From 9a07523ddb1b1afae67cf52e5ca264b755a8e494 Mon Sep 17 00:00:00 2001 From: Martin Czygan Date: Tue, 27 Jul 2021 13:17:58 +0200 Subject: minor tweaks and doc improvements --- skate/cmd/skate-map/main.go | 26 ++++++++-------- skate/cmd/skate-reduce/main.go | 68 ++++++++++++++++++++---------------------- 2 files changed, 45 insertions(+), 49 deletions(-) (limited to 'skate/cmd') diff --git a/skate/cmd/skate-map/main.go b/skate/cmd/skate-map/main.go index f87c02f..a437705 100644 --- a/skate/cmd/skate-map/main.go +++ b/skate/cmd/skate-map/main.go @@ -2,9 +2,9 @@ // extract a key from a json document. For simple cases, you can use `jq` and // other tools. Some key derivations require a bit more, hence a dedicated program. // -// An example with mostly unix tools. We want to extract (DOI, doc) tuples from -// newline delimited JSON and sort by it; we also want to do this fast, hence -// parallel, LC_ALL, etc. +// An example with mostly unix tools. We want to extract (DOI, doc) tuples +// (sorted by DOI) from newline delimited JSON; we also want to do this fast, +// hence GNU parallel, LC_ALL, etc. // // $ zstdcat -T0 file.zst | (1) // LC_ALL=C tr -d '\t' | (2) * @@ -20,7 +20,7 @@ // (1) zstd is fast! "~4x faster than zlib" (https://is.gd/HT1DUs) // (2) we use tab as column separator and we want clean this up before (could // be skipped, if we limit number of splits) -// (3) we pass the data to jq, with a bit larger buffer (default is 1MB) +// (3) we pass the data to jq, with a bit larger buffer for GNU parallel (default is 1MB, currently) // (4) we want no "null" output // (5) tostring prints the input as string, because we need to carry the document forward ... // (6) ... but we'll need some cleanup, too @@ -28,9 +28,9 @@ // (8) a custom filter to normalize a DOI in a specific column // (9) sorting by DOI // -// This is reasonably fast, but some cleanup is ugly. We also want more complex -// keys, e.g. more normalizations, etc; in short: we'd like to encapsulate (2) -// to (8) with `skate-map`. +// This is reasonably fast, but some data cleanup code is ugly. We also want +// more complex keys, e.g. more normalizations, etc; in short: we'd like to +// encapsulate (2) to (8) with `skate-map`. package main import ( @@ -92,19 +92,19 @@ func main() { } switch { case *mapperName != "": - if mapf, ok := availableMappers[*mapperName]; !ok { + if mapper, ok := availableMappers[*mapperName]; !ok { log.Fatalf("unknown mapper name: %v", *mapperName) } else { if *skipOnEmpty > 0 { - mapf = skate.WithSkipOnEmpty(mapf, *skipOnEmpty-1) + mapper = skate.WithSkipOnEmpty(mapper, *skipOnEmpty-1) } if *keyPrefix != "" { - mapf = skate.WithPrefix(mapf, *keyPrefix) + mapper = skate.WithPrefix(mapper, *keyPrefix) } if *bestEffort { - mapf = skate.WithBestEffort(mapf) + mapper = skate.WithBestEffort(mapper) } - pp := parallel.NewProcessor(os.Stdin, os.Stdout, mapf.AsTSV) + pp := parallel.NewProcessor(os.Stdin, os.Stdout, mapper.AsTSV) pp.NumWorkers = *numWorkers pp.BatchSize = *batchSize pp.Verbose = *verbose @@ -115,9 +115,9 @@ func main() { default: fmt.Println(help) w := tabwriter.NewWriter(os.Stdout, 0, 0, 4, ' ', 0) + defer w.Flush() for k, v := range availableMappers { fmt.Fprintf(w, "%s\t%s\n", k, skate.NameOf(v)) } - w.Flush() } } diff --git a/skate/cmd/skate-reduce/main.go b/skate/cmd/skate-reduce/main.go index 7918a28..6d743b7 100644 --- a/skate/cmd/skate-reduce/main.go +++ b/skate/cmd/skate-reduce/main.go @@ -1,6 +1,6 @@ -// skate-reduce takes prepared inputs (e.g. from skate-map or skate-cluster) -// and applies various verification and conversion functions. The output will -// often be a stream of biblioref schema docs. +// skate-reduce takes prepared inputs (e.g. from skate-map) and applies various +// verification and conversion functions. The output will often be a stream of +// biblioref schema docs. // // Support various "modes", e.g. exact, verify, ref, bref, wiki. Each mode may // work on one or two files, and may need extra args. @@ -9,38 +9,38 @@ // | will emit biblioref docs relating *one* element from releases with *all* // | elements from ref; this is for "doi", "pmid" and other id matches, where no // | further checks are necessary. The match reason, e.g. "doi" needs to be -// | supplied. +// | supplied // | // | $ skate-reduce -m exact -r doi -F a.tsv -L b.tsv // | // | // * fuzzy | takes two (key, doc) TSV files (one for release, one for refs), -// | runs verification within a group and will emit biblioref. +// | runs verification within a group and will emit biblioref // | // | $ skate-reduce -m fuzzy -F a.tsv -L b.tsv // | // | -// * wiki | zippy mode for releases and wikipedia inputs. +// * wiki | zippy mode for releases and wikipedia inputs // | // | $ skate-reduce -m wiki -L a.ndj -W b.ndj // | // | -// * oledt | zippy mode for releases and OL inputs, dumps table for debugging. +// * oledt | zippy mode for releases and OL inputs, dumps table for debugging // | // | $ skate-reduce -m oled -F a.ndj -O b.ndj // | // | -// * oled | zippy mode for releases and OL inputs, emit biblioref. +// * oled | zippy mode for releases and OL inputs, emit biblioref // | // | $ skate-reduce -m oled -F a.ndj -O b.ndj // | // | -// * rere | zippy mode for OL release and ref (as release) inputs, emit biblioref. +// * rere | zippy mode for OL release and ref (as release) inputs, emit biblioref // | // | $ skate-reduce -m rere -O a.ndj -F b.ndj // | // | -// * unmatched | join matched and unmatched reference data; do deduplicate on the fly +// * unmatched | join matched and unmatched reference data; deduplicate on the fly // | // | $ skate-reduce -m unmatched -B a.ndj -F b.ndj // | @@ -81,8 +81,8 @@ var ( cdxAdhoc = flag.String("C", "", "path to cdx adhoc schema") // Extra args. - reason = flag.String("r", "", "reason for match: doi, pmid, pmcid, arxiv, unknown") - reasonMap = map[string]skate.MatchResult{ + matchResult = flag.String("r", "", "reason for match: doi, pmid, pmcid, arxiv, unknown") + matchResultMap = map[string]skate.MatchResult{ "doi": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonDOI}, "pmid": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonPMID}, "pmcid": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonPMCID}, @@ -118,76 +118,72 @@ func main() { if *quite { log.SetOutput(ioutil.Discard) } - bw := bufio.NewWriter(os.Stdout) + var ( + bw = bufio.NewWriter(os.Stdout) + l, f, w, o, b, c *os.File + r skate.MatchResult + ok bool + err error + ) defer bw.Flush() switch *mode { case "exact": - l, f, err := xio.OpenTwo(*releases, *refs) - if err != nil { + if l, f, err = xio.OpenTwo(*releases, *refs); err != nil { log.Fatal(err) } - r, ok := reasonMap[*reason] - if !ok { - log.Fatalf("unknown reason: %v", *reason) + if r, ok = matchResultMap[*matchResult]; !ok { + log.Fatalf("unknown reason: %v", *matchResult) } if err := skate.ZippyExact(l, f, r, bw); err != nil { log.Fatal(err) } case "fuzzy": - l, f, err := xio.OpenTwo(*releases, *refs) - if err != nil { + if l, f, err = xio.OpenTwo(*releases, *refs); err != nil { log.Fatal(err) } if err := skate.ZippyVerifyRefs(l, f, bw); err != nil { log.Fatal(err) } case "wiki": - l, w, err := xio.OpenTwo(*releases, *wiki) - if err != nil { + if l, w, err = xio.OpenTwo(*releases, *wiki); err != nil { log.Fatal(err) } - if err := skate.ZippyExactWiki(l, w, reasonMap["doi"], bw); err != nil { + if err := skate.ZippyExactWiki(l, w, matchResultMap["doi"], bw); err != nil { log.Fatal(err) } case "oledt": - o, f, err := xio.OpenTwo(*openLibrary, *refs) - if err != nil { + if o, f, err = xio.OpenTwo(*openLibrary, *refs); err != nil { log.Fatal(err) } if err := skate.ZippyVerifyRefsOpenLibraryTable(o, f, bw); err != nil { log.Fatal(err) } case "oled": - o, f, err := xio.OpenTwo(*openLibrary, *refs) - if err != nil { + if o, f, err = xio.OpenTwo(*openLibrary, *refs); err != nil { log.Fatal(err) } if err := skate.ZippyVerifyRefsOpenLibrary(o, f, bw); err != nil { log.Fatal(err) } case "rere": - o, f, err := xio.OpenTwo(*releases, *refs) - if err != nil { + if o, f, err = xio.OpenTwo(*releases, *refs); err != nil { log.Fatal(err) } - r, ok := reasonMap[*reason] - if !ok { - log.Fatalf("unknown reason: %v", *reason) + if r, ok = matchResultMap[*matchResult]; !ok { + log.Fatalf("unknown reason: %v", *matchResult) } if err := skate.ZippyExactReleases(o, f, r, bw); err != nil { log.Fatal(err) } case "unmatched": - b, f, err := xio.OpenTwo(*bref, *refs) - if err != nil { + if b, f, err = xio.OpenTwo(*bref, *refs); err != nil { log.Fatal(err) } if err := skate.ZippyBrefAugment(b, f, bw); err != nil { log.Fatal(err) } case "wb": - f, c, err := xio.OpenTwo(*refs, *cdxAdhoc) - if err != nil { + if f, c, err = xio.OpenTwo(*refs, *cdxAdhoc); err != nil { log.Fatal(err) } if err := skate.ZippyWayback(f, c, bw); err != nil { -- cgit v1.2.3