i #260 Add commit and churn to issue notebook

When implementing the social smell metrics in Kaiaulu, churn and commits were accidentally removed. This commit adds them back. OpenSSL project configuration file was also updated to timestamp the analysis performed for OpenSSL in the Notebook. _pkgdown was updated so documentation for the package can be generated. Signed-off-by: Carlos Paradis <[email protected]>
sailuh · Dec 8, 2023 · 9294a9b · 9294a9b
1 parent 0bda3ea
commit 9294a9b
Show file tree

Hide file tree

Showing 3 changed files with 48 additions and 54 deletions.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -94,11 +94,18 @@ reference:
 - title: __IO__
   desc:  Functions to create and read temporary files in R.
 - contents:
+  - io_make_file
+  - io_make_folder
+  - io_delete_folder
   - make_temporary_file
   - read_temporary_file
 - title: __Git__
   desc:  Functions to interact with git interface to facilitate interval static code analysis.
 - contents:
+  - git_init
+  - git_mv
+  - git_add
+  - git_commit
   - git_checkout
   - git_head
   - git_log
@@ -214,5 +221,29 @@ reference:
 - title: __Fake Data Generator__
   desc:  Functions to create fake data for unit testing parsers
 - contents:
-  - jira_create_sample_log
-  - jira_delete_sample_log
+  - make_mbox_reply
+  - make_mbox_mailing_list
+  - make_jira_issue
+  - make_jira_issue_tracker
+- title: internal
+- contents:
+  - create_assignee
+  - create_base_info
+  - create_components
+  - create_creator
+  - create_ext_info
+  - create_issue_comments
+  - create_issue_type
+  - create_reporter
+  - create_resolution
+  - create_status
+  - example_different_branches
+  - example_empty_repo
+  - example_jira_issue_comments
+  - example_jira_issue_components
+  - example_jira_two_issues
+  - example_large_sized_commits
+  - example_mailing_list_two_threads
+  - example_renamed_file
+  - example_test_example_src_repo
+
diff --git a/conf/openssl.yml b/conf/openssl.yml
@@ -38,9 +38,10 @@ version_control:
   # The .git is hidden, so you can see it using `ls -a`
   log: ../../rawdata/git_repo/OpenSSL/.git
   # From where the git log was downloaded?
-  log_url: https://github.com/apache/apr
+  log_url: https://github.com/openssl/openssl
   # List of branches used for analysis
   branch:
+    - 3f5ea7dc0ca4affb1fbe5c9f6d25add8aa3535b3
     - master
 
 mailing_list:

diff --git a/vignettes/issue_social_smell_showcase.Rmd b/vignettes/issue_social_smell_showcase.Rmd
@@ -129,10 +129,6 @@ Remember: Kaiaulu will not throw errors if you omit relevant sources of develope
 
 ```{r eval = FALSE}
 project_mbox <- NULL
-project_jira <- NULL
-project_github_replies <- NULL
-
-
 
 if(!is.null(mbox_path)){
   project_mbox <- parse_mbox(perceval_path,mbox_path)  
@@ -142,8 +138,6 @@ if(!is.null(mbox_path)){
   
   project_mbox$reply_datetimetz <- as.POSIXct(project_mbox$reply_datetimetz,
                                         format = "%a, %d %b %Y %H:%M:%S %z", tz = "UTC")
-
-  
 }
 ```
 
@@ -208,8 +202,8 @@ project_reply <- project_log[["project_reply"]]
 
 
 ```{r echo=FALSE}
-project_git <- readRDS("~/Downloads/openssl_project_git.rds")
-project_reply <- readRDS("~/Downloads/openssl_project_reply.rds")
+project_git <- readRDS("~/Downloads/ist_openssl_project_git.rds")
+project_reply <- readRDS("~/Downloads/ist_openssl_project_reply.rds")
 ```
 
 
@@ -287,6 +281,7 @@ cve_ids <- unique(project_git_cves$commit_message_id)
 progress_i <- 1
 total <- length(cve_ids)
 cve_smell_interval <- list()
+
 for(cve_id in cve_ids){
   print(stringi::stri_c("Progress: ",progress_i,"/",total))
   progress_i <- progress_i + 1
@@ -343,6 +338,8 @@ for(cve_id in cve_ids){
     ml_only_devs <- NA
     ml_threads <- NA
     code_ml_both_devs <- NA
+    churn <- NA
+    n_commits <- NA
     
     i <- j - 1
   
@@ -420,6 +417,10 @@ for(cve_id in cve_ids){
       code_only_devs <- length(unique(project_git_slice$identity_id))
       code_files <- length(unique(project_git_slice$file_pathname))
       
+      churn <- sum(as.numeric(project_git_slice$lines_added) +
+                       as.numeric(project_git_slice$lines_removed),na.rm= TRUE)
+      n_commits <- length(unique(project_git_slice$commit_hash))
+      
     }  
     if(ml_exist){
       # Smell
@@ -468,7 +469,9 @@ for(cve_id in cve_ids){
                                      code_files,
                                      ml_only_devs,
                                      ml_threads,
-                                     code_ml_both_devs)
+                                     code_ml_both_devs,
+                                     churn,
+                                     n_commits)
   }
   cve_interval_id <- stri_c(cve_id,"|",start_date,"|",end_date)
   smells_interval <- rbindlist(smells)
@@ -478,48 +481,7 @@ for(cve_id in cve_ids){
 dt <- rbindlist(cve_smell_interval)
 ```
 
-
-```{r echo = FALSE}
-dt <- readRDS("~/Downloads/openssl_dt_cve_smell_interval.rds")
-git_network_authors <- readRDS("~/Downloads/openssl_git_network_authors.rds")
-code_clusters <- readRDS("~/Downloads/openssl_code_clusters.rds")
-mail_clusters <- readRDS("~/Downloads/openssl_mail_clusters.rds")
-reply_network_authors <- readRDS("~/Downloads/openssl_reply_network_authors.rds")
-```
-
 ```{r}
-kable(head(dt))
-```
-
-
-## Community Inspection per Time Slice
-
-This shows the last loop slice. Authors here are connected if they changed the same file in a given time window:
-
-```{r}
-project_collaboration_network <- recolor_network_by_community(git_network_authors,code_clusters)
-
-gcid <- igraph::graph_from_data_frame(d=project_collaboration_network[["edgelist"]], 
-                      directed = FALSE,
-                      vertices = project_collaboration_network[["nodes"]])
-
-visIgraph(gcid,randomSeed = 1)
-```
-
-In this network, the nodes are colored according to the communities identified by the community detection algorithm used, OSLOM. We can observe the classification is reasonable: The inter connected nodes were assigned as one community, where as the nodes without communication were considered their ``own community''. 
-
-You can also observe the identity match algorithm in action and its potential implications: Different identities matched to the same author are separated by the | ). Had it not performed as intended, single nodes would appear separately and very likely connected, thus biasing the social metrics.
-
-The following visualization shows similar information, however authors are only now connected if they exchanged e-mails on the same e-mail thread in the same time period as the previous graph:
-
-```{r eval = FALSE}
-project_collaboration_network <- recolor_network_by_community(reply_network_authors,mail_clusters)
-
-gcid <- igraph::graph_from_data_frame(d=project_collaboration_network[["edgelist"]], 
-                      directed = FALSE,
-                      vertices = project_collaboration_network[["nodes"]])
-
-visIgraph(gcid,randomSeed = 1)
+#fwrite(dt,"~/Downloads/ist_cve_smell_interval_dt.csv")
 ```
 
-The large absence of authors in the second visualization indicates communication was very sparse during that development time period. Because a large number of changes were performed, and sparse communication occurred, the various social metrics captured by comparing both graphs would be large.