From 9b730df843fb78c43738cdd27d1d6ed486fe46a9 Mon Sep 17 00:00:00 2001 From: Siddhartha Basu Date: Thu, 12 Aug 2021 21:21:21 -0500 Subject: [PATCH] feat: add CreateCollection function --- go.mod | 7 +++- go.sum | 30 +++++++++++++++ storage/arangodb/database.go | 72 ++++++++++++++++++++++++++++++++++++ 3 files changed, 107 insertions(+), 2 deletions(-) create mode 100644 storage/arangodb/database.go diff --git a/go.mod b/go.mod index a8a20e1..2e5542f 100644 --- a/go.mod +++ b/go.mod @@ -1,11 +1,14 @@ module github.com/dictyBase/go-obograph require ( - github.com/arangodb/go-driver v0.0.0-20210304082257-d7e0ea043b7f + github.com/arangodb/go-driver v0.0.0-20210804111724-721038b2c5bd github.com/dictyBase/arangomanager v0.3.1 - github.com/go-playground/validator/v10 v10.8.0 + github.com/go-playground/validator/v10 v10.9.0 github.com/sirupsen/logrus v1.8.1 github.com/urfave/cli v1.22.5 + golang.org/x/crypto v0.0.0-20210812204632-0ba0e8f03122 // indirect + golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e // indirect + golang.org/x/text v0.3.7 // indirect ) go 1.16 diff --git a/go.sum b/go.sum index 8ca0617..ee4043f 100644 --- a/go.sum +++ b/go.sum @@ -1,6 +1,8 @@ github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= github.com/arangodb/go-driver v0.0.0-20210304082257-d7e0ea043b7f h1:MEdxM6EhSFo2ecumBN0CC6s1zMWDpNvcmDIHEfMvl18= github.com/arangodb/go-driver v0.0.0-20210304082257-d7e0ea043b7f/go.mod h1:3NUekcRLpgheFIGEwcOvxilEW73MV1queNKW58k7sdc= +github.com/arangodb/go-driver v0.0.0-20210804111724-721038b2c5bd h1:ppc8E3GWM67RKfU4FjFecuQcu4JrOIkl181UZTs5vNA= +github.com/arangodb/go-driver v0.0.0-20210804111724-721038b2c5bd/go.mod h1:zdDkJJnCj8DAkfbtIjIXnsTrWIiy6VhP3Vy14p+uQeY= github.com/arangodb/go-velocypack v0.0.0-20200318135517-5af53c29c67e h1:Xg+hGrY2LcQBbxd0ZFdbGSyRKTYMZCfBbw/pMJFOk1g= github.com/arangodb/go-velocypack v0.0.0-20200318135517-5af53c29c67e/go.mod h1:mq7Shfa/CaixoDxiyAAc5jZ6CVBAyPaNQCGS7mkj4Ho= github.com/coreos/go-iptables v0.4.3/go.mod h1:/mVI274lEDI2ns62jHCDnCyBF9Iwsmekav8Dbxlm1MU= @@ -8,6 +10,7 @@ github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7 github.com/cpuguy83/go-md2man/v2 v2.0.0-20190314233015-f79a8a8ca69d/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= github.com/cpuguy83/go-md2man/v2 v2.0.0 h1:EoUDS0afbrsXAZ9YQ9jdu/mZ2sXgT1/2yyNng4PGlyM= github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= +github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E= github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= @@ -22,22 +25,38 @@ github.com/go-playground/assert/v2 v2.0.1 h1:MsBgLAaY856+nPRTKrp3/OZK38U/wa0CcBY github.com/go-playground/assert/v2 v2.0.1/go.mod h1:VDjEfimB/XKnb+ZQfWdccd7VUvScMdVu0Titje2rxJ4= github.com/go-playground/locales v0.13.0 h1:HyWk6mgj5qFqCT5fjGBuRArbVDfE4hi8+e8ceBS/t7Q= github.com/go-playground/locales v0.13.0/go.mod h1:taPMhCMXrRLJO55olJkUXHZBHCxTMfnGwq/HNwmWNS8= +github.com/go-playground/locales v0.14.0 h1:u50s323jtVGugKlcYeyzC0etD1HifMjqmJqb8WugfUU= +github.com/go-playground/locales v0.14.0/go.mod h1:sawfccIbzZTqEDETgFXqTho0QybSa7l++s0DH+LDiLs= github.com/go-playground/universal-translator v0.17.0 h1:icxd5fm+REJzpZx7ZfpaD876Lmtgy7VtROAbHHXk8no= github.com/go-playground/universal-translator v0.17.0/go.mod h1:UkSxE5sNxxRwHyU+Scu5vgOQjsIJAF8j9muTVoKLVtA= +github.com/go-playground/universal-translator v0.18.0 h1:82dyy6p4OuJq4/CByFNOn/jYrnRPArHwAcmLoJZxyho= +github.com/go-playground/universal-translator v0.18.0/go.mod h1:UvRDBj+xPUEGrFYl+lu/H90nyDXpg0fqeB/AQUGNTVA= github.com/go-playground/validator/v10 v10.5.0/go.mod h1:xm76BBt941f7yWdGnI2DVPFFg1UK3YY04qifoXU3lOk= github.com/go-playground/validator/v10 v10.8.0 h1:1kAa0fCrnpv+QYdkdcRzrRM7AyYs5o8+jZdJCz9xj6k= github.com/go-playground/validator/v10 v10.8.0/go.mod h1:9JhgTzTaE31GZDpH/HSvHiRJrJ3iKAgqqH0Bl/Ocjdk= +github.com/go-playground/validator/v10 v10.9.0 h1:NgTtmN58D0m8+UuxtYmGztBJB7VnPgjj221I1QHci2A= +github.com/go-playground/validator/v10 v10.9.0/go.mod h1:74x4gJWsvQexRdW8Pn3dXSGrTK4nAUsbPlLADvpJkos= +github.com/golang-jwt/jwt v3.2.2+incompatible/go.mod h1:8pz2t5EyA70fFQQSrl6XZXzqecmYZeUEB8OUGHkxJ+I= github.com/google/addlicense v0.0.0-20200817051935-6f4cd4aacc89/go.mod h1:EMjYTRimagHs1FwlIqKyX3wAM0u3rA+McvlIIWmSamA= github.com/google/uuid v1.1.1/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo= github.com/jinzhu/now v0.0.0-20181116074157-8ec929ed50c3/go.mod h1:oHTiXerJ20+SfYcrdlBO7rzZRJWGwSTQ0iUY2jI6Gfc= +github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo= +github.com/kr/pretty v0.2.1/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI= +github.com/kr/pretty v0.3.0/go.mod h1:640gp4NfQd8pI5XOwp5fnNeVWj67G7CFk/SaSQn7NBk= +github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ= +github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI= +github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE= github.com/leodido/go-urn v1.2.0/go.mod h1:+8+nEpDfqqsY+g338gtMEUOtuK+4dEMhiQEgxpxOKII= github.com/leodido/go-urn v1.2.1 h1:BqpAaACuzVSgi/VLzGZIobT2z4v53pjosyNd9Yv6n/w= github.com/leodido/go-urn v1.2.1/go.mod h1:zt4jvISO2HfUBqxjfIshjdMTYS56ZS/qv49ictyFfxY= +github.com/pkg/diff v0.0.0-20210226163009-20ebb0f2a09e/go.mod h1:pJLUxLENpZxwdsKMEsNbx1VGcRFpLqf3715MtcvvzbA= github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4= github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM= github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= +github.com/rogpeppe/go-internal v1.6.1/go.mod h1:xXDCJY+GAPziupqXw64V24skbSoqbTEfhy4qGm1nDQc= +github.com/rogpeppe/go-internal v1.8.0/go.mod h1:WmiCO8CzOY8rg0OYDC4/i/2WRWAB6poM+XZ2dLUbcbE= github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= github.com/russross/blackfriday/v2 v2.0.1 h1:lPqVAte+HuHNfhJ/0LC98ESWRz8afy9tM/0RK8m9o+Q= @@ -61,6 +80,8 @@ golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8U golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto= golang.org/x/crypto v0.0.0-20210711020723-a769d52b0f97 h1:/UOmuWzQfxxo9UtlXMwuQU8CMgg1eZXqTRwkSQJWKOI= golang.org/x/crypto v0.0.0-20210711020723-a769d52b0f97/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc= +golang.org/x/crypto v0.0.0-20210812204632-0ba0e8f03122 h1:AOT7vJYHE32m61R8d1WlcqhOO1AocesDsKpcMq+UOaA= +golang.org/x/crypto v0.0.0-20210812204632-0ba0e8f03122/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc= golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= @@ -77,12 +98,17 @@ golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c h1:F1jZWGFhYfh0Ci55sIpILtKKK8p3i2/krTr0H1rg74I= golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.0.0-20210806184541-e5e7981a1069/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= +golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e h1:WUoyKPm6nCo1BnNUvPGnFG3T5DUVem42yDJZZ4CNxMA= +golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk= golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/text v0.3.6 h1:aRYxNxv6iGQlyVaZmk6ZgYEDa+Jg18DxebPSrd6bg1M= golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= +golang.org/x/text v0.3.7 h1:olpwvP2KacW1ZWvsR7uQhoyTYvKAupfQrRGBFM352Gk= +golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ= golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= @@ -91,6 +117,10 @@ golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8T golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= +gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= +gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q= +gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= +gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= diff --git a/storage/arangodb/database.go b/storage/arangodb/database.go new file mode 100644 index 0000000..b376834 --- /dev/null +++ b/storage/arangodb/database.go @@ -0,0 +1,72 @@ +package arangodb + +import ( + "context" + + driver "github.com/arangodb/go-driver" + manager "github.com/dictyBase/arangomanager" +) + +type OntoCollection struct { + Term driver.Collection + Rel driver.Collection + Cv driver.Collection + Obog driver.Graph +} + +// CreateCollection creates all the necessary collections, graph and index required +// for persisting obojson ontology in arangodb +func CreateCollection(db *manager.Database, collP *CollectionParams) (*OntoCollection, error) { + oc, err := docCollection(db, collP) + if err != nil { + return oc, err + } + obog, err := db.FindOrCreateGraph( + collP.OboGraph, + []driver.EdgeDefinition{{ + Collection: oc.Rel.Name(), + From: []string{oc.Term.Name()}, + To: []string{oc.Term.Name()}, + }}) + if err != nil { + return oc, err + } + oc.Obog = obog + _, _, err = oc.Term.EnsurePersistentIndex( + context.Background(), + []string{"label"}, + &driver.EnsurePersistentIndexOptions{ + Name: "label-idx", + InBackground: true, + }) + return oc, err +} + +func docCollection(db *manager.Database, collP *CollectionParams) (*OntoCollection, error) { + oc := &OntoCollection{} + termc, err := db.FindOrCreateCollection( + collP.Term, + &driver.CreateCollectionOptions{}, + ) + if err != nil { + return oc, err + } + relc, err := db.FindOrCreateCollection( + collP.Relationship, + &driver.CreateCollectionOptions{Type: driver.CollectionTypeEdge}, + ) + if err != nil { + return oc, err + } + graphc, err := db.FindOrCreateCollection( + collP.GraphInfo, + &driver.CreateCollectionOptions{}, + ) + if err != nil { + return oc, err + } + oc.Term = termc + oc.Rel = relc + oc.Cv = graphc + return oc, nil +}