diff options
Diffstat (limited to 'lib/qmrf-report.rb')
| -rw-r--r-- | lib/qmrf-report.rb | 26 |
1 files changed, 17 insertions, 9 deletions
diff --git a/lib/qmrf-report.rb b/lib/qmrf-report.rb index 2c6cde8..a5cb86b 100644 --- a/lib/qmrf-report.rb +++ b/lib/qmrf-report.rb @@ -21,6 +21,8 @@ module OpenTox SCHEMA_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xsd") # QMRF XML Template file TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml") + # QMRF catalogs. Entries of a catalog can be referenced in certain tags. + CATALOGS = ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"] # QMRF XML tags with attributes to edit ATTRIBUTE_TAGS = ["training_set_availability", "training_set_data", "training_set_descriptors", "dependent_var_availability", "validation_set_availability", "validation_set_data", "validation_set_descriptors", "validation_dependent_var_availability"] @@ -46,7 +48,11 @@ module OpenTox end # Get or Set a value - # e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title> + # e.G.: + #@example change the title + # report.value "QSAR_title", "Title of My QSAR" + # #changes the QSAR_title tag to: + # #<QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title> # @param [String] key Nodename e.g.: "QSAR_title" # @param [String] value Value to change. If not set the function returns the current value # @return [Error] returns Error message if fails @@ -58,11 +64,13 @@ module OpenTox t.content end - # Set attributes of an report XML tag - # e.G.: <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/> + # Set attributes of an report XML tag. + # Some of the QMRF XML tags have attributes to be edited. This applies to 6.1 to 6.4 and 7.1 to 7.4 see also: {OpenTox::QMRFReport::ATTRIBUTE_TAGS ATTRIBUTE_TAGS}. + # e.G. "Available information for the training set" at 6.2 of the report: + # <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/> #@example change_attributes # report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"} - # @param [String] key Nodename e.g.: "training_set_data" + # @param [String] tagname Nodename e.g.: "training_set_data" # @param [Hash] valuehash Key-Value Hash of tag attributes to change. # @return [Error] returns Error message if fails def change_attributes tagname, valuehash @@ -74,7 +82,7 @@ module OpenTox end # Change a catalog - # @param [String] catalog Name of the catalog - One of "software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog" in QMRF v1.3 + # @param [String] catalog Name of the catalog - One of {OpenTox::QMRFReport::CATALOGS CATALOGS}. # @param [String] id Single entry node in the catalog e.G.: "<software contact='mycontact@mydomain.dom' description="My QSAR Software " id="software_catalog_2" name="MySoftware" number="" url="https://mydomain.dom"/> # @param [Hash] valuehash Key-Value Hash with attributes for a single catalog node # @return [Error] returns Error message if fails @@ -100,7 +108,7 @@ module OpenTox #@example ref_catalog # report.ref_catalog 'qmrf_authors', 'authors_catalog', 'firstauthor' # @param [String] chapter Name of the chapter to add the catalog reference. e.g.: qmrf_authors, model_authors, QSAR_software, ... - # @param [String] catalog Name of the catalog + # @param [String] catalog Name of the catalog. One of {OpenTox::QMRFReport::CATALOGS CATALOGS}. # @param [String] id entry node in the catalog def ref_catalog chapter, catalog, id catalog_exists? catalog @@ -117,7 +125,7 @@ module OpenTox end # get an attribute from a catalog entry - # @param [String] catalog Name of the catalog + # @param [String] catalog Name of the catalog. One of {OpenTox::QMRFReport::CATALOGS CATALOGS}. # @param [String] id entry id in the catalog # @param [String] key returns value of a key in a catalog node # @return [String, false] returns value of a key in a catalog node or false if catalog entry do not exists. @@ -132,9 +140,9 @@ module OpenTox # Check if a catalog exists in this QMRF version # @param [String] catalog Catalog - # @return [Error, true] returns true or Error if a catalog do not exists + # @return [Error, true] returns true or Error if a catalog do not exists. See also {OpenTox::QMRFReport::CATALOGS CATALOGS}. def catalog_exists? catalog - raise "Unknown catalog: #{catalog}" unless ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"].include? catalog.to_s + raise "Unknown catalog: #{catalog}" unless CATALOGS.include? catalog.to_s true end |