2013), lazar: a modular predictive toxicology framework ", :number => "1", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"}
+ report.change_catalog :publications_catalog, :publications_catalog_4, {:title => "Maunz A., Guetlein M., Rautenberg M., Vorgrimmler D., Gebele D. and Helma C. (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"}
+
+ report.ref_catalog :references, :publications_catalog, :publications_catalog_4
+
+ report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma C., Gebele D., Rautenberg M. (2017) lazar, software available at https://lazar.in-silico.ch,source code available at #{lazar_commit}", :url => "https://doi.org/10.5281/zenodo.215483"}
+
report.ref_catalog :references, :publications_catalog, :publications_catalog_1
- report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Helma C, Gebele D, Rautenberg M (2017) lazar, software available at https://lazar.in-silico.ch,source code available at #{lazar_commit}", :number => "2", :url => "https://doi.org/10.5281/zenodo.215483"}
- report.ref_catalog :references, :publications_catalog, :publications_catalog_2
-
# Availability of information about the model 2.8
report.value "info_availability", "Prediction interface and validation results available at https://lazar.in-silico.ch"
@@ -60,7 +61,7 @@ def qmrf_report id
report.value "endpoint_units", "#{prediction_model.unit}"
# Dependent variable 3.5
- report.value "endpoint_variable", "#{prediction_model.endpoint} #{prediction_model.regression? ? "regression" : "classification"}"
+ report.value "endpoint_variable", "#{prediction_model.endpoint}"
# Type of model 4.1
model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','')
@@ -72,7 +73,7 @@ def qmrf_report id
# Descriptors in the model 4.3
if model.algorithms["descriptors"][:type]
- report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "Molprint 2D (Bender et al. 2004)", :name => "#{model.algorithms["descriptors"][:type]} fingerprints", :publication_ref => "", :units => ""}
+ report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "(Bender et al. 2004)", :name => "#{model.algorithms["descriptors"][:type]} fingerprints", :publication_ref => "", :units => ""}
report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
end
@@ -198,7 +199,7 @@ def qmrf_report id
Please note that lazar predictions are based on neighbors.
- Descriptors are only used for the calculation of similarities.
+ Descriptors are only used for the calculation of similarities.