diff --git a/biobtree.go b/biobtree.go index bdba576..f1b6f35 100755 --- a/biobtree.go +++ b/biobtree.go @@ -20,8 +20,8 @@ import ( "github.com/urfave/cli" ) -const version = "1.1.4" -const versionTag = "v1.1.4" +const version = "1.2.0" +const versionTag = "v1.2.0" var config *conf.Conf @@ -148,6 +148,13 @@ func main() { return runWebCommand(c) }, }, + { + Name: "install", + Usage: "Install configuration files. Used for genomes and datasets listing", + Action: func(c *cli.Context) error { + return runInstallCommand(c) + }, + }, { Name: "alias", Usage: "Recreates alias db this is used if new aliases wants to added while keeping existing state", @@ -350,6 +357,17 @@ func runWebCommand(c *cli.Context) error { } +func runInstallCommand(c *cli.Context) error { + + confdir := c.GlobalString("confdir") + outDir := c.GlobalString("out_dir") + config = &conf.Conf{} + config.Init(confdir, versionTag, true, outDir) + + return nil + +} + func runProfileCommand(c *cli.Context) error { confdir := c.GlobalString("confdir") diff --git a/conf/optional.dataset.json b/conf/optional.dataset.json index 4046812..6f24f4e 100755 --- a/conf/optional.dataset.json +++ b/conf/optional.dataset.json @@ -269,12 +269,6 @@ "id": "544", "url": "http://mammoth.bcm.tmc.edu/cgi-bin/report_maker_ls/uniprotTraceServerResults.pl?identifier=£{id}" }, - "flybase": { - "aliases": "FlyBase", - "name": "FlyBase", - "id": "545", - "url": "http://flybase.org/reports/£{id}.html" - }, "foodb": { "aliases": "FooDB,FooDB accession", "name": "FooDB", @@ -755,12 +749,6 @@ "id": "625", "url": "" }, - "supfam": { - "aliases": "SUPFAM", - "name": "SUPFAM", - "id": "626", - "url": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=£{id}" - }, "swiss-2dpage": { "aliases": "SWISS-2DPAGE", "name": "SWISS-2DPAGE", diff --git a/ensembl/ensembl.paths.json b/ensembl/ensembl.paths.json index c411bff..a41ccac 100755 --- a/ensembl/ensembl.paths.json +++ b/ensembl/ensembl.paths.json @@ -1 +1 @@ -{"version":98,"jsons":{"acanthochromis_polyacanthus":["/pub/current_json/acanthochromis_polyacanthus/acanthochromis_polyacanthus.json"],"ailuropoda_melanoleuca":["/pub/current_json/ailuropoda_melanoleuca/ailuropoda_melanoleuca.json"],"amphilophus_citrinellus":["/pub/current_json/amphilophus_citrinellus/amphilophus_citrinellus.json"],"amphiprion_ocellaris":["/pub/current_json/amphiprion_ocellaris/amphiprion_ocellaris.json"],"amphiprion_percula":["/pub/current_json/amphiprion_percula/amphiprion_percula.json"],"anabas_testudineus":["/pub/current_json/anabas_testudineus/anabas_testudineus.json"],"anas_platyrhynchos_platyrhynchos":["/pub/current_json/anas_platyrhynchos_platyrhynchos/anas_platyrhynchos_platyrhynchos.json"],"anolis_carolinensis":["/pub/current_json/anolis_carolinensis/anolis_carolinensis.json"],"anser_brachyrhynchus":["/pub/current_json/anser_brachyrhynchus/anser_brachyrhynchus.json"],"aotus_nancymaae":["/pub/current_json/aotus_nancymaae/aotus_nancymaae.json"],"apteryx_haastii":["/pub/current_json/apteryx_haastii/apteryx_haastii.json"],"apteryx_owenii":["/pub/current_json/apteryx_owenii/apteryx_owenii.json"],"apteryx_rowi":["/pub/current_json/apteryx_rowi/apteryx_rowi.json"],"astatotilapia_calliptera":["/pub/current_json/astatotilapia_calliptera/astatotilapia_calliptera.json"],"astyanax_mexicanus":["/pub/current_json/astyanax_mexicanus/astyanax_mexicanus.json"],"astyanax_mexicanus_pachon":["/pub/current_json/astyanax_mexicanus_pachon/astyanax_mexicanus_pachon.json"],"betta_splendens":["/pub/current_json/betta_splendens/betta_splendens.json"],"bison_bison_bison":["/pub/current_json/bison_bison_bison/bison_bison_bison.json"],"bos_indicus_hybrid":["/pub/current_json/bos_indicus_hybrid/bos_indicus_hybrid.json"],"bos_mutus":["/pub/current_json/bos_mutus/bos_mutus.json"],"bos_taurus":["/pub/current_json/bos_taurus/bos_taurus.json"],"bos_taurus_hybrid":["/pub/current_json/bos_taurus_hybrid/bos_taurus_hybrid.json"],"caenorhabditis_elegans":["/pub/current_json/caenorhabditis_elegans/caenorhabditis_elegans.json"],"calidris_pugnax":["/pub/current_json/calidris_pugnax/calidris_pugnax.json"],"calidris_pygmaea":["/pub/current_json/calidris_pygmaea/calidris_pygmaea.json"],"callithrix_jacchus":["/pub/current_json/callithrix_jacchus/callithrix_jacchus.json"],"callorhinchus_milii":["/pub/current_json/callorhinchus_milii/callorhinchus_milii.json"],"canis_familiaris":["/pub/current_json/canis_familiaris/canis_familiaris.json"],"canis_lupus_dingo":["/pub/current_json/canis_lupus_dingo/canis_lupus_dingo.json"],"capra_hircus":["/pub/current_json/capra_hircus/capra_hircus.json"],"carlito_syrichta":["/pub/current_json/carlito_syrichta/carlito_syrichta.json"],"castor_canadensis":["/pub/current_json/castor_canadensis/castor_canadensis.json"],"cavia_aperea":["/pub/current_json/cavia_aperea/cavia_aperea.json"],"cavia_porcellus":["/pub/current_json/cavia_porcellus/cavia_porcellus.json"],"cebus_capucinus":["/pub/current_json/cebus_capucinus/cebus_capucinus.json"],"cercocebus_atys":["/pub/current_json/cercocebus_atys/cercocebus_atys.json"],"chelonoidis_abingdonii":["/pub/current_json/chelonoidis_abingdonii/chelonoidis_abingdonii.json"],"chinchilla_lanigera":["/pub/current_json/chinchilla_lanigera/chinchilla_lanigera.json"],"chlorocebus_sabaeus":["/pub/current_json/chlorocebus_sabaeus/chlorocebus_sabaeus.json"],"choloepus_hoffmanni":["/pub/current_json/choloepus_hoffmanni/choloepus_hoffmanni.json"],"chrysemys_picta_bellii":["/pub/current_json/chrysemys_picta_bellii/chrysemys_picta_bellii.json"],"ciona_intestinalis":["/pub/current_json/ciona_intestinalis/ciona_intestinalis.json"],"ciona_savignyi":["/pub/current_json/ciona_savignyi/ciona_savignyi.json"],"clupea_harengus":["/pub/current_json/clupea_harengus/clupea_harengus.json"],"colobus_angolensis_palliatus":["/pub/current_json/colobus_angolensis_palliatus/colobus_angolensis_palliatus.json"],"cottoperca_gobio":["/pub/current_json/cottoperca_gobio/cottoperca_gobio.json"],"coturnix_japonica":["/pub/current_json/coturnix_japonica/coturnix_japonica.json"],"cricetulus_griseus_chok1gshd":["/pub/current_json/cricetulus_griseus_chok1gshd/cricetulus_griseus_chok1gshd.json"],"cricetulus_griseus_crigri":["/pub/current_json/cricetulus_griseus_crigri/cricetulus_griseus_crigri.json"],"cricetulus_griseus_picr":["/pub/current_json/cricetulus_griseus_picr/cricetulus_griseus_picr.json"],"crocodylus_porosus":["/pub/current_json/crocodylus_porosus/crocodylus_porosus.json"],"cyanistes_caeruleus":["/pub/current_json/cyanistes_caeruleus/cyanistes_caeruleus.json"],"cynoglossus_semilaevis":["/pub/current_json/cynoglossus_semilaevis/cynoglossus_semilaevis.json"],"cyprinodon_variegatus":["/pub/current_json/cyprinodon_variegatus/cyprinodon_variegatus.json"],"danio_rerio":["/pub/current_json/danio_rerio/danio_rerio.json"],"dasypus_novemcinctus":["/pub/current_json/dasypus_novemcinctus/dasypus_novemcinctus.json"],"denticeps_clupeoides":["/pub/current_json/denticeps_clupeoides/denticeps_clupeoides.json"],"dipo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\ No newline at end of file diff --git a/service/mapfilter.go b/service/mapfilter.go index aa5d4c0..a057844 100644 --- a/service/mapfilter.go +++ b/service/mapfilter.go @@ -213,7 +213,7 @@ func (s *service) inputXrefs(ids []string, idsDomain uint32, filterq *query.Quer if pages == nil { - res, err := s.search(ids, idsDomain, rootPage, filterq, false, false) + res, err := s.search(ids, idsDomain, rootPage, filterq, true, false) if err != nil { return nil, "", err diff --git a/service/service.go b/service/service.go index df7b1df..c4528c4 100644 --- a/service/service.go +++ b/service/service.go @@ -7,6 +7,7 @@ import ( "io/ioutil" "log" "os" + "path/filepath" "sort" "strconv" "strings" @@ -45,7 +46,7 @@ type service struct { func (s *service) init() { meta := make(map[string]interface{}) - f, err := ioutil.ReadFile(config.Appconf["dbDir"] + "/db.meta.json") + f, err := ioutil.ReadFile(filepath.FromSlash(config.Appconf["dbDir"] + "/db.meta.json")) if err != nil { log.Fatalln("Error while reading meta information file which should be produced with generate command. Please make sure you did previous steps correctly.") fmt.Printf("Error: %v", err) diff --git a/service/web.go b/service/web.go index 28c6d2b..45a311b 100755 --- a/service/web.go +++ b/service/web.go @@ -36,7 +36,6 @@ func (web *Web) Start(c *conf.Conf) { web.service = s - // start grpc rpc := biobtreegrpc{ service: s, } @@ -46,17 +45,18 @@ func (web *Web) Start(c *conf.Conf) { web.metaRes = []byte(s.metajson()) searchGz := gziphandler.GzipHandler(http.HandlerFunc(web.search)) + metaGz := gziphandler.GzipHandler(http.HandlerFunc(web.meta)) searchEntryGz := gziphandler.GzipHandler(http.HandlerFunc(web.entry)) mapFilterGz := gziphandler.GzipHandler(http.HandlerFunc(web.mapFilter)) searchPageGz := gziphandler.GzipHandler(http.HandlerFunc(web.searchPage)) searchFilterGz := gziphandler.GzipHandler(http.HandlerFunc(web.searchFilter)) - metaGz := gziphandler.GzipHandler(http.HandlerFunc(web.meta)) + http.Handle("/ws/", searchGz) + http.Handle("/ws/meta/", metaGz) http.Handle("/ws/entry/", searchEntryGz) http.Handle("/ws/map/", mapFilterGz) http.Handle("/ws/page/", searchPageGz) http.Handle("/ws/filter/", searchFilterGz) - http.Handle("/ws/meta/", metaGz) //web ui fs := http.FileServer(http.Dir("website")) diff --git a/update/ensembl.go b/update/ensembl.go index b35aa14..d6aa4a0 100644 --- a/update/ensembl.go +++ b/update/ensembl.go @@ -63,14 +63,13 @@ func (e *ensembl) getEnsemblPaths() (*ensemblPaths, string) { } -func (e *ensembl) updateEnsemblPaths() (*ensemblPaths, string) { +func (e *ensembl) updateEnsemblPaths(version int) (*ensemblPaths, string) { var branch string var ftpAddress string var ftpJSONPath string var ftpMysqlPath string var ftpBiomartFolder string - var version int var err error switch e.source { diff --git a/update/update.go b/update/update.go index 35af17b..17bb94f 100755 --- a/update/update.go +++ b/update/update.go @@ -434,7 +434,8 @@ func (d *DataUpdate) setEnsemblPaths() { if _, ok := config.Appconf["disableEnsemblReleaseCheck"]; !ok { - if d.hasEnsemblNewRelease() { + hasNewRelease, version := d.hasEnsemblNewRelease() + if hasNewRelease { ensembls := [6]ensembl{} ensembls[0] = ensembl{source: "ensembl", d: d, branch: pbuf.Ensemblbranch_ENSEMBL} @@ -445,7 +446,7 @@ func (d *DataUpdate) setEnsemblPaths() { ensembls[5] = ensembl{source: "ensembl_protists", d: d, branch: pbuf.Ensemblbranch_PROTIST} for _, ens := range ensembls { - ens.updateEnsemblPaths() + ens.updateEnsemblPaths(version) time.Sleep(time.Duration(2) * time.Second) // just for not to kicked out from ensembl ftp } @@ -454,12 +455,13 @@ func (d *DataUpdate) setEnsemblPaths() { } -func (d *DataUpdate) hasEnsemblNewRelease() bool { +func (d *DataUpdate) hasEnsemblNewRelease() (bool, int) { epaths := ensemblPaths{} pathFile := filepath.FromSlash(config.Appconf["ensemblDir"] + "/ensembl_metazoa.paths.json") if !fileExists(pathFile) { - return true + + return true, d.getLatestEnsemblVersion() } f, err := os.Open(pathFile) check(err) @@ -472,6 +474,14 @@ func (d *DataUpdate) hasEnsemblNewRelease() bool { log.Fatal("Missing ensembl_version_url param") } + latestVersion := d.getLatestEnsemblVersion() + + return latestVersion != epaths.Version, latestVersion + +} + +func (d *DataUpdate) getLatestEnsemblVersion() int { + egversion := ensemblGLatestVersion{} res, err := http.Get(config.Appconf["ensembl_version_url"]) if err != nil { @@ -482,10 +492,7 @@ func (d *DataUpdate) hasEnsemblNewRelease() bool { log.Fatal("Error while getting ensembl release info from its rest service. This error could be temporary try again later or use param disableEnsemblReleaseCheck", err) } err = json.Unmarshal(body, &egversion) - - //fmt.Println(egversion.Version) - //fmt.Println(epaths.Version) - return egversion.Version != epaths.Version + return egversion.Version } func (d *DataUpdate) showProgres() { diff --git a/update/update_test.go b/update/update_test.go index e73f344..0e9e458 100644 --- a/update/update_test.go +++ b/update/update_test.go @@ -20,7 +20,7 @@ var loadConf = initConf() func initConf() bool { c := conf.Conf{} - c.Init("../", "", []string{}, []string{}, true) + c.Init("../", "", true, "") config = &c return true @@ -55,7 +55,7 @@ func TestHgnc(t *testing.T) { config.Appconf["kvgenCount"] = "4" config.Appconf["kvgenChunkSize"] = "13" - d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -68,7 +68,7 @@ func TestHgnc(t *testing.T) { } var m = generate.Merge{} - j, k, _ := m.Merge(config) + j, k, _ := m.Merge(config, false) if j != 18 { panic("merge write key value is invalid") @@ -110,7 +110,7 @@ func TestKeyLink(t *testing.T) { config.Appconf["kvgenChunkSize"] = "13" config.Appconf["pageSize"] = "2" - d := NewDataUpdate([]string{"uniprot"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"uniprot"}, []string{}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -123,7 +123,7 @@ func TestKeyLink(t *testing.T) { } var m = generate.Merge{} - j, k, l := m.Merge(config) + j, k, l := m.Merge(config, false) if j != 8 { panic("merge write key value is invalid") @@ -160,7 +160,7 @@ func TestPaging(t *testing.T) { //c.Appconf["kvgenChunkSize"] = "13" config.Appconf["pageSize"] = "2" - d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -173,7 +173,7 @@ func TestPaging(t *testing.T) { } var m = generate.Merge{} - j, k, _ := m.Merge(config) + j, k, _ := m.Merge(config, false) if j != 19 { // todo empty xref key hgnc:2 is not written?? panic("merge write key value is invalid") @@ -207,7 +207,7 @@ func TestTargetDbs(t *testing.T) { config.Appconf["kvgenCount"] = "4" config.Appconf["kvgenChunkSize"] = "13" - d := NewDataUpdate([]string{"hgnc"}, []string{"VEGA"}, []string{}, config, "1") + d := NewDataUpdate([]string{"hgnc"}, []string{"VEGA"}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -220,7 +220,7 @@ func TestTargetDbs(t *testing.T) { } var m = generate.Merge{} - j, k, _ := m.Merge(config) + j, k, _ := m.Merge(config, false) if j != 10 { panic("merge write key value is invalid") @@ -253,7 +253,7 @@ func TestDuplicateValue(t *testing.T) { config.Appconf["kvgenCount"] = "1" config.Appconf["kvgenChunkSize"] = "20" - d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"hgnc"}, []string{}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -266,7 +266,7 @@ func TestDuplicateValue(t *testing.T) { } var m = generate.Merge{} - j, k, _ := m.Merge(config) + j, k, _ := m.Merge(config, false) if j != 3 { panic("merge write key value is invalid") @@ -345,7 +345,7 @@ func TestEnsembl(t *testing.T) { config.Appconf["kvgenCount"] = "4" config.Appconf["kvgenChunkSize"] = "13" - d := NewDataUpdate([]string{"ensembl"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"ensembl"}, []string{}, []string{}, []string{}, config, "1") parsed, kvs := d.Update() @@ -358,7 +358,7 @@ func TestEnsembl(t *testing.T) { } var m = generate.Merge{} - j, k, l := m.Merge(config) + j, k, l := m.Merge(config, false) if j != 11 { panic("merge write key value is invalid") @@ -402,12 +402,12 @@ func TestSamples(t *testing.T) { config.Appconf["kvgenCount"] = "4" config.Appconf["kvgenChunkSize"] = "1000000" - d := NewDataUpdate([]string{"uniprot", "uniref100", "uniref90", "uniref50", "uniparc", "taxonomy", "interpro"}, []string{}, []string{}, config, "1") + d := NewDataUpdate([]string{"uniprot", "uniref100", "uniref90", "uniref50", "uniparc", "taxonomy", "interpro"}, []string{}, []string{}, []string{}, config, "1") d.Update() var m = generate.Merge{} - i, j, _ := m.Merge(config) + i, j, _ := m.Merge(config, false) fmt.Println("lmdb key value size", i) fmt.Println("max uid", j) diff --git a/web/dist/css/app.f3c239b1.css b/web/dist/css/app.2a610469.css similarity index 73% rename from web/dist/css/app.f3c239b1.css rename to web/dist/css/app.2a610469.css index b6abad6..3c20668 100644 --- a/web/dist/css/app.f3c239b1.css +++ b/web/dist/css/app.2a610469.css @@ -1 +1 @@ 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About
\n\n More information and some stats will come to this page. For any issue or error please contact from github\n page.\n
\nExample Use Cases
\n\nBulk Query
\nBulk Query allow to send query of large numbers of identifers or special keywords. Upload your text file which contains identifers or special keywords seperated by new line.
\n\nAPI
\n\n XrefMap has an API with following functions. Usage example with javascript can be found\n here.\n
\nSearch calls take list of comma separated identifiers as a parameter. Example,
\nwww.ebi.ac.uk/~tgur/xrefmap/api.php?ids=P15498
\nEach identifier search can have maximum 200 cross reference results. If it has more results, they are retrieved via pagination call. Pagination index starts from 0. Total page count is required to be specified with pageTotal parameter. This value is calculated via main search call. Example,
\nwww.ebi.ac.uk/~tgur/xrefmap/ws/api.php?ids=P15498&src=8&page=0&pageTotal=2
\nResults can be filtered based on datasets. Example,
\nwww.ebi.ac.uk/~tgur/ws/api.php?ids=P15498&src=8&filters=20,77
\nFor pagination and filtering calls, dataset identifiers needs to be specified. Dataset identifiers are accessed from main search response.
\n\n\n Limitations: API only supports binary response format. JSON format might be added in future.\n HTTP GET supported only, HTTP POST will be added later versions.\n
\nname | \nid | \nnumeric id | \n
---|---|---|
{{res.name}} | \n{{res.id}} | \n{{index}} | \n
\n | Source | \nMapping | \n
---|---|---|
{{index2+1}} | \n\n 0\">〃\n {{xref_conf[sub_res.source.dataset].name}} - \n 0\">{{sub_res.source.keyword}} - \n {{sub_res.source.identifier}}\n \n 0\">{{ sub_res.source.identifier}}\n \n \n \n \n\n | \n \n {{res.identifier}}\n \n 0\">{{ res.identifier}}\n \n \n \n \n | \n
Attributes
Mapped references
\n\n \n \n \n \n
\n\n \n \n \n \n \n Map\n \n
\n\n \n \n \n \n \n Search\n \n
\nAbout
\n\n More information and some stats will come to this page. For any issue or error please contact from github\n page.\n
\nExample Use Cases
\n\nBulk Query
\nBulk Query allow to send query of large numbers of identifers or special keywords. Upload your text file which contains identifers or special keywords seperated by new line.
\n\nAPI
\n\n XrefMap has an API with following functions. Usage example with javascript can be found\n here.\n
\nSearch calls take list of comma separated identifiers as a parameter. Example,
\nwww.ebi.ac.uk/~tgur/xrefmap/api.php?ids=P15498
\nEach identifier search can have maximum 200 cross reference results. If it has more results, they are retrieved via pagination call. Pagination index starts from 0. Total page count is required to be specified with pageTotal parameter. This value is calculated via main search call. Example,
\nwww.ebi.ac.uk/~tgur/xrefmap/ws/api.php?ids=P15498&src=8&page=0&pageTotal=2
\nResults can be filtered based on datasets. Example,
\nwww.ebi.ac.uk/~tgur/ws/api.php?ids=P15498&src=8&filters=20,77
\nFor pagination and filtering calls, dataset identifiers needs to be specified. Dataset identifiers are accessed from main search response.
\n\n\n Limitations: API only supports binary response format. JSON format might be added in future.\n HTTP GET supported only, HTTP POST will be added later versions.\n
\nname | \nid | \nnumeric id | \n
---|---|---|
{{res.name}} | \n{{res.id}} | \n{{index}} | \n
\n | Source | \nMapping | \n
---|---|---|
{{index2+1}} | \n\n 0\">〃\n {{xref_conf[sub_res.source.dataset].name}} - \n 0\">{{sub_res.source.keyword}} - \n {{sub_res.source.identifier}}\n \n 0\">{{ sub_res.source.identifier}}\n \n \n \n\n | \n \n {{res.identifier}}\n \n 0\">{{ res.identifier}}\n \n \n \n | \n
Attributes
Mapped references
\n\n \n \n \n \n
\n\n \n \n \n \n \n Map\n \n
\n\n \n \n \n \n \n Search\n \n
\n