Refactor doctor (#12264)

* Refactor Logger

Refactor Logger to make a logger interface and make it possible to
wrap loggers for specific purposes.

* Refactor Doctor

    Move the gitea doctor functions into its own module.
    Use a logger for its messages instead of returning a results string[]

Signed-off-by: Andrew Thornton <art27@cantab.net>

* Update modules/doctor/misc.go

Co-authored-by: 6543 <6543@obermui.de>

* Update modules/doctor/misc.go

Co-authored-by: 6543 <6543@obermui.de>

Co-authored-by: 6543 <6543@obermui.de>
Co-authored-by: techknowlogick <techknowlogick@gitea.io>

cmd/doctor.go

@@ -5,27 +5,19 @@
 package cmd
 
 import (
-	"bufio"
-	"bytes"
 	"context"
 	"fmt"
-	"io/ioutil"
 	golog "log"
 	"os"
-	"os/exec"
-	"path/filepath"
 	"strings"
 	"text/tabwriter"
 
 	"code.gitea.io/gitea/models"
 	"code.gitea.io/gitea/models/migrations"
-	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/doctor"
 	"code.gitea.io/gitea/modules/log"
-	"code.gitea.io/gitea/modules/options"
-	"code.gitea.io/gitea/modules/repository"
 	"code.gitea.io/gitea/modules/setting"
-	"code.gitea.io/gitea/modules/util"
+
-	"xorm.io/builder"
 	"xorm.io/xorm"
 
 	"github.com/urfave/cli"
@@ -62,6 +54,10 @@ var CmdDoctor = cli.Command{
 			Name:  "log-file",
 			Usage: `Name of the log file (default: "doctor.log"). Set to "-" to output to stdout, set to "" to disable`,
 		},
+		cli.BoolFlag{
+			Name:  "color, H",
+			Usage: "Use color for outputted information",
+		},
 	},
 	Subcommands: []cli.Command{
 		cmdRecreateTable,
@@ -86,78 +82,6 @@ You should back-up your database before doing this and ensure that your database
 	Action: runRecreateTable,
 }
 
-type check struct {
-	title            string
-	name             string
-	isDefault        bool
-	f                func(ctx *cli.Context) ([]string, error)
-	abortIfFailed    bool
-	skipDatabaseInit bool
-}
-
-// checklist represents list for all checks
-var checklist = []check{
-	{
-		// NOTE: this check should be the first in the list
-		title:            "Check paths and basic configuration",
-		name:             "paths",
-		isDefault:        true,
-		f:                runDoctorPathInfo,
-		abortIfFailed:    true,
-		skipDatabaseInit: true,
-	},
-	{
-		title:         "Check Database Version",
-		name:          "check-db-version",
-		isDefault:     true,
-		f:             runDoctorCheckDBVersion,
-		abortIfFailed: false,
-	},
-	{
-		title:     "Check consistency of database",
-		name:      "check-db-consistency",
-		isDefault: false,
-		f:         runDoctorCheckDBConsistency,
-	},
-	{
-		title:     "Check if OpenSSH authorized_keys file is up-to-date",
-		name:      "authorized_keys",
-		isDefault: true,
-		f:         runDoctorAuthorizedKeys,
-	},
-	{
-		title:     "Check if SCRIPT_TYPE is available",
-		name:      "script-type",
-		isDefault: false,
-		f:         runDoctorScriptType,
-	},
-	{
-		title:     "Check if hook files are up-to-date and executable",
-		name:      "hooks",
-		isDefault: false,
-		f:         runDoctorHooks,
-	},
-	{
-		title:     "Recalculate merge bases",
-		name:      "recalculate_merge_bases",
-		isDefault: false,
-		f:         runDoctorPRMergeBase,
-	},
-	{
-		title:     "Recalculate Stars number for all user",
-		name:      "recalculate_stars_number",
-		isDefault: false,
-		f:         runDoctorUserStarNum,
-	},
-	{
-		title:     "Enable push options",
-		name:      "enable-push-options",
-		isDefault: false,
-		f:         runDoctorEnablePushOptions,
-	},
-	// more checks please append here
-}
-
 func runRecreateTable(ctx *cli.Context) error {
 	// Redirect the default golog to here
 	golog.SetFlags(0)
@@ -211,10 +135,15 @@ func runDoctor(ctx *cli.Context) error {
 		logFile = "doctor.log"
 	}
 
+	colorize := log.CanColorStdout
+	if ctx.IsSet("color") {
+		colorize = ctx.Bool("color")
+	}
+
 	if len(logFile) == 0 {
-		log.NewLogger(1000, "doctor", "console", `{"level":"NONE","stacktracelevel":"NONE","colorize":"%t"}`)
+		log.NewLogger(1000, "doctor", "console", fmt.Sprintf(`{"level":"NONE","stacktracelevel":"NONE","colorize":%t}`, colorize))
 	} else if logFile == "-" {
-		log.NewLogger(1000, "doctor", "console", `{"level":"trace","stacktracelevel":"NONE"}`)
+		log.NewLogger(1000, "doctor", "console", fmt.Sprintf(`{"level":"trace","stacktracelevel":"NONE","colorize":%t}`, colorize))
 	} else {
 		log.NewLogger(1000, "doctor", "file", fmt.Sprintf(`{"filename":%q,"level":"trace","stacktracelevel":"NONE"}`, logFile))
 	}
@@ -225,24 +154,24 @@ func runDoctor(ctx *cli.Context) error {
 	golog.SetOutput(log.NewLoggerAsWriter("INFO", log.GetLogger(log.DEFAULT)))
 
 	if ctx.IsSet("list") {
-		w := tabwriter.NewWriter(os.Stdout, 0, 8, 0, '\t', 0)
+		w := tabwriter.NewWriter(os.Stdout, 0, 8, 1, '\t', 0)
 		_, _ = w.Write([]byte("Default\tName\tTitle\n"))
-		for _, check := range checklist {
+		for _, check := range doctor.Checks {
-			if check.isDefault {
+			if check.IsDefault {
 				_, _ = w.Write([]byte{'*'})
 			}
 			_, _ = w.Write([]byte{'\t'})
-			_, _ = w.Write([]byte(check.name))
+			_, _ = w.Write([]byte(check.Name))
 			_, _ = w.Write([]byte{'\t'})
-			_, _ = w.Write([]byte(check.title))
+			_, _ = w.Write([]byte(check.Title))
 			_, _ = w.Write([]byte{'\n'})
 		}
 		return w.Flush()
 	}
 
-	var checks []check
+	var checks []*doctor.Check
 	if ctx.Bool("all") {
-		checks = checklist
+		checks = doctor.Checks
 	} else if ctx.IsSet("run") {
 		addDefault := ctx.Bool("default")
 		names := ctx.StringSlice("run")
@@ -250,452 +179,37 @@ func runDoctor(ctx *cli.Context) error {
 			names[i] = strings.ToLower(strings.TrimSpace(name))
 		}
 
-		for _, check := range checklist {
+		for _, check := range doctor.Checks {
-			if addDefault && check.isDefault {
+			if addDefault && check.IsDefault {
 				checks = append(checks, check)
 				continue
 			}
 			for _, name := range names {
-				if name == check.name {
+				if name == check.Name {
 					checks = append(checks, check)
 					break
 				}
 			}
 		}
 	} else {
-		for _, check := range checklist {
+		for _, check := range doctor.Checks {
-			if check.isDefault {
+			if check.IsDefault {
 				checks = append(checks, check)
 			}
 		}
 	}
 
-	dbIsInit := false
+	// Now we can set up our own logger to return information about what the doctor is doing
-
+	if err := log.NewNamedLogger("doctorouter",
-	for i, check := range checks {
+		1000,
-		if !dbIsInit && !check.skipDatabaseInit {
+		"console",
-			// Only open database after the most basic configuration check
+		"console",
-			setting.EnableXORMLog = false
+		fmt.Sprintf(`{"level":"INFO","stacktracelevel":"NONE","colorize":%t,"flags":-1}`, colorize)); err != nil {
-			if err := initDBDisableConsole(true); err != nil {
+		fmt.Println(err)
-				fmt.Println(err)
-				fmt.Println("Check if you are using the right config file. You can use a --config directive to specify one.")
-				return nil
-			}
-			dbIsInit = true
-		}
-		fmt.Println("[", i+1, "]", check.title)
-		messages, err := check.f(ctx)
-		for _, message := range messages {
-			fmt.Println("-", message)
-		}
-		if err != nil {
-			fmt.Println("Error:", err)
-			if check.abortIfFailed {
-				return nil
-			}
-		} else {
-			fmt.Println("OK.")
-		}
-		fmt.Println()
-	}
-	return nil
-}
-
-func runDoctorPathInfo(ctx *cli.Context) ([]string, error) {
-
-	res := make([]string, 0, 10)
-
-	if fi, err := os.Stat(setting.CustomConf); err != nil || !fi.Mode().IsRegular() {
-		res = append(res, fmt.Sprintf("Failed to find configuration file at '%s'.", setting.CustomConf))
-		res = append(res, fmt.Sprintf("If you've never ran Gitea yet, this is normal and '%s' will be created for you on first run.", setting.CustomConf))
-		res = append(res, "Otherwise check that you are running this command from the correct path and/or provide a `--config` parameter.")
-		return res, fmt.Errorf("can't proceed without a configuration file")
-	}
-
-	setting.NewContext()
-
-	fail := false
-
-	check := func(name, path string, is_dir, required, is_write bool) {
-		res = append(res, fmt.Sprintf("%-25s  '%s'", name+":", path))
-		fi, err := os.Stat(path)
-		if err != nil {
-			if os.IsNotExist(err) && ctx.Bool("fix") && is_dir {
-				if err := os.MkdirAll(path, 0777); err != nil {
-					res = append(res, fmt.Sprintf("    ERROR: %v", err))
-					fail = true
-					return
-				}
-				fi, err = os.Stat(path)
-			}
-		}
-		if err != nil {
-			if required {
-				res = append(res, fmt.Sprintf("    ERROR: %v", err))
-				fail = true
-				return
-			}
-			res = append(res, fmt.Sprintf("    NOTICE: not accessible (%v)", err))
-			return
-		}
-
-		if is_dir && !fi.IsDir() {
-			res = append(res, "    ERROR: not a directory")
-			fail = true
-			return
-		} else if !is_dir && !fi.Mode().IsRegular() {
-			res = append(res, "    ERROR: not a regular file")
-			fail = true
-		} else if is_write {
-			if err := runDoctorWritableDir(path); err != nil {
-				res = append(res, fmt.Sprintf("    ERROR: not writable: %v", err))
-				fail = true
-			}
-		}
-	}
-
-	// Note print paths inside quotes to make any leading/trailing spaces evident
-	check("Configuration File Path", setting.CustomConf, false, true, false)
-	check("Repository Root Path", setting.RepoRootPath, true, true, true)
-	check("Data Root Path", setting.AppDataPath, true, true, true)
-	check("Custom File Root Path", setting.CustomPath, true, false, false)
-	check("Work directory", setting.AppWorkPath, true, true, false)
-	check("Log Root Path", setting.LogRootPath, true, true, true)
-
-	if options.IsDynamic() {
-		// Do not check/report on StaticRootPath if data is embedded in Gitea (-tags bindata)
-		check("Static File Root Path", setting.StaticRootPath, true, true, false)
-	}
-
-	if fail {
-		return res, fmt.Errorf("please check your configuration file and try again")
-	}
-
-	return res, nil
-}
-
-func runDoctorWritableDir(path string) error {
-	// There's no platform-independent way of checking if a directory is writable
-	// https://stackoverflow.com/questions/20026320/how-to-tell-if-folder-exists-and-is-writable
-
-	tmpFile, err := ioutil.TempFile(path, "doctors-order")
-	if err != nil {
 		return err
 	}
-	if err := util.Remove(tmpFile.Name()); err != nil {
+
-		fmt.Printf("Warning: can't remove temporary file: '%s'\n", tmpFile.Name())
+	logger := log.GetLogger("doctorouter")
-	}
+	defer logger.Close()
-	tmpFile.Close()
+	return doctor.RunChecks(logger, ctx.Bool("fix"), checks)
-	return nil
-}
-
-const tplCommentPrefix = `# gitea public key`
-
-func runDoctorAuthorizedKeys(ctx *cli.Context) ([]string, error) {
-	if setting.SSH.StartBuiltinServer || !setting.SSH.CreateAuthorizedKeysFile {
-		return nil, nil
-	}
-
-	fPath := filepath.Join(setting.SSH.RootPath, "authorized_keys")
-	f, err := os.Open(fPath)
-	if err != nil {
-		if ctx.Bool("fix") {
-			return []string{fmt.Sprintf("Error whilst opening authorized_keys: %v. Attempting regeneration", err)}, models.RewriteAllPublicKeys()
-		}
-		return nil, err
-	}
-	defer f.Close()
-
-	linesInAuthorizedKeys := map[string]bool{}
-
-	scanner := bufio.NewScanner(f)
-	for scanner.Scan() {
-		line := scanner.Text()
-		if strings.HasPrefix(line, tplCommentPrefix) {
-			continue
-		}
-		linesInAuthorizedKeys[line] = true
-	}
-	f.Close()
-
-	// now we regenerate and check if there are any lines missing
-	regenerated := &bytes.Buffer{}
-	if err := models.RegeneratePublicKeys(regenerated); err != nil {
-		return nil, err
-	}
-	scanner = bufio.NewScanner(regenerated)
-	for scanner.Scan() {
-		line := scanner.Text()
-		if strings.HasPrefix(line, tplCommentPrefix) {
-			continue
-		}
-		if ok := linesInAuthorizedKeys[line]; ok {
-			continue
-		}
-		if ctx.Bool("fix") {
-			return []string{"authorized_keys is out of date, attempting regeneration"}, models.RewriteAllPublicKeys()
-		}
-		return nil, fmt.Errorf(`authorized_keys is out of date and should be regenerated with "gitea admin regenerate keys" or "gitea doctor --run authorized_keys --fix"`)
-	}
-	return nil, nil
-}
-
-func runDoctorCheckDBVersion(ctx *cli.Context) ([]string, error) {
-	if err := models.NewEngine(context.Background(), migrations.EnsureUpToDate); err != nil {
-		if ctx.Bool("fix") {
-			return []string{fmt.Sprintf("WARN: Got Error %v during ensure up to date", err), "Attempting to migrate to the latest DB version to fix this."}, models.NewEngine(context.Background(), migrations.Migrate)
-		}
-		return nil, err
-	}
-	return nil, nil
-}
-
-func iterateRepositories(each func(*models.Repository) ([]string, error)) ([]string, error) {
-	results := []string{}
-	err := models.Iterate(
-		models.DefaultDBContext(),
-		new(models.Repository),
-		builder.Gt{"id": 0},
-		func(idx int, bean interface{}) error {
-			res, err := each(bean.(*models.Repository))
-			results = append(results, res...)
-			return err
-		},
-	)
-	return results, err
-}
-
-func iteratePRs(repo *models.Repository, each func(*models.Repository, *models.PullRequest) ([]string, error)) ([]string, error) {
-	results := []string{}
-	err := models.Iterate(
-		models.DefaultDBContext(),
-		new(models.PullRequest),
-		builder.Eq{"base_repo_id": repo.ID},
-		func(idx int, bean interface{}) error {
-			res, err := each(repo, bean.(*models.PullRequest))
-			results = append(results, res...)
-			return err
-		},
-	)
-	return results, err
-}
-
-func runDoctorHooks(ctx *cli.Context) ([]string, error) {
-	// Need to iterate across all of the repositories
-	return iterateRepositories(func(repo *models.Repository) ([]string, error) {
-		results, err := repository.CheckDelegateHooks(repo.RepoPath())
-		if err != nil {
-			return nil, err
-		}
-		if len(results) > 0 && ctx.Bool("fix") {
-			return []string{fmt.Sprintf("regenerated hooks for %s", repo.FullName())}, repository.CreateDelegateHooks(repo.RepoPath())
-		}
-
-		return results, nil
-	})
-}
-
-func runDoctorPRMergeBase(ctx *cli.Context) ([]string, error) {
-	numRepos := 0
-	numPRs := 0
-	numPRsUpdated := 0
-	results, err := iterateRepositories(func(repo *models.Repository) ([]string, error) {
-		numRepos++
-		return iteratePRs(repo, func(repo *models.Repository, pr *models.PullRequest) ([]string, error) {
-			numPRs++
-			results := []string{}
-			pr.BaseRepo = repo
-			repoPath := repo.RepoPath()
-
-			oldMergeBase := pr.MergeBase
-
-			if !pr.HasMerged {
-				var err error
-				pr.MergeBase, err = git.NewCommand("merge-base", "--", pr.BaseBranch, pr.GetGitRefName()).RunInDir(repoPath)
-				if err != nil {
-					var err2 error
-					pr.MergeBase, err2 = git.NewCommand("rev-parse", git.BranchPrefix+pr.BaseBranch).RunInDir(repoPath)
-					if err2 != nil {
-						results = append(results, fmt.Sprintf("WARN: Unable to get merge base for PR ID %d, #%d onto %s in %s/%s", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name))
-						log.Error("Unable to get merge base for PR ID %d, Index %d in %s/%s. Error: %v & %v", pr.ID, pr.Index, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err, err2)
-						return results, nil
-					}
-				}
-			} else {
-				parentsString, err := git.NewCommand("rev-list", "--parents", "-n", "1", pr.MergedCommitID).RunInDir(repoPath)
-				if err != nil {
-					results = append(results, fmt.Sprintf("WARN: Unable to get parents for merged PR ID %d, #%d onto %s in %s/%s", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name))
-					log.Error("Unable to get parents for merged PR ID %d, Index %d in %s/%s. Error: %v", pr.ID, pr.Index, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err)
-					return results, nil
-				}
-				parents := strings.Split(strings.TrimSpace(parentsString), " ")
-				if len(parents) < 2 {
-					return results, nil
-				}
-
-				args := append([]string{"merge-base", "--"}, parents[1:]...)
-				args = append(args, pr.GetGitRefName())
-
-				pr.MergeBase, err = git.NewCommand(args...).RunInDir(repoPath)
-				if err != nil {
-					results = append(results, fmt.Sprintf("WARN: Unable to get merge base for merged PR ID %d, #%d onto %s in %s/%s", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name))
-					log.Error("Unable to get merge base for merged PR ID %d, Index %d in %s/%s. Error: %v", pr.ID, pr.Index, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err)
-					return results, nil
-				}
-			}
-			pr.MergeBase = strings.TrimSpace(pr.MergeBase)
-			if pr.MergeBase != oldMergeBase {
-				if ctx.Bool("fix") {
-					if err := pr.UpdateCols("merge_base"); err != nil {
-						return results, err
-					}
-				} else {
-					results = append(results, fmt.Sprintf("#%d onto %s in %s/%s: MergeBase should be %s but is %s", pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, oldMergeBase, pr.MergeBase))
-				}
-				numPRsUpdated++
-			}
-			return results, nil
-		})
-	})
-
-	if ctx.Bool("fix") {
-		results = append(results, fmt.Sprintf("%d PR mergebases updated of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos))
-	} else {
-		if numPRsUpdated > 0 && err == nil {
-			return results, fmt.Errorf("%d PRs with incorrect mergebases of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos)
-		}
-		results = append(results, fmt.Sprintf("%d PRs with incorrect mergebases of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos))
-	}
-
-	return results, err
-}
-
-func runDoctorUserStarNum(ctx *cli.Context) ([]string, error) {
-	return nil, models.DoctorUserStarNum()
-}
-
-func runDoctorScriptType(ctx *cli.Context) ([]string, error) {
-	path, err := exec.LookPath(setting.ScriptType)
-	if err != nil {
-		return []string{fmt.Sprintf("ScriptType %s is not on the current PATH", setting.ScriptType)}, err
-	}
-	return []string{fmt.Sprintf("ScriptType %s is on the current PATH at %s", setting.ScriptType, path)}, nil
-}
-
-func runDoctorCheckDBConsistency(ctx *cli.Context) ([]string, error) {
-	var results []string
-
-	// make sure DB version is uptodate
-	if err := models.NewEngine(context.Background(), migrations.EnsureUpToDate); err != nil {
-		return nil, fmt.Errorf("model version on the database does not match the current Gitea version. Model consistency will not be checked until the database is upgraded")
-	}
-
-	//find labels without existing repo or org
-	count, err := models.CountOrphanedLabels()
-	if err != nil {
-		return nil, err
-	}
-	if count > 0 {
-		if ctx.Bool("fix") {
-			if err = models.DeleteOrphanedLabels(); err != nil {
-				return nil, err
-			}
-			results = append(results, fmt.Sprintf("%d labels without existing repository/organisation deleted", count))
-		} else {
-			results = append(results, fmt.Sprintf("%d labels without existing repository/organisation", count))
-		}
-	}
-
-	//find issues without existing repository
-	count, err = models.CountOrphanedIssues()
-	if err != nil {
-		return nil, err
-	}
-	if count > 0 {
-		if ctx.Bool("fix") {
-			if err = models.DeleteOrphanedIssues(); err != nil {
-				return nil, err
-			}
-			results = append(results, fmt.Sprintf("%d issues without existing repository deleted", count))
-		} else {
-			results = append(results, fmt.Sprintf("%d issues without existing repository", count))
-		}
-	}
-
-	//find pulls without existing issues
-	count, err = models.CountOrphanedObjects("pull_request", "issue", "pull_request.issue_id=issue.id")
-	if err != nil {
-		return nil, err
-	}
-	if count > 0 {
-		if ctx.Bool("fix") {
-			if err = models.DeleteOrphanedObjects("pull_request", "issue", "pull_request.issue_id=issue.id"); err != nil {
-				return nil, err
-			}
-			results = append(results, fmt.Sprintf("%d pull requests without existing issue deleted", count))
-		} else {
-			results = append(results, fmt.Sprintf("%d pull requests without existing issue", count))
-		}
-	}
-
-	//find tracked times without existing issues/pulls
-	count, err = models.CountOrphanedObjects("tracked_time", "issue", "tracked_time.issue_id=issue.id")
-	if err != nil {
-		return nil, err
-	}
-	if count > 0 {
-		if ctx.Bool("fix") {
-			if err = models.DeleteOrphanedObjects("tracked_time", "issue", "tracked_time.issue_id=issue.id"); err != nil {
-				return nil, err
-			}
-			results = append(results, fmt.Sprintf("%d tracked times without existing issue deleted", count))
-		} else {
-			results = append(results, fmt.Sprintf("%d tracked times without existing issue", count))
-		}
-	}
-
-	count, err = models.CountNullArchivedRepository()
-	if err != nil {
-		return nil, err
-	}
-	if count > 0 {
-		if ctx.Bool("fix") {
-			updatedCount, err := models.FixNullArchivedRepository()
-			if err != nil {
-				return nil, err
-			}
-			results = append(results, fmt.Sprintf("%d repositories with null is_archived updated", updatedCount))
-		} else {
-			results = append(results, fmt.Sprintf("%d repositories with null is_archived", count))
-		}
-	}
-
-	//ToDo: function to recalc all counters
-
-	return results, nil
-}
-
-func runDoctorEnablePushOptions(ctx *cli.Context) ([]string, error) {
-	numRepos := 0
-	_, err := iterateRepositories(func(repo *models.Repository) ([]string, error) {
-		numRepos++
-		r, err := git.OpenRepository(repo.RepoPath())
-		if err != nil {
-			return nil, err
-		}
-		defer r.Close()
-
-		if ctx.Bool("fix") {
-			_, err := git.NewCommand("config", "receive.advertisePushOptions", "true").RunInDir(r.Path)
-			return nil, err
-		}
-
-		return nil, nil
-	})
-
-	var prefix string
-	if !ctx.Bool("fix") {
-		prefix = "DRY RUN: "
-	}
-	return []string{fmt.Sprintf("%sEnabled push options for %d repositories.", prefix, numRepos)}, err
 }

modules/doctor/authorizedkeys.go

@@ -0,0 +1,95 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/setting"
+)
+
+const tplCommentPrefix = `# gitea public key`
+
+func checkAuthorizedKeys(logger log.Logger, autofix bool) error {
+	if setting.SSH.StartBuiltinServer || !setting.SSH.CreateAuthorizedKeysFile {
+		return nil
+	}
+
+	fPath := filepath.Join(setting.SSH.RootPath, "authorized_keys")
+	f, err := os.Open(fPath)
+	if err != nil {
+		if !autofix {
+			logger.Critical("Unable to open authorized_keys file. ERROR: %v", err)
+			return fmt.Errorf("Unable to open authorized_keys file. ERROR: %v", err)
+		}
+		logger.Warn("Unable to open authorized_keys. (ERROR: %v). Attempting to rewrite...", err)
+		if err = models.RewriteAllPublicKeys(); err != nil {
+			logger.Critical("Unable to rewrite authorized_keys file. ERROR: %v", err)
+			return fmt.Errorf("Unable to rewrite authorized_keys file. ERROR: %v", err)
+		}
+	}
+	defer f.Close()
+
+	linesInAuthorizedKeys := map[string]bool{}
+
+	scanner := bufio.NewScanner(f)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if strings.HasPrefix(line, tplCommentPrefix) {
+			continue
+		}
+		linesInAuthorizedKeys[line] = true
+	}
+	f.Close()
+
+	// now we regenerate and check if there are any lines missing
+	regenerated := &bytes.Buffer{}
+	if err := models.RegeneratePublicKeys(regenerated); err != nil {
+		logger.Critical("Unable to regenerate authorized_keys file. ERROR: %v", err)
+		return fmt.Errorf("Unable to regenerate authorized_keys file. ERROR: %v", err)
+	}
+	scanner = bufio.NewScanner(regenerated)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if strings.HasPrefix(line, tplCommentPrefix) {
+			continue
+		}
+		if ok := linesInAuthorizedKeys[line]; ok {
+			continue
+		}
+		if !autofix {
+			logger.Critical(
+				"authorized_keys file %q is out of date.\nRegenerate it with:\n\t\"%s\"\nor\n\t\"%s\"",
+				fPath,
+				"gitea admin regenerate keys",
+				"gitea doctor --run authorized_keys --fix")
+			return fmt.Errorf(`authorized_keys is out of date and should be regenerated with "gitea admin regenerate keys" or "gitea doctor --run authorized_keys --fix"`)
+		}
+		logger.Warn("authorized_keys is out of date. Attempting rewrite...")
+		err = models.RewriteAllPublicKeys()
+		if err != nil {
+			logger.Critical("Unable to rewrite authorized_keys file. ERROR: %v", err)
+			return fmt.Errorf("Unable to rewrite authorized_keys file. ERROR: %v", err)
+		}
+	}
+	return nil
+}
+
+func init() {
+	Register(&Check{
+		Title:     "Check if OpenSSH authorized_keys file is up-to-date",
+		Name:      "authorized-keys",
+		IsDefault: true,
+		Run:       checkAuthorizedKeys,
+		Priority:  4,
+	})
+}

modules/doctor/dbconsistency.go

@@ -0,0 +1,127 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"context"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/models/migrations"
+	"code.gitea.io/gitea/modules/log"
+)
+
+func checkDBConsistency(logger log.Logger, autofix bool) error {
+	// make sure DB version is uptodate
+	if err := models.NewEngine(context.Background(), migrations.EnsureUpToDate); err != nil {
+		logger.Critical("Model version on the database does not match the current Gitea version. Model consistency will not be checked until the database is upgraded")
+		return err
+	}
+
+	// find labels without existing repo or org
+	count, err := models.CountOrphanedLabels()
+	if err != nil {
+		logger.Critical("Error: %v whilst counting orphaned labels")
+		return err
+	}
+
+	if count > 0 {
+		if autofix {
+			if err = models.DeleteOrphanedLabels(); err != nil {
+				logger.Critical("Error: %v whilst deleting orphaned labels")
+				return err
+			}
+			logger.Info("%d labels without existing repository/organisation deleted", count)
+		} else {
+			logger.Warn("%d labels without existing repository/organisation", count)
+		}
+	}
+
+	// find issues without existing repository
+	count, err = models.CountOrphanedIssues()
+	if err != nil {
+		logger.Critical("Error: %v whilst counting orphaned issues")
+		return err
+	}
+	if count > 0 {
+		if autofix {
+			if err = models.DeleteOrphanedIssues(); err != nil {
+				logger.Critical("Error: %v whilst deleting orphaned issues")
+				return err
+			}
+			logger.Info("%d issues without existing repository deleted", count)
+		} else {
+			logger.Warn("%d issues without existing repository", count)
+		}
+	}
+
+	// find pulls without existing issues
+	count, err = models.CountOrphanedObjects("pull_request", "issue", "pull_request.issue_id=issue.id")
+	if err != nil {
+		logger.Critical("Error: %v whilst counting orphaned objects")
+		return err
+	}
+	if count > 0 {
+		if autofix {
+			if err = models.DeleteOrphanedObjects("pull_request", "issue", "pull_request.issue_id=issue.id"); err != nil {
+				logger.Critical("Error: %v whilst deleting orphaned objects")
+				return err
+			}
+			logger.Info("%d pull requests without existing issue deleted", count)
+		} else {
+			logger.Warn("%d pull requests without existing issue", count)
+		}
+	}
+
+	// find tracked times without existing issues/pulls
+	count, err = models.CountOrphanedObjects("tracked_time", "issue", "tracked_time.issue_id=issue.id")
+	if err != nil {
+		logger.Critical("Error: %v whilst counting orphaned objects")
+		return err
+	}
+	if count > 0 {
+		if autofix {
+			if err = models.DeleteOrphanedObjects("tracked_time", "issue", "tracked_time.issue_id=issue.id"); err != nil {
+				logger.Critical("Error: %v whilst deleting orphaned objects")
+				return err
+			}
+			logger.Info("%d tracked times without existing issue deleted", count)
+		} else {
+			logger.Warn("%d tracked times without existing issue", count)
+		}
+	}
+
+	// find null archived repositories
+	count, err = models.CountNullArchivedRepository()
+	if err != nil {
+		logger.Critical("Error: %v whilst counting null archived repositories")
+		return err
+	}
+	if count > 0 {
+		if autofix {
+			updatedCount, err := models.FixNullArchivedRepository()
+			if err != nil {
+				logger.Critical("Error: %v whilst fixing null archived repositories")
+				return err
+			}
+			logger.Info("%d repositories with null is_archived updated", updatedCount)
+		} else {
+			logger.Warn("%d repositories with null is_archived", count)
+		}
+	}
+
+	// TODO: function to recalc all counters
+
+	return nil
+}
+
+func init() {
+	Register(&Check{
+		Title:     "Check consistency of database",
+		Name:      "check-db-consistency",
+		IsDefault: false,
+		Run:       checkDBConsistency,
+		Priority:  3,
+	})
+}

modules/doctor/dbversion.go

@@ -0,0 +1,42 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"context"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/models/migrations"
+	"code.gitea.io/gitea/modules/log"
+)
+
+func checkDBVersion(logger log.Logger, autofix bool) error {
+	if err := models.NewEngine(context.Background(), migrations.EnsureUpToDate); err != nil {
+		if !autofix {
+			logger.Critical("Error: %v during ensure up to date", err)
+			return err
+		}
+		logger.Warn("Got Error: %v during ensure up to date", err)
+		logger.Warn("Attempting to migrate to the latest DB version to fix this.")
+
+		err = models.NewEngine(context.Background(), migrations.Migrate)
+		if err != nil {
+			logger.Critical("Error: %v during migration")
+		}
+		return err
+	}
+	return nil
+}
+
+func init() {
+	Register(&Check{
+		Title:         "Check Database Version",
+		Name:          "check-db-version",
+		IsDefault:     true,
+		Run:           checkDBVersion,
+		AbortIfFailed: false,
+		Priority:      2,
+	})
+}

modules/doctor/doctor.go

@@ -0,0 +1,105 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"fmt"
+	"sort"
+	"strings"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/setting"
+)
+
+// Check represents a Doctor check
+type Check struct {
+	Title                      string
+	Name                       string
+	IsDefault                  bool
+	Run                        func(logger log.Logger, autofix bool) error
+	AbortIfFailed              bool
+	SkipDatabaseInitialization bool
+	Priority                   int
+}
+
+type wrappedLevelLogger struct {
+	log.LevelLogger
+}
+
+func (w *wrappedLevelLogger) Log(skip int, level log.Level, format string, v ...interface{}) error {
+	return w.LevelLogger.Log(
+		skip+1,
+		level,
+		" - %s "+format,
+		append(
+			[]interface{}{
+				log.NewColoredValueBytes(
+					fmt.Sprintf("[%s]", strings.ToUpper(level.String()[0:1])),
+					level.Color()),
+			}, v...)...)
+}
+
+func initDBDisableConsole(disableConsole bool) error {
+	setting.NewContext()
+	setting.InitDBConfig()
+
+	setting.NewXORMLogService(disableConsole)
+	if err := models.SetEngine(); err != nil {
+		return fmt.Errorf("models.SetEngine: %v", err)
+	}
+	return nil
+}
+
+// Checks is the list of available commands
+var Checks []*Check
+
+// RunChecks runs the doctor checks for the provided list
+func RunChecks(logger log.Logger, autofix bool, checks []*Check) error {
+	wrappedLogger := log.LevelLoggerLogger{
+		LevelLogger: &wrappedLevelLogger{logger},
+	}
+
+	dbIsInit := false
+	for i, check := range checks {
+		if !dbIsInit && !check.SkipDatabaseInitialization {
+			// Only open database after the most basic configuration check
+			setting.EnableXORMLog = false
+			if err := initDBDisableConsole(true); err != nil {
+				logger.Error("Error whilst initializing the database: %v", err)
+				logger.Error("Check if you are using the right config file. You can use a --config directive to specify one.")
+				return nil
+			}
+			dbIsInit = true
+		}
+		logger.Info("[%d] %s", log.NewColoredIDValue(i+1), check.Title)
+		logger.Flush()
+		if err := check.Run(&wrappedLogger, autofix); err != nil {
+			if check.AbortIfFailed {
+				logger.Critical("FAIL")
+				return err
+			}
+			logger.Error("ERROR")
+		} else {
+			logger.Info("OK")
+			logger.Flush()
+		}
+	}
+	return nil
+}
+
+// Register registers a command with the list
+func Register(command *Check) {
+	Checks = append(Checks, command)
+	sort.SliceStable(Checks, func(i, j int) bool {
+		if Checks[i].Priority == Checks[j].Priority {
+			return Checks[i].Name < Checks[j].Name
+		}
+		if Checks[i].Priority == 0 {
+			return false
+		}
+		return Checks[i].Priority < Checks[j].Priority
+	})
+}

modules/doctor/mergebase.go

@@ -0,0 +1,110 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"fmt"
+	"strings"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/log"
+	"xorm.io/builder"
+)
+
+func iteratePRs(repo *models.Repository, each func(*models.Repository, *models.PullRequest) error) error {
+	return models.Iterate(
+		models.DefaultDBContext(),
+		new(models.PullRequest),
+		builder.Eq{"base_repo_id": repo.ID},
+		func(idx int, bean interface{}) error {
+			return each(repo, bean.(*models.PullRequest))
+		},
+	)
+}
+
+func checkPRMergeBase(logger log.Logger, autofix bool) error {
+	numRepos := 0
+	numPRs := 0
+	numPRsUpdated := 0
+	err := iterateRepositories(func(repo *models.Repository) error {
+		numRepos++
+		return iteratePRs(repo, func(repo *models.Repository, pr *models.PullRequest) error {
+			numPRs++
+			pr.BaseRepo = repo
+			repoPath := repo.RepoPath()
+
+			oldMergeBase := pr.MergeBase
+
+			if !pr.HasMerged {
+				var err error
+				pr.MergeBase, err = git.NewCommand("merge-base", "--", pr.BaseBranch, pr.GetGitRefName()).RunInDir(repoPath)
+				if err != nil {
+					var err2 error
+					pr.MergeBase, err2 = git.NewCommand("rev-parse", git.BranchPrefix+pr.BaseBranch).RunInDir(repoPath)
+					if err2 != nil {
+						logger.Warn("Unable to get merge base for PR ID %d, #%d onto %s in %s/%s. Error: %v & %v", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err, err2)
+						return nil
+					}
+				}
+			} else {
+				parentsString, err := git.NewCommand("rev-list", "--parents", "-n", "1", pr.MergedCommitID).RunInDir(repoPath)
+				if err != nil {
+					logger.Warn("Unable to get parents for merged PR ID %d, #%d onto %s in %s/%s. Error: %v", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err)
+					return nil
+				}
+				parents := strings.Split(strings.TrimSpace(parentsString), " ")
+				if len(parents) < 2 {
+					return nil
+				}
+
+				args := append([]string{"merge-base", "--"}, parents[1:]...)
+				args = append(args, pr.GetGitRefName())
+
+				pr.MergeBase, err = git.NewCommand(args...).RunInDir(repoPath)
+				if err != nil {
+					logger.Warn("Unable to get merge base for merged PR ID %d, #%d onto %s in %s/%s. Error: %v", pr.ID, pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, err)
+					return nil
+				}
+			}
+			pr.MergeBase = strings.TrimSpace(pr.MergeBase)
+			if pr.MergeBase != oldMergeBase {
+				if autofix {
+					if err := pr.UpdateCols("merge_base"); err != nil {
+						logger.Critical("Failed to update merge_base. ERROR: %v", err)
+						return fmt.Errorf("Failed to update merge_base. ERROR: %v", err)
+					}
+				} else {
+					logger.Info("#%d onto %s in %s/%s: MergeBase should be %s but is %s", pr.Index, pr.BaseBranch, pr.BaseRepo.OwnerName, pr.BaseRepo.Name, oldMergeBase, pr.MergeBase)
+				}
+				numPRsUpdated++
+			}
+			return nil
+		})
+	})
+
+	if autofix {
+		logger.Info("%d PR mergebases updated of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos)
+	} else {
+		if numPRsUpdated > 0 && err == nil {
+			logger.Critical("%d PRs with incorrect mergebases of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos)
+			return fmt.Errorf("%d PRs with incorrect mergebases of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos)
+		}
+
+		logger.Warn("%d PRs with incorrect mergebases of %d PRs total in %d repos", numPRsUpdated, numPRs, numRepos)
+	}
+
+	return err
+}
+
+func init() {
+	Register(&Check{
+		Title:     "Recalculate merge bases",
+		Name:      "recalculate-merge-bases",
+		IsDefault: false,
+		Run:       checkPRMergeBase,
+		Priority:  7,
+	})
+}

modules/doctor/misc.go

@@ -0,0 +1,146 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"fmt"
+	"os/exec"
+	"strings"
+
+	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/modules/git"
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/repository"
+	"code.gitea.io/gitea/modules/setting"
+	"xorm.io/builder"
+)
+
+func iterateRepositories(each func(*models.Repository) error) error {
+	err := models.Iterate(
+		models.DefaultDBContext(),
+		new(models.Repository),
+		builder.Gt{"id": 0},
+		func(idx int, bean interface{}) error {
+			return each(bean.(*models.Repository))
+		},
+	)
+	return err
+}
+
+func checkScriptType(logger log.Logger, autofix bool) error {
+	path, err := exec.LookPath(setting.ScriptType)
+	if err != nil {
+		logger.Critical("ScriptType \"%q\" is not on the current PATH. Error: %v", setting.ScriptType, err)
+		return fmt.Errorf("ScriptType \"%q\" is not on the current PATH. Error: %v", setting.ScriptType, err)
+	}
+	logger.Info("ScriptType %s is on the current PATH at %s", setting.ScriptType, path)
+	return nil
+}
+
+func checkHooks(logger log.Logger, autofix bool) error {
+	if err := iterateRepositories(func(repo *models.Repository) error {
+		results, err := repository.CheckDelegateHooks(repo.RepoPath())
+		if err != nil {
+			logger.Critical("Unable to check delegate hooks for repo %-v. ERROR: %v", repo, err)
+			return fmt.Errorf("Unable to check delegate hooks for repo %-v. ERROR: %v", repo, err)
+		}
+		if len(results) > 0 && autofix {
+			logger.Warn("Regenerated hooks for %s", repo.FullName())
+			if err := repository.CreateDelegateHooks(repo.RepoPath()); err != nil {
+				logger.Critical("Unable to recreate delegate hooks for %-v. ERROR: %v", repo, err)
+				return fmt.Errorf("Unable to recreate delegate hooks for %-v. ERROR: %v", repo, err)
+			}
+		}
+		for _, result := range results {
+			logger.Warn(result)
+		}
+		return nil
+	}); err != nil {
+		logger.Critical("Errors noted whilst checking delegate hooks.")
+		return err
+	}
+	return nil
+}
+
+func checkUserStarNum(logger log.Logger, autofix bool) error {
+	if err := models.DoctorUserStarNum(); err != nil {
+		logger.Critical("Unable update User Stars numbers")
+		return err
+	}
+	return nil
+}
+
+func checkEnablePushOptions(logger log.Logger, autofix bool) error {
+	numRepos := 0
+	numNeedUpdate := 0
+	if err := iterateRepositories(func(repo *models.Repository) error {
+		numRepos++
+		r, err := git.OpenRepository(repo.RepoPath())
+		if err != nil {
+			return err
+		}
+		defer r.Close()
+
+		if autofix {
+			_, err := git.NewCommand("config", "receive.advertisePushOptions", "true").RunInDir(r.Path)
+			return err
+		}
+
+		value, err := git.NewCommand("config", "receive.advertisePushOptions").RunInDir(r.Path)
+		if err != nil {
+			return err
+		}
+
+		result, valid := git.ParseBool(strings.TrimSpace(value))
+		if !result || !valid {
+			numNeedUpdate++
+			logger.Info("%s: does not have receive.advertisePushOptions set correctly: %q", repo.FullName(), value)
+		}
+		return nil
+	}); err != nil {
+		logger.Critical("Unable to EnablePushOptions: %v", err)
+		return err
+	}
+
+	if autofix {
+		logger.Info("Enabled push options for %d repositories.", numRepos)
+	} else {
+		logger.Info("Checked %d repositories, %d need updates.", numRepos, numNeedUpdate)
+
+	}
+
+	return nil
+}
+
+func init() {
+	Register(&Check{
+		Title:     "Check if SCRIPT_TYPE is available",
+		Name:      "script-type",
+		IsDefault: false,
+		Run:       checkScriptType,
+		Priority:  5,
+	})
+	Register(&Check{
+		Title:     "Check if hook files are up-to-date and executable",
+		Name:      "hooks",
+		IsDefault: false,
+		Run:       checkHooks,
+		Priority:  6,
+	})
+	Register(&Check{
+		Title:     "Recalculate Stars number for all user",
+		Name:      "recalculate-stars-number",
+		IsDefault: false,
+		Run:       checkUserStarNum,
+		Priority:  6,
+	})
+	Register(&Check{
+		Title:     "Enable push options",
+		Name:      "enable-push-options",
+		IsDefault: false,
+		Run:       checkEnablePushOptions,
+		Priority:  7,
+	})
+}

modules/doctor/paths.go

@@ -0,0 +1,126 @@
+// Copyright 2020 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package doctor
+
+import (
+	"fmt"
+	"io/ioutil"
+	"os"
+
+	"code.gitea.io/gitea/modules/log"
+	"code.gitea.io/gitea/modules/options"
+	"code.gitea.io/gitea/modules/setting"
+)
+
+type configurationFile struct {
+	Name        string
+	Path        string
+	IsDirectory bool
+	Required    bool
+	Writable    bool
+}
+
+func checkConfigurationFile(logger log.Logger, autofix bool, fileOpts configurationFile) error {
+	logger.Info(`%-26s  %q`, log.NewColoredValue(fileOpts.Name+":", log.Reset), fileOpts.Path)
+	fi, err := os.Stat(fileOpts.Path)
+	if err != nil {
+		if os.IsNotExist(err) && autofix && fileOpts.IsDirectory {
+			if err := os.MkdirAll(fileOpts.Path, 0777); err != nil {
+				logger.Error("    Directory does not exist and could not be created. ERROR: %v", err)
+				return fmt.Errorf("Configuration directory: \"%q\" does not exist and could not be created. ERROR: %v", fileOpts.Path, err)
+			}
+			fi, err = os.Stat(fileOpts.Path)
+		}
+	}
+	if err != nil {
+		if fileOpts.Required {
+			logger.Error("    Is REQUIRED but is not accessible. ERROR: %v", err)
+			return fmt.Errorf("Configuration file \"%q\" is not accessible but is required. Error: %v", fileOpts.Path, err)
+		}
+		logger.Warn("    NOTICE: is not accessible (Error: %v)", err)
+		// this is a non-critical error
+		return nil
+	}
+
+	if fileOpts.IsDirectory && !fi.IsDir() {
+		logger.Error("    ERROR: not a directory")
+		return fmt.Errorf("Configuration directory \"%q\" is not a directory. Error: %v", fileOpts.Path, err)
+	} else if !fileOpts.IsDirectory && !fi.Mode().IsRegular() {
+		logger.Error("    ERROR: not a regular file")
+		return fmt.Errorf("Configuration file \"%q\" is not a regular file. Error: %v", fileOpts.Path, err)
+	} else if fileOpts.Writable {
+		if err := isWritableDir(fileOpts.Path); err != nil {
+			logger.Error("    ERROR: is required to be writable but is not writable: %v", err)
+			return fmt.Errorf("Configuration file \"%q\" is required to be writable but is not. Error: %v", fileOpts.Path, err)
+		}
+	}
+	return nil
+}
+
+func checkConfigurationFiles(logger log.Logger, autofix bool) error {
+	if fi, err := os.Stat(setting.CustomConf); err != nil || !fi.Mode().IsRegular() {
+		logger.Error("Failed to find configuration file at '%s'.", setting.CustomConf)
+		logger.Error("If you've never ran Gitea yet, this is normal and '%s' will be created for you on first run.", setting.CustomConf)
+		logger.Error("Otherwise check that you are running this command from the correct path and/or provide a `--config` parameter.")
+		logger.Critical("Cannot proceed without a configuration file")
+		return err
+	}
+
+	setting.NewContext()
+
+	configurationFiles := []configurationFile{
+		{"Configuration File Path", setting.CustomConf, false, true, false},
+		{"Repository Root Path", setting.RepoRootPath, true, true, true},
+		{"Data Root Path", setting.AppDataPath, true, true, true},
+		{"Custom File Root Path", setting.CustomPath, true, false, false},
+		{"Work directory", setting.AppWorkPath, true, true, false},
+		{"Log Root Path", setting.LogRootPath, true, true, true},
+	}
+
+	if options.IsDynamic() {
+		configurationFiles = append(configurationFiles, configurationFile{"Static File Root Path", setting.StaticRootPath, true, true, false})
+	}
+
+	numberOfErrors := 0
+	for _, configurationFile := range configurationFiles {
+		if err := checkConfigurationFile(logger, autofix, configurationFile); err != nil {
+			numberOfErrors++
+		}
+	}
+
+	if numberOfErrors > 0 {
+		logger.Critical("Please check your configuration files and try again.")
+		return fmt.Errorf("%d configuration files with errors", numberOfErrors)
+	}
+
+	return nil
+}
+
+func isWritableDir(path string) error {
+	// There's no platform-independent way of checking if a directory is writable
+	// https://stackoverflow.com/questions/20026320/how-to-tell-if-folder-exists-and-is-writable
+
+	tmpFile, err := ioutil.TempFile(path, "doctors-order")
+	if err != nil {
+		return err
+	}
+	if err := os.Remove(tmpFile.Name()); err != nil {
+		fmt.Printf("Warning: can't remove temporary file: '%s'\n", tmpFile.Name())
+	}
+	tmpFile.Close()
+	return nil
+}
+
+func init() {
+	Register(&Check{
+		Title:                      "Check paths and basic configuration",
+		Name:                       "paths",
+		IsDefault:                  true,
+		Run:                        checkConfigurationFiles,
+		AbortIfFailed:              true,
+		SkipDatabaseInitialization: true,
+		Priority:                   1,
+	})
+}