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seanlaidlaw/iRODS-Downloader

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irods_downloader.go

Summary

Maintainability
F
1 wk
Test Coverage

Function main has a Cognitive Complexity of 284 (exceeds 20 allowed). Consider refactoring.
Open

func main() {
    // we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
    viper.SetConfigName("irods_downloader_config")
    viper.SetConfigType("yaml")
    viper.AddConfigPath(".")              // look for config in the working directory first
Severity: Minor
Found in irods_downloader.go - About 5 days to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function main has 566 lines of code (exceeds 50 allowed). Consider refactoring.
Open

func main() {
    // we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
    viper.SetConfigName("irods_downloader_config")
    viper.SetConfigType("yaml")
    viper.AddConfigPath(".")              // look for config in the working directory first
Severity: Major
Found in irods_downloader.go - About 2 days to fix

    File irods_downloader.go has 686 lines of code (exceeds 500 allowed). Consider refactoring.
    Open

    package main

import (
    "bytes"
    "encoding/json"
    Severity: Minor
    Found in irods_downloader.go - About 6 hrs to fix

      Function main has 8 return statements (exceeds 4 allowed).
      Open

      func main() {
    // we want to load a config file named "irods_downloader_config.yaml" if it exists in WD or in ~/.config
    viper.SetConfigName("irods_downloader_config")
    viper.SetConfigType("yaml")
    viper.AddConfigPath(".")              // look for config in the working directory first
      Severity: Major
      Found in irods_downloader.go - About 50 mins to fix

        Avoid deeply nested control flow statements.
        Open

                            if err != nil {
                        // Display everything we got if error.
                        log.Println("Error when running command.  Output:")
                        log.Println(string(output))
                        log.Printf("Got command status: %s\n", err.Error())
        Severity: Major
        Found in irods_downloader.go - About 45 mins to fix

          2: cannot find package "github.com/spf13/viper" in any of:
          Open

              "github.com/spf13/viper"
          Severity: Minor
          Found in irods_downloader.go by govet

          Similar blocks of code found in 2 locations. Consider refactoring.
          Open

          func indexBam(cram_list []cram_file, i int, samtools_exec string) {
    cram := &cram_list[i]

    bam_filename := cram.Realigned_bam_path
    output, err := exec.Command(samtools_exec, "index", bam_filename).CombinedOutput()
          Severity: Major
          Found in irods_downloader.go and 1 other location - About 1 hr to fix
          irods_downloader.go on lines 91..107

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 154.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Similar blocks of code found in 2 locations. Consider refactoring.
          Open

          func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
    cram := &cram_list[i]

    bam_filename := cram.Realigned_bam_path
    output, err := exec.Command(samtools_exec, "quickcheck", bam_filename).CombinedOutput()
          Severity: Major
          Found in irods_downloader.go and 1 other location - About 1 hr to fix
          irods_downloader.go on lines 109..125

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 154.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          don't use underscores in Go names; func parameter submitted_jobs_map should be submittedJobsMap
          Open

              submitted_jobs_map map[string]string,
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter attribute_name should be attributeName
          Open

              attribute_name string,
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Cram_dl_path should be CramDlPath
          Open

              Cram_dl_path                 string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bwa_align_libraries should be bwaAlignLibraries
          Open

              bwa_align_libraries := viper.GetStringSlice("bwa_align_libraries")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var genome_annot should be genomeAnnot
          Open

              genome_annot := viper.GetString("genome_annot")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var sample_name should be sampleName
          Open

                          sample_name := ""
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var fq_filename should be fqFilename
          Open

                          fq_filename := strings.ReplaceAll(cram.Filename, ".cram", "")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var rna_bams_featurecounts_input should be rnaBamsFeaturecountsInput
          Open

                  var rna_bams_featurecounts_input []string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter cram_list should be cramList
          Open

          func writeCheckpoint(cram_list []cram_file, step int) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter cram_list should be cramList
          Open

          func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter samtools_exec should be samtoolsExec
          Open

          func indexBam(cram_list []cram_file, i int, samtools_exec string) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Realigned_bam_path should be RealignedBamPath
          Open

              Realigned_bam_path           string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var imeta_file should be imetaFile
          Open

                          imeta_file, err := os.Create(cram.Imeta_path)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var lib_type_dir should be libTypeDir
          Open

                          lib_type_dir := strings.ReplaceAll(cram.Library_type, " ", "_")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var checkpoint_file should be checkpointFile
          Open

              checkpoint_file := fmt.Sprintf("checkpoint_%d.json", step)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter cram_list should be cramList
          Open

              cram_list *[]cram_file,
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bjobs_output_filename should be bjobsOutputFilename
          Open

                      bjobs_output_filename := submitted_jobs_map[func_cram.Filename]
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Imeta_downloaded should be ImetaDownloaded
          Open

              Imeta_downloaded             bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Cram_is_phix should be CramIsPhix
          Open

              Cram_is_phix                 bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Fastq_2_path should be Fastq2Path
          Open

              Fastq_2_path                 string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Fastq_extracted_success should be FastqExtractedSuccess
          Open

              Fastq_extracted_success      bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Cram_download_success should be CramDownloadSuccess
          Open

              Cram_download_success        bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Symlinked_fq_1 should be SymlinkedFq1
          Open

              Symlinked_fq_1               string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Imeta_parsed should be ImetaParsed
          Open

              Imeta_parsed                 bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bwa_ram should be bwaRAM
          Open

              bwa_ram := viper.GetString("bwa_ram")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Realigned_quickcheck_success should be RealignedQuickcheckSuccess
          Open

              Realigned_quickcheck_success bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var job_err should be jobErr
          Open

                          job_err := out_folder + "/D_realignement_RNA_" + cram.Sample_name + ".e"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var cram_list should be cramList
          Open

          var cram_list []cram_file
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var star_exec should be starExec
          Open

              star_exec := viper.GetString("star_exec")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var cram_exists_map should be cramExistsMap
          Open

                  cram_exists_map := make(map[string]string)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var library_type should be libraryType
          Open

                          library_type := ""
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var attribute_with_sample_name should be attributeWithSampleName
          Open

              attribute_with_sample_name := viper.GetString("attribute_with_sample_name")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var realignment_map should be realignmentMap
          Open

                  realignment_map := make(map[string]string)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var job_err should be jobErr
          Open

                  job_err := "E_Counts_matrix_RNA/featurecounts_run.e"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bam_filename should be bamFilename
          Open

              bam_filename := cram.Realigned_bam_path
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var star_genome_dir should be starGenomeDir
          Open

              star_genome_dir := viper.GetString("star_genome_dir")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var sample_names_map should be sampleNamesMap
          Open

                  sample_names_map := make(map[string][]string)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var out_folder should be outFolder
          Open

                          out_folder := "D_realignments/" + strings.ReplaceAll(cram.Library_type, " ", "_") + "/"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var matrix_out should be matrixOut
          Open

                  matrix_out := "E_Counts_matrix_RNA/featurecounts_matrix.tsv"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func quickcheck_alignments should be quickcheckAlignments
          Open

          func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var star_align_libraries should be starAlignLibraries
          Open

              star_align_libraries := viper.GetStringSlice("star_align_libraries")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var split_filename should be splitFilename
          Open

                      split_filename := strings.Split(filename, "_")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var func_cram should be funcCram
          Open

                      func_cram := &((*cram_list)[i])
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter samtools_exec should be samtoolsExec
          Open

          func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; func parameter cram_list should be cramList
          Open

          func indexBam(cram_list []cram_file, i int, samtools_exec string) {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field File_exists_in_irods should be FileExistsInIrods
          Open

              File_exists_in_irods         bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var cram_dl_dir should be cramDlDir
          Open

                  cram_dl_dir := "A_iRODS_CRAM_Downloads/"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var undownloaded_cram_map should be undownloadedCramMap
          Open

                  undownloaded_cram_map := make(map[string]string)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bam_filename should be bamFilename
          Open

              bam_filename := cram.Realigned_bam_path
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bwa_exec should be bwaExec
          Open

              bwa_exec := viper.GetString("bwa_exec")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var current_step should be currentStep
          Open

              var current_step int
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var phix_status should be phixStatus
          Open

                      phix_status := false
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var split_imeta should be splitImeta
          Open

                          split_imeta := bytes.Split(imeta, []byte("----"))
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var line_split should be lineSplit
          Open

                                  line_split := strings.Split(strings.TrimSuffix(string(line), "\n"), "\n")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var job_out should be jobOut
          Open

                          job_out := out_folder + "/D_realignement_RNA_" + cram.Sample_name + ".o"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Sample_name should be SampleName
          Open

              Sample_name                  string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var star_ram should be starRAM
          Open

              star_ram := viper.GetString("star_ram")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var cram_list_len should be cramListLen
          Open

                  cram_list_len := len(cram_list)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var line_split should be lineSplit
          Open

                                  line_split := strings.Split(strings.TrimSuffix(string(line), "\n"), "\n")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var job_out should be jobOut
          Open

                  job_out := "E_Counts_matrix_RNA/featurecounts_run.o"
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; type cram_file should be cramFile
          Open

          type cram_file struct {
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Imeta_path should be ImetaPath
          Open

              Imeta_path                   string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Realigned_succesful should be RealignedSuccesful
          Open

              Realigned_succesful          bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bwa_genome_ref should be bwaGenomeRef
          Open

              bwa_genome_ref := viper.GetString("bwa_genome_ref")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var featurecounts_exec should be featurecountsExec
          Open

              featurecounts_exec := viper.GetString("featurecounts_exec")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var featurecounts_ram should be featurecountsRAM
          Open

              featurecounts_ram := viper.GetString("featurecounts_ram")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var fastq_cram_map should be fastqCramMap
          Open

                  fastq_cram_map := make(map[string]string)
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Realigned_index_success should be RealignedIndexSuccess
          Open

              Realigned_index_success      bool
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var samtools_exec should be samtoolsExec
          Open

              samtools_exec := viper.GetString("samtools_exec")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var split_output should be splitOutput
          Open

                  split_output := bytes.Split(output, []byte("----"))
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var run_lane should be runLane
          Open

                      run_lane := strings.Split(split_filename[1], "#")[0] // this gets between _ and # which is lane
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Irods_path should be IrodsPath
          Open

              Irods_path                   string
          Severity: Minor
          Found in irods_downloader.go by golint

          var rankingsJson should be rankingsJSON
          Open

              rankingsJson, _ := json.MarshalIndent(cram_list, "", "  ")
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Library_type should be LibraryType
          Open

              Library_type                 string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Fastq_1_path should be Fastq1Path
          Open

              Fastq_1_path                 string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; struct field Symlinked_fq_2 should be SymlinkedFq2
          Open

              Symlinked_fq_2               string
          Severity: Minor
          Found in irods_downloader.go by golint

          don't use underscores in Go names; var bam_output should be bamOutput
          Open

                          bam_output := out_folder + cram.Sample_name + ".bam"
          Severity: Minor
          Found in irods_downloader.go by golint

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