qsar-report 0.0.2 → 0.0.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +17 -4
- data/VERSION +1 -1
- data/lib/qmrf-report.rb +2 -2
- data/lib/qprf-report.rb +3 -3
- data/test/qmrf-report.rb +9 -9
- data/test/qprf-report.rb +5 -5
- metadata +1 -1
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: 64a39f9e1511d0f8f585aa3fa316dbd349d6c30f
|
|
4
|
+
data.tar.gz: 1fe77d4ed35aeba2d7927eae6608f7a1ddee36c1
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: eff30e0c0d94da86a568f967a46fb13cc5e6fcf893b953aa1bb809748946b12151fa271b04945049c04017c56d419385c7cbc5c1b2c0c1215c865df991619bfb
|
|
7
|
+
data.tar.gz: 18a34a213877e2025b9aebe47ec61e4921a4152645dca17b742a3bda525dd1341eaceb954687dd3725d9e4a3ba507ccdcc6a8bbcc763d1ce46608d6b699ab07f
|
data/README.md
CHANGED
|
@@ -1,12 +1,12 @@
|
|
|
1
1
|
# QSAR-Report
|
|
2
2
|
QMRF and QPRF reporting extension to OpenTox ruby modules and lazar
|
|
3
3
|
## About
|
|
4
|
-
Class for QMRF and QPRF reporting.
|
|
4
|
+
Class for QMRF and QPRF reporting.
|
|
5
5
|
* QMRF:
|
|
6
6
|
Provides a ruby OpenTox class to prepare an initial version of a QMRF report.
|
|
7
7
|
The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 (https://sourceforge.net/projects/qmrf/)
|
|
8
8
|
* QPRF:
|
|
9
|
-
Provides a ruby OpenTox class to prepare an initial version of a QPRF report in JSON or HTML.
|
|
9
|
+
Provides a ruby OpenTox class to prepare an initial version of a QPRF (version 1.1) report in JSON or HTML.
|
|
10
10
|
|
|
11
11
|
## Usage
|
|
12
12
|
### QMRF
|
|
@@ -18,7 +18,7 @@ require "qsar-report"
|
|
|
18
18
|
report = OpenTox::QMRFReport.new
|
|
19
19
|
|
|
20
20
|
# add a title
|
|
21
|
-
report.
|
|
21
|
+
report.value "QSAR_title", "My QSAR Title"
|
|
22
22
|
|
|
23
23
|
# add a publication to the publication catalog
|
|
24
24
|
report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
|
|
@@ -50,7 +50,7 @@ report.Version = "1"
|
|
|
50
50
|
report.Date = Time.now.strftime("%Y/%m/%d")
|
|
51
51
|
|
|
52
52
|
# Set the CAS number in chapter 1.1
|
|
53
|
-
report.
|
|
53
|
+
report.value "1.1", "7732-18-5" # set CAS number for H²O
|
|
54
54
|
|
|
55
55
|
# print HTML version
|
|
56
56
|
puts report.to_html
|
|
@@ -60,4 +60,17 @@ puts report.pretty_json
|
|
|
60
60
|
|
|
61
61
|
```
|
|
62
62
|
|
|
63
|
+
Installation
|
|
64
|
+
------------
|
|
65
|
+
|
|
66
|
+
gem install qsar-report
|
|
67
|
+
|
|
68
|
+
Documentation
|
|
69
|
+
-------------
|
|
70
|
+
* [RubyDoc.info Code documentation](http://www.rubydoc.info/gems/qsar-report)
|
|
71
|
+
* For full information on QSAR reporting see: [JRC QSAR Model Database and QSAR Model Reporting Formats](https://eurl-ecvam.jrc.ec.europa.eu/databases/jrc-qsar-model-database-and-qsar-model-reporting-formats)
|
|
72
|
+
|
|
73
|
+
Copyright
|
|
74
|
+
---------
|
|
75
|
+
Copyright (c) 2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
|
|
63
76
|
|
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
0.0.
|
|
1
|
+
0.0.3
|
data/lib/qmrf-report.rb
CHANGED
|
@@ -10,7 +10,7 @@ module OpenTox
|
|
|
10
10
|
#@example Report
|
|
11
11
|
# require "qsar-report"
|
|
12
12
|
# report = OpenTox::QMRFReport.new
|
|
13
|
-
# report.
|
|
13
|
+
# report.value "QSAR_title", "My QSAR Title"
|
|
14
14
|
# report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
|
|
15
15
|
# report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
|
|
16
16
|
# puts report.to_xml
|
|
@@ -48,7 +48,7 @@ module OpenTox
|
|
|
48
48
|
# @param [String] value Value to change. If not set the function returns the current value
|
|
49
49
|
# @return [Error] returns Error message if fails
|
|
50
50
|
# @return [String] returns value
|
|
51
|
-
def
|
|
51
|
+
def value key, value=nil
|
|
52
52
|
raise "Can not edit attribute #{key} directly. Edit the catalog with 'report.change_catalog(catalog, key, value)'." if ["QSAR_software","QSAR_Algorithm", ""].include? key
|
|
53
53
|
t = @report.at_css key
|
|
54
54
|
t.content = value unless value.nil?
|
data/lib/qprf-report.rb
CHANGED
|
@@ -14,7 +14,7 @@ module OpenTox
|
|
|
14
14
|
# report.Title = "My QPRF Report"
|
|
15
15
|
# report.Version = "1"
|
|
16
16
|
# report.Date = Time.now.strftime("%Y/%m/%d")
|
|
17
|
-
# report.
|
|
17
|
+
# report.value "1.1", "7732-18-5" # set CAS number for H²O
|
|
18
18
|
# puts report.to_html
|
|
19
19
|
|
|
20
20
|
class QPRFReport
|
|
@@ -56,12 +56,12 @@ module OpenTox
|
|
|
56
56
|
# Set or Get a value in the QPRF report
|
|
57
57
|
#@example for CAS Number
|
|
58
58
|
# report = OpenTox::QPRFReport.new
|
|
59
|
-
# report.
|
|
59
|
+
# report.value "1.1", "7732-18-5"
|
|
60
60
|
#
|
|
61
61
|
# @param [String] chapter Name of the chapter - e.g.: "1.1", "1.2", "1.3", "1.4", "1.5 General", "1.5 a.", "1.5 b.", "1.5 c.", "1.5 d.", "2.1" ...
|
|
62
62
|
# @param [String] value Value to set. If not set the function returns the current value
|
|
63
63
|
# @return [String] returns Value
|
|
64
|
-
def
|
|
64
|
+
def value chapter, value=nil
|
|
65
65
|
case chapter
|
|
66
66
|
when /^1\.\d*/
|
|
67
67
|
block = "1. Substance"
|
data/test/qmrf-report.rb
CHANGED
|
@@ -19,17 +19,17 @@ class QMRFReportTest < MiniTest::Test
|
|
|
19
19
|
|
|
20
20
|
def test_3_write_some_values
|
|
21
21
|
report = OpenTox::QMRFReport.new
|
|
22
|
-
report.
|
|
23
|
-
report.
|
|
24
|
-
assert_equal report.
|
|
25
|
-
assert_equal report.
|
|
26
|
-
refute_equal report.
|
|
22
|
+
report.value "QSAR_title", "My QSAR Title"
|
|
23
|
+
report.value "QSAR_models", "My QSAR Model"
|
|
24
|
+
assert_equal report.value("QSAR_title"), "My QSAR Title"
|
|
25
|
+
assert_equal report.value("QSAR_models"), "My QSAR Model"
|
|
26
|
+
refute_equal report.value("QSAR_title"), "lazar"
|
|
27
27
|
end
|
|
28
28
|
|
|
29
29
|
def test_4_write_check
|
|
30
30
|
report = OpenTox::QMRFReport.new
|
|
31
|
-
report.
|
|
32
|
-
report.
|
|
31
|
+
report.value "QSAR_title", "My QSAR Title"
|
|
32
|
+
report.value "QSAR_models", "My QSAR Model"
|
|
33
33
|
assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t4.xml")))
|
|
34
34
|
end
|
|
35
35
|
|
|
@@ -52,8 +52,8 @@ class QMRFReportTest < MiniTest::Test
|
|
|
52
52
|
|
|
53
53
|
def test_7_write_alot
|
|
54
54
|
report = OpenTox::QMRFReport.new
|
|
55
|
-
report.
|
|
56
|
-
report.
|
|
55
|
+
report.value "QSAR_title", "My QSAR Title"
|
|
56
|
+
report.value "QSAR_models", "My QSAR Model"
|
|
57
57
|
report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :contact => "in-silico toxicology gmbh", :url => "https://lazar.in-silico.ch", :description => "lazar toxicity predictions"}
|
|
58
58
|
report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
|
|
59
59
|
report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "MyName M (2016) My Second Publication Title, Hornblower, 101ff.", :url => "http://hornblower.dom"}
|
data/test/qprf-report.rb
CHANGED
|
@@ -25,7 +25,7 @@ class QMRFReportTest < MiniTest::Test
|
|
|
25
25
|
assert_equal report.Title, "QSAR Prediction Reporting Format (QPRF)"
|
|
26
26
|
end
|
|
27
27
|
|
|
28
|
-
def
|
|
28
|
+
def test_4_set_values
|
|
29
29
|
report = OpenTox::QPRFReport.new
|
|
30
30
|
report.Title = "My Test Title"
|
|
31
31
|
report.Version = "12"
|
|
@@ -36,16 +36,16 @@ class QMRFReportTest < MiniTest::Test
|
|
|
36
36
|
|
|
37
37
|
def test_5_get_11
|
|
38
38
|
report = OpenTox::QPRFReport.new
|
|
39
|
-
report.
|
|
40
|
-
assert_equal report.
|
|
39
|
+
report.value "1.1", "7732-18-5"
|
|
40
|
+
assert_equal report.value("1.1"), "7732-18-5"
|
|
41
41
|
end
|
|
42
42
|
|
|
43
|
-
def
|
|
43
|
+
def test_6_set_more_values
|
|
44
44
|
report = OpenTox::QPRFReport.new
|
|
45
45
|
report.Title = "My QPRF Report"
|
|
46
46
|
report.Version = "2.1"
|
|
47
47
|
report.Date = "2016/08/21"
|
|
48
|
-
report.
|
|
48
|
+
report.value "1.1", "7732-18-5"
|
|
49
49
|
assert_equal report.pretty_json, File.read(File.join(DATA_DIR,'qprf-t6.json'))
|
|
50
50
|
end
|
|
51
51
|
|