i #223 Add GoF Module and QoL for Text Module

The GoF Module slighly extends the previous GoF Notebook API to facilitate integration to other analysis in Kaiaulu. - De-coupled GoF Parser into Parser/Writer - Sub-setting of GoF Output from Classes/Methods/Variables -> Classes - Mapping from Classes to Filepaths - Reorganization of functions into a dedicated GoF module. Signed-off-by: Carlos Paradis <[email protected]>
sailuh · Sep 1, 2023 · ad6efa7 · ad6efa7
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diff --git a/NAMESPACE b/NAMESPACE
@@ -73,6 +73,8 @@ export(metric_file_non_bug_churn)
 export(metric_file_non_bug_frequency)
 export(model_directed_graph)
 export(motif_factory)
+export(motif_factory_anti_square)
+export(motif_factory_anti_triangle)
 export(motif_factory_square)
 export(motif_factory_triangle)
 export(normalized_levenshtein)
@@ -105,13 +107,15 @@ export(parse_r_function_dependencies)
 export(parse_rfile_ast)
 export(query_src_text)
 export(query_src_text_class_names)
+export(query_src_text_namespace)
 export(read_temporary_file)
 export(recolor_network_by_community)
 export(smell_missing_links)
 export(smell_organizational_silo)
 export(smell_radio_silence)
 export(smell_sociotechnical_congruence)
 export(split_name_email)
+export(subset_gof_class)
 export(transform_commit_message_id_to_network)
 export(transform_cve_cwe_file_to_network)
 export(transform_dependencies_to_network)
@@ -126,6 +130,7 @@ export(transform_reply_to_bipartite_network)
 export(transform_temporal_gitlog_to_adsmj)
 export(weight_scheme_count_deleted_nodes)
 export(weight_scheme_sum_edges)
+export(write_gof_patterns)
 importFrom(data.table,":=")
 importFrom(data.table,.N)
 importFrom(data.table,as.data.table)

diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,7 @@ __kaiaulu 0.0.0.9700 (in development)__
 
 ### NEW FEATURES
 
+ * Adds GoF module and various utility functions to facilitate integrating identified pattern classes to files. [#223](https://github.com/sailuh/kaiaulu/issues/223)
  * Adds `parse_jira_rss_xml()`, which enables reusing the full 26 projects dataset of our prior TSE work. [#218](https://github.com/sailuh/kaiaulu/issues/218)
  * Adds `metric_file_bug_frequency()`, `metric_file_non_bug_frequency()`, `metric_file_bug_churn()`, `metric_file_non_bug_churn()`, `metric_file_churn()` to `R/metric.R` [#214](https://github.com/sailuh/kaiaulu/issues/214)
  * Adds Gang of Four parser for Tsantalis' parser4.jar [#211](https://github.com/sailuh/kaiaulu/issues/211)

diff --git a/R/gof.R b/R/gof.R
@@ -0,0 +1,141 @@
+# Kaiaulu - https://github.com/sailuh/kaiaulu
+#
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+#' Write GoF Patterns
+#'
+#' Write GoF patterns generated by `pattern4.jar` into a a table.
+#' \url{https://www.srcml.org/documentation.html}.
+#' Pattern4.jar is available on
+#' [Tsantalis' homepage](https://users.encs.concordia.ca/~nikolaos/pattern_detection.html)).
+#'
+#' @param pattern4_path The path to Tsantalis' pattern4 jar
+#' @param class_folder_path The path to a folder one
+#' level above subdirectories that contain the class files.
+#' @param output_filepath Optional path to store the XML generated by pattern4. If not
+#' specified, it will be saved to `/tmp/gof.xml`.
+#'
+#' @return A data.table containing the parsed gof patterns per class.
+#' @references N. Tsantalis, A. Chatzigeorgiou, G. Stephanides, S. T. Halkidis,
+#' "Design Pattern Detection Using Similarity Scoring",
+#' IEEE Transactions on Software Engineering,
+#' vol. 32, no. 11, pp. 896-909, November, 2006.
+#' @export
+write_gof_patterns <- function(pattern4_path,class_folder_path,output_filepath='/tmp/gof.xml'){
+
+  pattern4_path <- path.expand(pattern4_path)
+  class_folder_path <- path.expand(class_folder_path)
+
+  if(!file.exists(pattern4_path)) stop("The specified pattern4_path does not exist!")
+  if(!dir.exists(class_folder_path)) stop("The specified class_folder_path does not exist!")
+
+  # java -Xms32m -Xmx512m -jar pattern4.jar -target "C:\foo\myclasses" -output "C:\foo\output.xml"
+  gof_pattern_xml_path <- system2("java",
+                                  args = c('-Xms64m','-Xmx100000m','-jar',
+                                           pattern4_path,
+                                           '-target',paste0('"',class_folder_path,'"'),
+                                           '-output',paste0('"',output_filepath,'"')),
+                                  stdout = TRUE,
+                                  stderr = FALSE)
+}
+
+#' Parse GoF Patterns
+#'
+#' Parses GoF patterns generated by \code{\link{write_gof_patterns}} into a a table.
+#' \url{https://www.srcml.org/documentation.html}.
+#' Pattern4.jar is available on
+#' [Tsantalis' homepage](https://users.encs.concordia.ca/~nikolaos/pattern_detection.html)).
+#'
+#' @param output_filepath Optional path to read the XML generated by \code{\link{write_gof_patterns}}.  If not
+#' specified, it will be assumed saved to the temporary folder path `/tmp/gof.xml`.
+#'
+#' @return A data.table containing the parsed gof patterns per class.
+#' @references N. Tsantalis, A. Chatzigeorgiou, G. Stephanides, S. T. Halkidis,
+#' "Design Pattern Detection Using Similarity Scoring",
+#' IEEE Transactions on Software Engineering,
+#' vol. 32, no. 11, pp. 896-909, November, 2006.
+#' @export
+parse_gof_patterns <- function(output_filepath='/tmp/gof.xml'){
+  gof_pattern_xml <- XML::xmlTreeParse(output_filepath)
+
+  # The <system> root node enumerates a fixed number of <pattern> tags.
+  gof_root <- XML::xmlRoot(gof_pattern_xml) #class => XML Node
+  patterns <- XML::xmlChildren(gof_root) #class => XMLNodeList (lapply safe)
+
+  parse_instance <- function(instance){
+
+    roles <- XML::xmlChildren(instance)
+    role_names <- sapply(roles,XML::xmlGetAttr,"name")
+    element <- sapply(roles,XML::xmlGetAttr,"element")
+
+    instance <- data.table(instance_id,
+                           role_name = role_names,
+                           element = element)
+
+    instance_id <<- instance_id + 1
+
+    return(instance)
+  }
+
+  parse_pattern <- function(pattern){
+    # Each GoF pattern, if occurring on the code, is assigned an instance
+    n_instances <- XML::xmlSize(pattern)
+
+    # The XML mentions the pattern name even with no instances detected. We do not
+    # include the pattern name if no instances are detected.
+    if(n_instances > 0){
+
+      # Note counter bypasses lapply scope <<-
+      instance_id <<- 1
+
+      pattern_name <- XML::xmlGetAttr(pattern,"name")
+
+      instances <- XML::xmlChildren(pattern)
+      instances_dt <- rbindlist(lapply(instances,parse_instance))
+      instances_dt$pattern_name <- pattern_name
+      return(instances_dt)
+    }else{
+      return(data.table())
+    }
+  }
+  patterns_dt <- rbindlist(lapply(patterns,parse_pattern))
+
+  patterns_dt <- patterns_dt[,.(pattern_name,instance_id,role_name,element)]
+  return(patterns_dt)
+}
+
+
+#' Subset GoF Classes
+#'
+#' The \code{\link{write_gof_patterns}} contains not only
+#' the participation of a class in a GoF Pattern, but also
+#' the participation of methods and variables when applicable.
+#' To distinguish a row entry among class, method or variable,
+#' we must subset the role names that are associated to classes.
+#' This information can be obtained by inspecting the source code
+#' of a similar tool to pattern4 by Tsantalis.
+#'
+#' More specifically, every pattern that pattern4.jar can identify is
+#' defined as a PatternDescriptor in DPD4Eclipse/src/gr/uom/java/pattern
+#' /PatternGenerator.java (see: https://github.com/tsantalis/DPD4Eclipse).
+#'
+#' E.g. The PatternDescriptor Decorator has rowNameList.add("Component");
+#' rowNameList.add("Decorator"); Therefore, in the XML output by pattern4.jar,
+#' it is guaranteed when (pattern_name == "Decorator" & role_name == "Component") or
+#' (pattern_name == "Decorator" & role_name == "Decorator").
+#'
+#' By following this process, a list of role names can be defined to subset the table
+#' to only contain classes.
+#'
+#' Note pattern4 executes in bytecode, hence the classes are identified by their namespace.
+#' Refer to \code{\link{query_src_text_namespace}} to obtain a table to map namespace classes
+#'  to filepaths.
+#' @param gof_patterns A table of parsed GoF Patterns
+#' obtained from \code{\link{parse_gof_patterns}}.
+#' @export
+subset_gof_class <- function(gof_patterns){
+  lead_patterns <- c('Creator', 'Abstraction', 'Adapter', 'Singleton', 'Prototype', 'Decorator', 'AbstractClass', 'Composite', 'Subject', 'State', 'Visitor', 'Strategy', 'Observer', 'Command', 'Handler', 'Component', 'Context', 'Implementor', 'ConcreteElement', 'Prototype', 'Client', 'Proxy', 'RealSubject', 'Subject', 'FamilyHead', 'Redirecter')
+  return(gof_patterns[role_name %in% lead_patterns])
+}
diff --git a/R/parser.R b/R/parser.R
@@ -1537,92 +1537,6 @@ parse_r_dependencies <- function(folder_path){
   return(edgelists)
 }
 
-#' Parse GoF Patterns
-#'
-#' Parses GoF patterns generated by `pattern4.jar` into a a table.
-#' \url{https://www.srcml.org/documentation.html}.
-#' Pattern4.jar is available on
-#' [Tsantalis' homepage](https://users.encs.concordia.ca/~nikolaos/pattern_detection.html)).
-#'
-#' @param pattern4_path The path to Tsantalis' pattern4 jar
-#' @param class_folder_path The path to a folder one
-#' level above subdirectories that contain the class files.
-#' @param output_filepath Optional path to store the XML generated by pattern4. If not
-#' specified, it will be saved to `/tmp/gof.xml`.
-#'
-#' @return A data.table containing the parsed gof patterns per class.
-#' @references N. Tsantalis, A. Chatzigeorgiou, G. Stephanides, S. T. Halkidis,
-#' "Design Pattern Detection Using Similarity Scoring",
-#' IEEE Transactions on Software Engineering,
-#' vol. 32, no. 11, pp. 896-909, November, 2006.
-#' @export
-parse_gof_patterns <- function(pattern4_path,class_folder_path,output_filepath='/tmp/gof.xml'){
-
-  pattern4_path <- path.expand(pattern4_path)
-  class_folder_path <- path.expand(class_folder_path)
-
-  if(!file.exists(pattern4_path)) stop("The specified pattern4_path does not exist!")
-  if(!dir.exists(class_folder_path)) stop("The specified class_folder_path does not exist!")
-
-  # java -Xms32m -Xmx512m -jar pattern4.jar -target "C:\foo\myclasses" -output "C:\foo\output.xml"
-  gof_pattern_xml_path <- system2("java",
-                                  args = c('-Xms32m','-Xmx512m','-jar',
-                                           pattern4_path,
-                                           '-target',paste0('"',class_folder_path,'"'),
-                                           '-output',paste0('"',output_filepath,'"')),
-                                  stdout = TRUE,
-                                  stderr = FALSE)
-
-
-
-  gof_pattern_xml <- XML::xmlTreeParse(output_filepath)
-
-  # The <system> root node enumerates a fixed number of <pattern> tags.
-  gof_root <- XML::xmlRoot(gof_pattern_xml) #class => XML Node
-  patterns <- XML::xmlChildren(gof_root) #class => XMLNodeList (lapply safe)
-
-  parse_instance <- function(instance){
-
-    roles <- XML::xmlChildren(instance)
-    role_names <- lapply(roles,XML::xmlGetAttr,"name")
-    element <- lapply(roles,XML::xmlGetAttr,"element")
-
-    instance <- data.table(instance_id,
-                           role_name = role_names,
-                           element = element)
-
-    instance_id <<- instance_id + 1
-
-    return(instance)
-  }
-
-  parse_pattern <- function(pattern){
-    # Each GoF pattern, if occurring on the code, is assigned an instance
-    n_instances <- XML::xmlSize(pattern)
-
-    # The XML mentions the pattern name even with no instances detected. We do not
-    # include the pattern name if no instances are detected.
-    if(n_instances > 0){
-
-      # Note counter bypasses lapply scope <<-
-      instance_id <<- 1
-
-      pattern_name <- XML::xmlGetAttr(pattern,"name")
-
-      instances <- XML::xmlChildren(pattern)
-      instances_dt <- rbindlist(lapply(instances,parse_instance))
-      instances_dt$pattern_name <- pattern_name
-      return(instances_dt)
-    }else{
-      return(data.table())
-    }
-  }
-  patterns_dt <- rbindlist(lapply(patterns,parse_pattern))
-
-  patterns_dt <- patterns_dt[,.(pattern_name,instance_id,role_name,element)]
-  return(patterns_dt)
-}
-
 # Various imports
 utils::globalVariables(c("."))
 #' @importFrom magrittr %>%

diff --git a/R/text.R b/R/text.R
@@ -107,3 +107,56 @@ query_src_text_class_names <- function(srcml_path,srcml_filepath){
   return(dt_filepath_classname)
 
 }
+
+#' Query srcML Namespace
+#'
+#' This is a convenience function to parse namespace names out of a project.
+#' \url{https://www.srcml.org/documentation.html}.
+#'
+#'
+#' @param srcml_path The path to srcML binary
+#' @param srcml_filepath The path to the srcML file to be queried
+#' (see \code{\link{annotate_src_text}}).
+#'
+#' @return A data.table containing Namespace.
+#' @references For details, see \url{https://www.srcml.org/documentation.html}.
+#' @export
+query_src_text_namespace <- function(srcml_path,srcml_filepath){
+  srcml_path <- path.expand(srcml_path)
+  srcml_filepath <- path.expand(srcml_filepath)
+
+  xpath_query <- "//src:package"
+
+  srcml_output <- query_src_text(srcml_path,xpath_query,srcml_filepath)
+
+  srcml_output <- XML::xmlTreeParse(srcml_output)
+  srcml_root <- XML::xmlRoot(srcml_output)
+
+  # The children of the root node is a list of unit nodes
+  srcml_class_names <- XML::xmlChildren(srcml_root)
+  # Each unit node is of the form:
+  # <unit revision="1.0.0" language="Java" filename="/Users/lzhan/Desktop/rawdata/git_repo/iotdb/tsfile/src/test/java/org/apache/iotdb/tsfile/read/reader/FakedMultiBatchReader.java" item="1"><package>package <name><name>org</name><operator>.</operator><name>apache</name><operator>.</operator><name>iotdb</name><operator>.</operator><name>tsfile</name><operator>.</operator><name>read</name><operator>.</operator><name>reader</name></name>;</package></unit>
+
+
+  parse_namespace <- function(unit){
+    # The class name is a child node of each node
+    class_name <- XML::xmlValue(unit[[1]])
+    class_name <- sub("^package", "", class_name)
+    class_name <- sub(";$","",class_name)
+    # The attribute filename contains the filename the class belongs to
+    filepath <- XML::xmlGetAttr(unit,"filename")
+
+    project_name <- 'iotdb'
+    # Create a regular expression pattern using project_name
+    pattern <- paste0('.*?', project_name, '/')
+    # Get relative path
+    filepath <- sub(pattern, '', filepath)
+
+    filename <- sub("\\.java$", "", basename(filepath))
+    full_path <- paste(class_name, filename, sep=".")
+    return(data.table(filepath=filepath, namespace=full_path))
+  }
+  dt_filepath_classname <- rbindlist(lapply(srcml_class_names,parse_namespace))
+
+  return(dt_filepath_classname)
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -25,7 +25,6 @@ reference:
   - parse_line_metrics
   - parse_line_type_file
   - parse_commit_message_id
-  - parse_gof_patterns
 - title: __Filters__
   desc:  Filters for file extensions, and substrings, such as test files, and time intervals.
 - contents:
@@ -65,6 +64,8 @@ reference:
   - motif_factory
   - motif_factory_triangle
   - motif_factory_square
+  - motif_factory_anti_triangle
+  - motif_factory_anti_square
 - title: __Identity__
   desc:  Provide the same id to authors who use variations of names or emails.
 - contents:
@@ -202,3 +203,11 @@ reference:
   - annotate_src_text
   - query_src_text
   - query_src_text_class_names
+  - query_src_text_namespace
+
+- title: __Gang of Four Patterns__
+  desc:  Functions related to Gang of Four Patterns
+- contents:
+  - parse_gof_patterns
+  - write_gof_patterns
+  - subset_gof_class
diff --git a/man/parse_gof_patterns.Rd b/man/parse_gof_patterns.Rd