#21 Add Filters for instrument, pagecount

cmd/mb3server/src/api-impl.go

@@ -126,7 +126,7 @@ func GetRecords(limit int32, page int32, contributor string, instrumentType []st
  }
  log.Println(ionModeLokal)
  it := &instrumentType
- if len(*it) == 0 {
+ if len(*it) == 0 || (len(*it) == 1 && (*it)[0] == "") {
  it = nil
  }
 
@@ -136,7 +136,7 @@ func GetRecords(limit int32, page int32, contributor string, instrumentType []st
  }
 
  var filters = database.Filters{
- InstrumentType: nil,
+ InstrumentType: it,
  Splash: "",
  MsType: msTypeLokal,
  IonMode: ionModeLokal,
@@ -152,7 +152,7 @@ func GetRecords(limit int32, page int32, contributor string, instrumentType []st
  Limit: int64(limit),
  Offset: int64(offset),
  }
- records, err := db.GetRecords(filters)
+ records, count, err := db.GetRecords(filters)
  if err != nil {
  return nil, err
  }
@@ -168,6 +168,7 @@ func GetRecords(limit int32, page int32, contributor string, instrumentType []st
  }
  result.Data = append(result.Data, val)
  }
+ result.Metadata.ResultCount = int32(count)
  return &result, nil
 }
 

go.mod

@@ -10,7 +10,7 @@ require (
  github.com/go-git/go-git/v5 v5.5.2
  github.com/lib/pq v1.10.7
  github.com/nullism/bqb v1.3.1
- go.mongodb.org/mongo-driver v1.11.1
+ go.mongodb.org/mongo-driver v1.11.6
  gopkg.in/mgo.v2 v2.0.0-20190816093944-a6b53ec6cb22
 )
 

go.sum

@@ -96,6 +96,8 @@ github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d/go.mod h1:rHwXgn7Jul
 github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY=
 go.mongodb.org/mongo-driver v1.11.1 h1:QP0znIRTuL0jf1oBQoAoM0C6ZJfBK4kx0Uumtv1A7w8=
 go.mongodb.org/mongo-driver v1.11.1/go.mod h1:s7p5vEtfbeR1gYi6pnj3c3/urpbLv2T5Sfd6Rp2HBB8=
+go.mongodb.org/mongo-driver v1.11.6 h1:XM7G6PjiGAO5betLF13BIa5TlLUUE3uJ/2Ox3Lz1K+o=
+go.mongodb.org/mongo-driver v1.11.6/go.mod h1:G9TgswdsWjX4tmDA5zfs2+6AEPpYJwqblyjsfuh8oXY=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
 golang.org/x/crypto v0.0.0-20220525230936-793ad666bf5e/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=

pkg/database/db_interface.go

@@ -139,7 +139,7 @@ type MB3Database interface {
  // GetRecords Get an array of MassBank records by filtering
  //
  // Will return an empty list if the filter does not match any records.
- GetRecords(filters Filters) ([]*massbank.Massbank, error)
+ GetRecords(filters Filters) ([]*massbank.Massbank, int64, error)
 
  // GetUniqueValues is used to get the values for filter frontend
  GetUniqueValues(filters Filters) (MB3Values, error)

pkg/database/db_interface_test.go

@@ -487,7 +487,7 @@ func TestMB3Database_GetRecords(t *testing.T) {
  }
  for _, tt := range tests {
  t.Run(tt.name, func(t *testing.T) {
- got, err := tt.db.db.GetRecords(tt.args)
+ got, _, err := tt.db.db.GetRecords(tt.args)
  if (err != nil) != tt.wantErr {
  t.Errorf("%s: GetRecords() error = %v, wantErr %v", tt.db.name, err, tt.wantErr)
  return

pkg/database/mongodb.go

@@ -389,12 +389,13 @@ func (db *Mb3MongoDB) GetRecord(s *string) (*massbank.Massbank, error) {
 // GetRecords see [MB3Database.GetRecords]
 func (db *Mb3MongoDB) GetRecords(
  filters Filters,
-) ([]*massbank.Massbank, error) {
+) ([]*massbank.Massbank, int64, error) {
  if db.database == nil {
- return nil, errors.New("database not ready")
+ return nil, 0, errors.New("database not ready")
  }
  var err error
  var cur *mongo.Cursor
+ var count int64
  if filters.Limit <= 0 {
  filters.Limit = DefaultValues.Limit
  }
@@ -412,23 +413,24 @@ func (db *Mb3MongoDB) GetRecords(
  } else {
  query := getQuery(filters)
  cur, err = db.database.Collection(mbCollection).Find(context.Background(), query, options.Find().SetLimit(filters.Limit).SetSkip(filters.Offset))
+ count, err = db.database.Collection(mbCollection).CountDocuments(context.Background(), query)
  }
  if err != nil {
- return nil, err
+ return nil, 0, err
  }
  var bsonResult []bson.M
  if err := cur.All(context.Background(), &bsonResult); err != nil {
- return nil, err
+ return nil, 0, err
  }
  var mbResult = []*massbank.Massbank{}
  for _, val := range bsonResult {
  mb, err := unmarshal2Massbank(err, &val)
  if err != nil {
- return nil, err
+ return nil, 0, err
  }
  mbResult = append(mbResult, mb)
  }
- return mbResult, nil
+ return mbResult, count, nil
 }
 
 func getQuery(filters Filters) bson.D {

web-frontend/src/lib/components/MainNav.svelte

@@ -18,7 +18,7 @@
  <a href="https://github.com/MassBank/MassBank-data/releases/latest" target="_blank" class="pure-menu-link">Download</a>
  </li>
  <li class="pure-menu-item">
- <input type="search" placeholder="Accession" bind:value="{acc}"><button on:click={() => goto('/record/'+acc)}>Go</button>{acc}
+ <input type="search" placeholder="Accession" bind:value="{acc}"><button on:click={() => goto('/record/'+acc)}>Go</button>
  </li>
  <li class="pure-menu-item pure-menu-has-children pure-menu-allow-hover">
  <a href="#" id="moreLink" class="pure-menu-link">More</a>

web-frontend/src/routes/contents/+page.svelte

@@ -7,8 +7,8 @@
  /** @type {import('./$types').PageData} */
  export let data: any;
  let base: string;
- let page: bigint = 1;
- let pages: bigint = 10;
+ let cur_page: number = 1;
+ let pages: number = 10;
  async function getFilters(base) {
  let resp = await fetch(base + "/v1/filter/browse");
  let jsonData = await resp.json();
@@ -24,16 +24,20 @@
  async function getResults(page) {
  let url = new URL("/v1/records",base)
  url.searchParams.append('page',page.toString())
- contribuors.forEach(element => url.searchParams.append('contributor',element))
- msType.forEach(element => url.searchParams.append('ms_type',element))
- instrumentType.forEach(element => url.searchParams.append('instrument_type',element))
- ionMode.forEach(element => url.searchParams.append('ion-mode',element))
+ url.searchParams.append('instrument_type',instrumentType.join())
+ url.searchParams.append('ms_type',msType.join())
+ url.searchParams.append('ion-mode',ionMode.join())
+ url.searchParams.append('contributor',contributors.join())
 
  console.log(url)
  let resp = await fetch(url)
  let jsonData = await resp.json();
  if(resp.ok) {
  console.log(JSON.stringify(jsonData))
+ pages = Math.floor(Number(jsonData.metadata.result_count)/20+1)
+ if (cur_page>pages) {
+ cur_page=1
+ }
  return jsonData
 
  } else {
@@ -42,14 +46,12 @@
  }
  }
 
- let contribuors = [];
+ let contributors = [];
  let msType = [];
  let instrumentType = [];
  let ionMode = [];
  $: base = data.baseurl
 </script>
-{base}
-{contribuors}
 <div class="pure-g">
  <div class="pure-u-1-5">
  {#await getFilters(base)}
@@ -58,7 +60,7 @@
  <div class="card">
  <h2>Filters</h2>
  <h3>Contributor</h3>
- <FilterButton bind:result={contribuors} group="cont" values={filters.contributor}></FilterButton>
+ <FilterButton bind:result={contributors} group="cont" values={filters.contributor}></FilterButton>
  <h3>Instrument Type</h3>
  <FilterButton bind:result={instrumentType} group="itype" values={filters.instrument_type}></FilterButton>
  <h3>MS Type</h3>
@@ -72,11 +74,11 @@
  </div>
  <div class="pure-u-4-5">
  <h2>Results</h2>
- {#key ionMode,msType,contribuors,instrumentType}
- {#await getResults(page)}
+ {#key ionMode,msType,contributors,instrumentType}
+ {#await getResults(cur_page)}
  <div class="info">Loading results...</div>
  {:then records}
- <Pagination bind:currentPage={page} pages={pages}>
+ <Pagination bind:currentPage={cur_page} pages={pages}>
  {#each records.data as record}
  <ShortRecordSummary record="{record}"></ShortRecordSummary>
  {/each}