diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 92cb937..5d25790 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -60,13 +60,13 @@ As one final guideline please be welcoming to newcomers and encourage new contri Unsure where to begin contributing to ark? You can start by looking through these beginner and help-wanted issues: -[Beginner issues](https://github.com/TimothyStiles/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two. +[Beginner issues](https://github.com/bebop/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two. -[Good first issues](https://github.com/TimothyStiles/ark/contribute) - issues which are good for first time contributors. +[Good first issues](https://github.com/bebop/ark/contribute) - issues which are good for first time contributors. -[Help wanted issues](https://github.com/TimothyStiles/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues. +[Help wanted issues](https://github.com/bebop/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues. -[Feature requests](https://github.com/TimothyStiles/ark/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag! +[Feature requests](https://github.com/bebop/ark/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag! ### Working on your first Pull Request? @@ -108,11 +108,11 @@ If the answer to either of those two questions are "yes", then you're probably d ### Non-security related bugs -For non-security bug reports please [submit it using this template!](https://github.com/TimothyStiles/ark/issues/new?assignees=&labels=&template=bug_report.md&title=) +For non-security bug reports please [submit it using this template!](https://github.com/bebop/ark/issues/new?assignees=&labels=&template=bug_report.md&title=) # How to suggest a feature or enhancement -If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/TimothyStiles/ark/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/TimothyStiles/ark/labels/enhancement) +If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/bebop/ark/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/bebop/ark/labels/enhancement) # How add a recommended VSCode Plugin diff --git a/db/cmd/download.go b/db/cmd/download.go index cbdc632..165bf74 100644 --- a/db/cmd/download.go +++ b/db/cmd/download.go @@ -39,6 +39,6 @@ var downloadCmd = &cobra.Command{ Short: "Download data for standard deploy build. Run at your own risk.", Long: "Download literally downloads all the base data needed to build a standard ark deployment the amount of data is dummy high to casually test on your personal machine. Run at your own risk.", Run: func(cmd *cobra.Command, args []string) { - download.ark() + // download.ark() }, } diff --git a/go.mod b/go.mod index b71a812..0a86783 100644 --- a/go.mod +++ b/go.mod @@ -1,4 +1,4 @@ -module github.com/TimothyStiles/ark +module github.com/bebop/ark go 1.18 diff --git a/pkg/config/config.go b/pkg/config/config.go index f8d7de2..b59ce27 100644 --- a/pkg/config/config.go +++ b/pkg/config/config.go @@ -5,7 +5,7 @@ import ( "os" "path/filepath" - "github.com/TimothyStiles/ark/pkg/env" + "github.com/bebop/ark/pkg/env" ) // Read reads the config file and returns the config. @@ -43,8 +43,8 @@ type Config struct { // DataPath is the data directory of the project. DataPath string `json:"data_path"` - // arkPath is the path to the ark sqlite database. - arkPath string `json:"ark_path"` + // ArkPath is the path to the ark sqlite database. + ArkPath string `json:"ark_path"` // RheaRDF is the path to the Rhea RDF file. RheaRDF string `json:"rhea_rdf"` @@ -80,7 +80,7 @@ func DevDefault() Config { IsProd: false, RootPath: env.RootPath(), DataPath: devPath, - arkPath: filepath.Join(devPath, "ark.sqlite"), + ArkPath: filepath.Join(devPath, "ark.sqlite"), RheaRDF: filepath.Join(devPath, "rhea_mini.rdf.gz"), RheaToUniprotSprot: filepath.Join(devPath, "rhea_to_uniprot_sprot.tsv.gz"), RheaToUniprotTrembl: filepath.Join(devPath, "rhea_to_uniprot_trembl.tsv.gz"), @@ -101,7 +101,7 @@ func ProdDefault() Config { IsProd: true, RootPath: env.RootPath(), DataPath: prodPath, - arkPath: filepath.Join(prodPath, "ark.sqlite"), + ArkPath: filepath.Join(prodPath, "ark.sqlite"), RheaRDF: filepath.Join(prodPath, "rhea.rdf.gz"), RheaToUniprotSprot: filepath.Join(prodPath, "rhea_to_uniprot_sprot.tsv"), RheaToUniprotTrembl: filepath.Join(prodPath, "rhea_to_uniprot_trembl.tsv"), diff --git a/pkg/download/file_test.go b/pkg/download/file_test.go index 2950f49..6f392f2 100644 --- a/pkg/download/file_test.go +++ b/pkg/download/file_test.go @@ -5,7 +5,7 @@ import ( "os" "testing" - "github.com/TimothyStiles/ark/pkg/download" + "github.com/bebop/ark/pkg/download" ) func TestFile(t *testing.T) { diff --git a/pkg/download/links_test.go b/pkg/download/links_test.go index 46aafbb..013ba7f 100644 --- a/pkg/download/links_test.go +++ b/pkg/download/links_test.go @@ -3,7 +3,7 @@ package download_test import ( "testing" - "github.com/TimothyStiles/ark/pkg/download" + "github.com/bebop/ark/pkg/download" ) func TestGetPageLinks(t *testing.T) { diff --git a/pkg/download/tarball_test.go b/pkg/download/tarball_test.go index cbe5bbb..32bd65f 100644 --- a/pkg/download/tarball_test.go +++ b/pkg/download/tarball_test.go @@ -6,7 +6,7 @@ import ( "os" "testing" - "github.com/TimothyStiles/ark/pkg/download" + "github.com/bebop/ark/pkg/download" ) func TestTarball(t *testing.T) { diff --git a/pkg/insert/rhea.go b/pkg/insert/rhea.go index 37baa87..06717e0 100644 --- a/pkg/insert/rhea.go +++ b/pkg/insert/rhea.go @@ -3,8 +3,8 @@ package insert import ( "context" - "github.com/TimothyStiles/ark/pkg/config" - "github.com/TimothyStiles/ark/pkg/rhea" + "github.com/bebop/ark/pkg/config" + "github.com/bebop/ark/pkg/rhea" "github.com/jmoiron/sqlx" "github.com/volatiletech/sqlboiler/v4/boil" ) diff --git a/pkg/insert/rhea_test.go b/pkg/insert/rhea_test.go index 1f5a62e..afe5d2e 100644 --- a/pkg/insert/rhea_test.go +++ b/pkg/insert/rhea_test.go @@ -8,8 +8,8 @@ import ( "path/filepath" "testing" - "github.com/TimothyStiles/ark/pkg/config" - "github.com/TimothyStiles/ark/schema" + "github.com/bebop/ark/pkg/config" + "github.com/bebop/ark/schema" "github.com/jmoiron/sqlx" _ "modernc.org/sqlite" ) @@ -23,12 +23,12 @@ func TestRhea(t *testing.T) { } defer os.RemoveAll(tmpDataDir) - tmpConfig.arkPath = filepath.Join(tmpDataDir, "rheaTest.db") + tmpConfig.ArkPath = filepath.Join(tmpDataDir, "rheaTest.db") //create test database err = schema.CreateDatabase(tmpConfig) - db, err := sqlx.Open("sqlite", tmpConfig.arkPath) + db, err := sqlx.Open("sqlite", tmpConfig.ArkPath) if err != nil { log.Fatalf("Failed to open sqlite in ark.db: %s", err) } diff --git a/pkg/rhea/rhea.go b/pkg/rhea/rhea.go index 4eaad27..ed01bf6 100644 --- a/pkg/rhea/rhea.go +++ b/pkg/rhea/rhea.go @@ -12,7 +12,7 @@ import ( "strconv" "strings" - "github.com/TimothyStiles/ark/models" + "github.com/bebop/ark/models" "github.com/volatiletech/null/v8" ) diff --git a/pkg/rhea/rhea_test.go b/pkg/rhea/rhea_test.go index 5df7884..c4dcf4d 100644 --- a/pkg/rhea/rhea_test.go +++ b/pkg/rhea/rhea_test.go @@ -6,7 +6,7 @@ import ( "os" "testing" - "github.com/TimothyStiles/ark/pkg/config" + "github.com/bebop/ark/pkg/config" _ "github.com/mattn/go-sqlite3" ) diff --git a/schema/schema.go b/schema/schema.go index 00f2125..05a4bc3 100644 --- a/schema/schema.go +++ b/schema/schema.go @@ -5,7 +5,7 @@ import ( "log" "strings" - "github.com/TimothyStiles/ark/pkg/config" + "github.com/bebop/ark/pkg/config" "github.com/huandu/go-sqlbuilder" "github.com/jmoiron/sqlx" @@ -17,7 +17,7 @@ func CreateDatabase(config config.Config) error { // Begin SQLite log.Println("Creating database...") - db, err := sqlx.Open("sqlite", config.arkPath) + db, err := sqlx.Open("sqlite", config.ArkPath) if err != nil { log.Fatalf("Failed to open sqlite database: %s", err) @@ -41,7 +41,7 @@ func CreateDatabase(config config.Config) error { log.Fatalf("Failed to execute schema: %s", err) } - err = chemblAttach(db, config.arkPath) + err = chemblAttach(db, config.ArkPath) if err != nil { log.Fatalf("Failed to attach chembl with error %s", err) } diff --git a/schema/schema_test.go b/schema/schema_test.go index 8484a5b..5e1a701 100644 --- a/schema/schema_test.go +++ b/schema/schema_test.go @@ -12,7 +12,7 @@ import ( "path/filepath" "testing" - "github.com/TimothyStiles/ark/pkg/config" + "github.com/bebop/ark/pkg/config" "github.com/jmoiron/sqlx" //"github.com/minio/minio-go/v7" @@ -30,7 +30,7 @@ var db *sqlx.DB func TestCreateDatabase(t *testing.T) { tmpDataDir, err := ioutil.TempDir("", "data-*") tmparkConfig := config.DevDefault() - tmparkConfig.arkPath = filepath.Join(tmpDataDir, "test.db") + tmparkConfig.ArkPath = filepath.Join(tmpDataDir, "test.db") if err != nil { t.Errorf("Failed to create temporary data directory") }