src/main.rs

[weswc]

Metadata

• initial qc commit: 482f952
• git branch: comment
• author: wes-a2ai (wes@a2-ai.com)
• file contents at initial qc commit

Data Assembly

Reproducibility and Organization

• Script is a quarto document
• Script renders free of error within the Rproject space
• .rv$summary() present at beginning of script and passes
• Relative paths are used
• .Rprofile is present in same directory as final script
• Parquet files are used where available
  Files that should be parquet:
  • [INSERT]
• Data hash codes are printed and match source and output data
  Expected hash files:
  • [INSERT]
• Correct source data files are read in
  Correct source data:
  • [INSERT]
• Final dataset outputs to expected location as a csv, converts all NA values to a period, and outputs a hash
• All code chunks are labeled
• sessioninfo() included at the conclusion of script

yspec

• All yspec files can be found in <project>/data/derived and are excluded from the gitignore
• All variables have descriptions. All descriptions are easy to read and understand. All variables have units where applicable
• All categorical variables have all options outlined and a 1:1 numerical decoded value. All categorical variables match the decoding present in the yspec
• All continuous variables specify units and all units match those of the final dataset. If multiple analytes are included in a single column, units are clear for each analyte
• The yspec file contains all necessary variables for analysis, including both project specific variables and NONMEM required variables

Dataset Assumptions - Automated

These can be done using pointblank and QCer can just confirm these pass!

• List pointblank assumptions:
  • [INSERT]
• The final dataset includes both a numeric (ID) and character (e.g. USUBJID) version of the unique subject identifier
• The final dataset includes all columns listed in the corresponding yspec file
• Any missing columns or observations are confirmed to be missing in source data and marked as -999
• Missing data is documented appropriately in dataset

Data Assumptions - Manual

These can't be done using pointblank and QCer must look closely at specific sections of code

• All manual conversions are accurate and consistent
• All manual imputations are well documented to outside sources or sufficiently justified
• All manual imputations are accurate according to their specified source
• All assumptions are well justified (e.g. by the protocol, project lead decision, client decision, etc.), documented, and reasonable
• All records to be excluded (e.g. for all analyses, for sensitivity analysis only) are properly identified, justified, and documented (i.e., CFLAG or other flag column)

Misc

• Code is easily readable and follows general coding guidelines (link to code hub)
• Helper functions are well documented, make sense, make reasonable assumptions, and follow good coding practices
• Helper function arguments match as stated in yspec (e.g. SEX variable in Cockcroft-Gault equation matches decoding in yspec)

[weswc]

QC Notification

Metadata

• current commit: 482f952
• previous commit: 7b7030c
• commit comparison

File Difference

@@ previous script: lines 1-13 @@
@@  current script: lines 1-17 @@
- 1 use anyhow::Result;
+ 1 use anyhow::{Result, anyhow, bail};
  2 use clap::{Parser, Subcommand};
  3 use clap_verbosity_flag::{InfoLevel, Verbosity};
  4 use std::path::PathBuf;
  5 
- 6 use ghqctoolkit::cli::{CliContext, RelevantFileParser};
- 7 use ghqctoolkit::{Configuration, GitInfo, RelevantFile, create_issue};
+ 6 use ghqctoolkit::cli::{CreateContext, CommentContext, RelevantFileParser};
+ 7 use ghqctoolkit::utils::StdEnvProvider;
+ 8 use ghqctoolkit::{
+ 9     Configuration, GitActionImpl, GitHubApi, GitInfo, RelevantFile, create_issue, determine_config_info,
+ 10     setup_configuration,
+ 11 };
  12 
  13 #[derive(Parser)]
  14 #[command(author, version, about, long_about = None)]
  15 struct Cli {
  16     #[command(subcommand)]
  17     command: Commands,
@@ previous script: lines 13-24 @@
@@  current script: lines 17-32 @@
  17     command: Commands,
  18 
  19     /// the git project directory for which to QC on
- 16     #[clap(short, long, default_value = ".", global = true)]
- 17     project: PathBuf,
+ 20     #[clap(short = 'd', long, default_value = ".", global = true)]
+ 21     directory: PathBuf,
  22 
+ 23     /// Configuration directory path
+ 24     #[arg(short, long)]
+ 25     config_dir: Option<PathBuf>,
+ 26 
  27     #[command(flatten)]
  28     verbose: Verbosity<InfoLevel>,
  29 }
  30 
  31 #[derive(Subcommand)]
  32 enum Commands {
@@ previous script: lines 27-35 @@
@@  current script: lines 35-48 @@
  35         #[command(subcommand)]
  36         issue_command: IssueCommands,
  37     },
+ 38     /// Configuration management commands
+ 39     Configuration {
+ 40         #[command(subcommand)]
+ 41         configuration_command: ConfigurationCommands,
+ 42     },
  43 }
  44 
  45 #[derive(Subcommand)]
  46 enum IssueCommands {
  47     /// Create a new issue for quality control
  48     Create {
@@ previous script: lines 41-53 @@
@@  current script: lines 54-62 @@
  54         #[arg(short, long)]
  55         file: Option<PathBuf>,
  56 
- 44         /// Configuration directory path
- 45         #[arg(short, long)]
- 46         config_dir: Option<PathBuf>,
- 47 
  57         /// Name of the checklist to use (will prompt if not provided)
  58         #[arg(short = 'l', long)]
  59         checklist_name: Option<String>,
  60 
  61         /// Assignees for the issue (usernames)
  62         #[arg(short, long)]
@@ previous script: lines 57-67 @@
@@  current script: lines 66-101 @@
  66         #[arg(short = 'r', long, value_parser = RelevantFileParser)]
  67         relevant_files: Option<Vec<RelevantFile>>,
  68     },
+ 69     Comment {
+ 70         /// Milestone for the issue (will prompt if not provided)
+ 71         #[arg(short, long)]
+ 72         milestone: Option<String>,
+ 73 
+ 74         /// File path to create issue for (will prompt if not provided)
+ 75         #[arg(short, long)]
+ 76         file: Option<PathBuf>,
+ 77 
+ 78         /// Current commit (defaults to most recent file commit if not in interactive mode)
+ 79         #[arg(short, long)]
+ 80         current_commit: Option<String>,
+ 81 
+ 82         /// Previous commit (defaults to second most recent file commit if not in interactive mode)
+ 83         #[arg(short, long)]
+ 84         previous_commit: Option<String>,
+ 85     }
  86 }
  87 
+ 88 #[derive(Subcommand)]
+ 89 enum ConfigurationCommands {
+ 90     Setup {
+ 91         /// git repository url to be cloned to config_dir
+ 92         git: Option<String>,
+ 93     },
+ 94 }
+ 95 
  96 #[cfg(feature = "cli")]
  97 #[tokio::main]
  98 async fn main() -> Result<()> {
  99     let cli = Cli::parse();
  100 
  101     let log_level = cli.verbose.log_level_filter();
@@ previous script: lines 71-133 @@
@@  current script: lines 105-241 @@
  105         .filter(Some("octocrab"), log_level) // Allow logs from octocrab
  106         .init();
  107 
- 74     let git_info = GitInfo::from_path(&cli.project)?;
+ 108     let env = StdEnvProvider;
  109 
  110     match cli.command {
- 77         Commands::Issue { issue_command } => match issue_command {
- 78             IssueCommands::Create {
- 79                 milestone,
- 80                 file,
- 81                 config_dir,
- 82                 checklist_name,
- 83                 assignees,
- 84                 relevant_files,
- 85             } => {
- 86                 let configuartion = if let Some(c) = config_dir {
- 87                     Configuration::from_path(&c)?
- 88                 } else {
- 89                     log::debug!("Configuration not specified, using default.");
- 90                     Configuration::default()
- 91                 };
+ 111         Commands::Issue { issue_command } => {
+ 112             let git_info = GitInfo::from_path(&cli.directory, &env)?;
  113 
- 93                 let context = match (milestone, file, checklist_name) {
- 94                     (Some(milestone), Some(file), Some(checklist_name)) => {
- 95                         CliContext::from_args(
- 96                             milestone,
- 97                             file,
- 98                             checklist_name,
- 99                             assignees,
- 100                             relevant_files,
- 101                             configuartion,
- 102                             git_info,
- 103                         )
- 104                         .await?
+ 114             match issue_command {
+ 115                 IssueCommands::Create {
+ 116                     milestone,
+ 117                     file,
+ 118                     checklist_name,
+ 119                     assignees,
+ 120                     relevant_files,
+ 121                 } => {
+ 122                     let config_dir = determine_config_info(cli.config_dir, &env)?;
+ 123                     let mut configuration = Configuration::from_path(&config_dir);
+ 124                     configuration.load_checklists();
+ 125                     
+ 126                     // Fetch milestones first
+ 127                     let milestones = git_info.get_milestones().await?;
+ 128 
+ 129                     let context = match (milestone, file, checklist_name) {
+ 130                         (Some(milestone), Some(file), Some(checklist_name)) => {
+ 131                             CreateContext::from_args(
+ 132                                 milestone,
+ 133                                 file,
+ 134                                 checklist_name,
+ 135                                 assignees,
+ 136                                 relevant_files,
+ 137                                 configuration,
+ 138                                 git_info,
+ 139                             )
+ 140                             .await?
+ 141                         }
+ 142                         (None, None, None) => {
+ 143                             CreateContext::from_interactive(&cli.directory, &milestones, configuration, git_info)
+ 144                                 .await?
+ 145                         }
+ 146                         _ => {
+ 147                             bail!(
+ 148                                 "Either provide all three arguments (--milestone, --file, --checklist-name) or none to enter interactive mode"
+ 149                             );
+ 150                         }
+ 151                     };
+ 152 
+ 153                     create_issue(
+ 154                         &context.file,
+ 155                         &context.milestone_status,
+ 156                         &context.checklist,
+ 157                         context.assignees,
+ 158                         &context.git_info,
+ 159                         context.relevant_files,
+ 160                     )
+ 161                     .await?;
+ 162 
+ 163                     println!("✅ Issue created successfully!");
+ 164                 }
+ 165                 IssueCommands::Comment { milestone, file, current_commit, previous_commit } => {
+ 166                     // Fetch milestones first
+ 167                     let milestones = git_info.get_milestones().await?;
+ 168                     
+ 169                     let context = match (milestone, file) {
+ 170                         (None, None) => {
+ 171                             // Interactive mode
+ 172                             CommentContext::from_interactive(&milestones, git_info).await?
+ 173                         }
+ 174                         (Some(milestone), Some(file)) => {
+ 175                             // Non-interactive mode
+ 176                             CommentContext::from_args(
+ 177                                 milestone,
+ 178                                 file,
+ 179                                 current_commit,
+ 180                                 previous_commit,
+ 181                                 &milestones,
+ 182                                 git_info,
+ 183                             ).await?
+ 184                         }
+ 185                         _ => {
+ 186                             bail!("Must provide both --milestone and --file arguments or neither to enter interactive mode")
+ 187                         }
+ 188                     };
+ 189                     
+ 190                     // Display what would happen
+ 191                     println!("Creating comment for file: {}", context.file.display());
+ 192                     println!("Issue: #{} - {}", context.issue.number, context.issue.title);
+ 193                     println!("Current commit: {}", context.current_commit);
+ 194                     if let Some(prev) = &context.previous_commit {
+ 195                         println!("Previous commit: {}", prev);
+ 196                     } else {
+ 197                         println!("Previous commit: None (this is the first commit for this file)");
  198                     }
- 106                     (None, None, None) => {
- 107                         CliContext::from_interactive(&cli.project, configuartion, git_info).await?
+ 199                     
+ 200                     // TODO: Implement actual comment creation logic
+ 201                     println!("✅ Comment would be created here!");
+ 202                 }
+ 203             }
+ 204         }
+ 205         Commands::Configuration {
+ 206             configuration_command,
+ 207         } => match configuration_command {
+ 208             ConfigurationCommands::Setup { git } => {
+ 209                 let url = if let Some(git) = git {
+ 210                     gix::url::parse(git.as_str().into())
+ 211                         .map_err(|e| anyhow!("provided url {git} is not a valid git url: {e}"))?
+ 212                 } else {
+ 213                     if let Ok(git) = std::env::var("GHQC_CONFIG_HOME") {
+ 214                         gix::url::parse(git.as_str().into()).map_err(|e| {
+ 215                             anyhow!("GHQC_CONFIG_HOME value {git} is not a valid git url: {e}")
+ 216                         })?
+ 217                     } else {
+ 218                         bail!(
+ 219                             "Must provide `git` flag or have the environment variable `GHQC_CONFIG_HOME` set"
+ 220                         );
  221                     }
- 109                     _ => {
- 110                         return Err(anyhow::anyhow!(
- 111                             "Either provide all three arguments (--milestone, --file, --checklist-name) or none to enter interactive mode"
- 112                         ));
- 113                     }
  222                 };
  223 
- 116                 create_issue(
- 117                     &context.file,
- 118                     &context.milestone_status,
- 119                     &context.checklist,
- 120                     context.assignees,
- 121                     &context.configuration,
- 122                     &context.git_info,
- 123                     context.relevant_files,
- 124                 )
- 125                 .await?;
+ 224                 let config_dir = determine_config_info(cli.config_dir, &StdEnvProvider::default())?;
  225 
- 127                 println!("✅ Issue created successfully!");
+ 226                 let git_action = GitActionImpl;
+ 227 
+ 228                 setup_configuration(&config_dir, url, git_action)
+ 229                     .await
+ 230                     .map_err(|e| anyhow!("{e}"))?;
+ 231 
+ 232                 println!(
+ 233                     "✅ Configuration successfully setup at {}",
+ 234                     config_dir.display()
+ 235                 );
  236             }
  237         },
  238     }
  239 
  240     Ok(())
  241 }