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Add iterative searcher to Foldseek #97

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Add iterative searcher to Foldseek #97

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116d574
Add iterative searches to worker.go
martin-steinegger Dec 24, 2024
a0401b9
Add iterative searches to Foldseek
martin-steinegger Dec 25, 2024
0e64e0f
Fix Search.vue
martin-steinegger Dec 25, 2024
23a713a
Fix issues raised
martin-steinegger Dec 26, 2024
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5 changes: 4 additions & 1 deletion backend/server.go
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Original file line number Diff line number Diff line change
Expand Up @@ -264,6 +264,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
var dbs []string
var mode string
var email string
var iterativesearch bool
var taxfilter string

if strings.HasPrefix(req.Header.Get("Content-Type"), "multipart/form-data") {
Expand All @@ -285,6 +286,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
dbs = req.Form["database[]"]
mode = req.FormValue("mode")
email = req.FormValue("email")
iterativesearch = req.FormValue("iterativesearch") == "true"
taxfilter = req.FormValue("taxfilter")
} else {
err := req.ParseForm()
Expand All @@ -296,6 +298,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
dbs = req.Form["database[]"]
mode = req.FormValue("mode")
email = req.FormValue("email")
iterativesearch = req.FormValue("iterativesearch") == "true"
taxfilter = req.FormValue("taxfilter")
}

Expand All @@ -315,7 +318,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
modeWithoutComplex := strings.Join(append(modes[:modeIdx], modes[modeIdx+1:]...), "-")
request, err = NewComplexSearchJobRequest(query, dbs, databases, modeWithoutComplex, config.Paths.Results, email, taxfilter)
} else {
request, err = NewStructureSearchJobRequest(query, dbs, databases, mode, config.Paths.Results, email, taxfilter)
request, err = NewStructureSearchJobRequest(query, dbs, databases, mode, config.Paths.Results, email, iterativesearch, taxfilter)
}
} else {
http.Error(w, "Job type not supported by this server", http.StatusBadRequest)
Expand Down
15 changes: 10 additions & 5 deletions backend/structuresearchjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,11 @@ import (
)

type StructureSearchJob struct {
Size int `json:"size" validate:"required"`
Database []string `json:"database" validate:"required"`
Mode string `json:"mode" validate:"oneof=3di tmalign 3diaa"`
TaxFilter string `json:"taxfilter"`
Size int `json:"size" validate:"required"`
Database []string `json:"database" validate:"required"`
Mode string `json:"mode" validate:"oneof=3di tmalign 3diaa"`
IterativeSearch bool `json:"iterativesearch"`
TaxFilter string `json:"taxfilter"
query string
}

Expand All @@ -22,6 +23,9 @@ func (r StructureSearchJob) Hash() Id {
h.Write(([]byte)(JobStructureSearch))
h.Write([]byte(r.query))
h.Write([]byte(r.Mode))
if r.IterativeSearch {
h.Write([]byte("Iterative"))
}
if r.TaxFilter != "" {
h.Write([]byte(r.TaxFilter))
}
Expand All @@ -48,11 +52,12 @@ func (r StructureSearchJob) WritePDB(path string) error {
return nil
}

func NewStructureSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string) (JobRequest, error) {
func NewStructureSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, iterativeSearch bool, taxfilter string) (JobRequest, error) {
job := StructureSearchJob{
max(strings.Count(query, "HEADER"), 1),
dbs,
mode,
iterativeSearch,
taxfilter,
query,
}
Expand Down
4 changes: 4 additions & 0 deletions backend/worker.go
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Original file line number Diff line number Diff line change
Expand Up @@ -405,6 +405,10 @@ mv -f -- "${BASE}/query.lookup_tmp" "${BASE}/query.lookup"
parameters = append(parameters, "0")
}

if job.IterativeSearch {
parameters = append(parameters, "--num-iterations")
parameters = append(parameters, "3")
}
cmd, done, err := execCommand(config.Verbose, parameters...)
if err != nil {
errChan <- &JobExecutionError{err}
Expand Down
245 changes: 154 additions & 91 deletions frontend/Search.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -35,102 +35,147 @@
v-model="query">
</query-textarea>

<div class="actions input-buttons-panel">
<div class="input-buttons-left">
<load-acession-button v-if="$APP == 'foldseek'" @select="query = $event" @loading="accessionLoading = $event" :preload-source="preloadSource" :preload-accession="preloadAccession"></load-acession-button>
<file-button id="file" :label="$STRINGS.UPLOAD_LABEL" v-on:upload="upload"></file-button>
<PredictStructureButton v-if="$APP == 'foldseek'" :query="query" v-model="predictable" v-on:predict="query = $event"></PredictStructureButton>
<file-button id="localFile" label="Upload previous results" @upload="uploadJSON"></file-button>
</div>
</div>
</template>
</panel>
</v-flex>
<v-flex xs12>
<panel collapsible collapsed render-collapsed>
<template slot="header">
<template v-if="!$vuetify.breakpoint.smAndDown">
Databases
</template>
<template v-else>
DBs
</template>
&amp; search settings
</template>
<div slot="content">
<databases
:selected="database"
:all-databases="databases"
@update:selected="database = $event"
@update:all-databases="databases = $event"
:hideEmail="hideEmail"
></databases>
<div class="actions input-buttons-panel">
<div class="input-buttons-left">
<load-acession-button v-if="$APP == 'foldseek'" @select="query = $event" @loading="accessionLoading = $event" :preload-source="preloadSource" :preload-accession="preloadAccession"></load-acession-button>
<file-button id="file" :label="$STRINGS.UPLOAD_LABEL" v-on:upload="upload"></file-button>
<PredictStructureButton v-if="$APP == 'foldseek'" :query="query" v-model="predictable" v-on:predict="query = $event"></PredictStructureButton>
</div>
<file-button id="localFile" label="Upload previous results" @upload="uploadJSON"></file-button>
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Please revert unrelated changes

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done

</div>
</template>
</panel>
</v-flex>
<v-flex xs12>
<!-- Databases Section -->
<panel collapsible collapsed>
<template slot="header">
<template v-if="!$vuetify.breakpoint.smAndDown">
Databases
</template>
<template v-else>
DBs
</template>
</template>
<div slot="content">
<!-- Existing Database Selection -->
<div class="input-group">
<v-tooltip open-delay="300" top>
<template v-slot:activator="{ on }">
<label v-on="on">Databases&nbsp;<v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label>
</template>
<span v-if="$ELECTRON || hideEmail">Choose the databases to search against and the result mode.</span>
<span v-else>Choose the databases to search against, the result mode, and optionally an email to notify you when the job is done.</span>
</v-tooltip>
</div>

<template v-if="databases.length > 0">
<v-checkbox v-for="(db, index) in databases" v-model="database" :key="index" :value="db.path" :label="db.name + ' ' + db.version" :append-icon="(db.status == 'ERROR' || db.status == 'UNKNOWN') ? $MDI.AlertCircleOutline : ((db.status == 'PENDING' || db.status == 'RUNNING') ? $MDI.ProgressWrench : undefined)" :disabled="db.status != 'COMPLETE'" hide-details></v-checkbox>
</template>

<div v-if="databasesNotReady" class="alert alert-info mt-1">
<span>Databases are loading...</span>
</div>
</div>
</panel>

<v-radio-group v-model="mode">
<v-tooltip open-delay="300" top>
<template v-slot:activator="{ on }">
<label v-on="on">Mode&nbsp;<v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label>
<!-- Search Parameters Section -->
<panel collapsible collapsed>
<template slot="header">
<template v-if="!$vuetify.breakpoint.smAndDown">
Search Parameters
</template>
<template v-else>
Params
</template>
</template>
<span v-html="$STRINGS.MODE_HELP"></span>
</v-tooltip>
<v-radio hide-details
v-for="i in ($STRINGS.MODE_COUNT - 0)"
:key="i"
:value="$STRINGS['MODE_KEY_' + i]"
:label="$STRINGS['MODE_TITLE_' + i]"
></v-radio>
</v-radio-group>
<div slot="content">
<!-- Mode Section -->
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Please revert unrelated changes

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done

<v-radio-group v-model="mode">
<v-tooltip open-delay="300" top>
<template v-slot:activator="{ on }">
<label v-on="on">Mode&nbsp;<v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label>
</template>
<span v-html="$STRINGS.MODE_HELP"></span>
</v-tooltip>
<v-radio hide-details
v-for="i in ($STRINGS.MODE_COUNT - 0)"
:key="i"
:value="$STRINGS['MODE_KEY_' + i]"
:label="$STRINGS['MODE_TITLE_' + i]">
</v-radio>
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Please revert the whitespace changes

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done

</v-radio-group>

<TaxonomyAutocomplete v-model="taxFilter"></TaxonomyAutocomplete>
<TaxonomyAutocomplete v-model="taxFilter"></TaxonomyAutocomplete>

<v-tooltip v-if="!$ELECTRON && !hideEmail" open-delay="300" top>
<template v-slot:activator="{ on }">
<v-text-field v-on="on" label="Notification Email (Optional)" placeholder="[email protected]" v-model="email"></v-text-field>
</template>
<span>Send an email when the job is done.</span>
</v-tooltip>
</div>
</panel>
</v-flex>
<v-flex>
<panel>
<template slot="content">
<div class="actions" :style="!$vuetify.breakpoint.xsOnly ?'display:flex; align-items: center;' : null">
<v-item-group class="v-btn-toggle">
<v-btn color="primary" :block="false" x-large v-on:click="search" :disabled="searchDisabled"><v-icon>{{ $MDI.Magnify }}</v-icon>&nbsp;Search</v-btn>
<v-btn v-if="isMultimer" color="secondary" :block="false" x-large v-on:click="goToMultimer"><v-icon>{{ $MDI.Multimer }}</v-icon>&nbsp;Go to Multimer</v-btn>
</v-item-group>
<div :style="!$vuetify.breakpoint.xsOnly ? 'margin-left: 1em;' : 'margin-top: 1em;'">
<span><strong>Summary</strong></span><br>
Search <template v-if="taxFilter">
<strong>{{ taxFilter.text }}</strong> in
</template>
<template v-if="database.length == databases.length">
<strong>all available</strong> databases
<v-divider class="my-2"></v-divider>

<v-radio-group v-model="iterativeSearch">
<v-tooltip open-delay="300" top>
<template v-slot:activator="{ on }">
<label v-on="on">
Iterative search
<v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon>
</label>
</template>
<span>Improve sensitivity of search by performing an iterative search (--num-iterations 3).</span>
</v-tooltip>

<v-radio label="On" :value="true"></v-radio>
<v-radio label="Off" :value="false"></v-radio>
</v-radio-group>
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Please keep email in addition to the new iterative search

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done

</div>
</panel>


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Please remove empty newlines

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done

</v-flex>
<v-flex>
<panel>
<template slot="content">
<div class="actions" :style="!$vuetify.breakpoint.xsOnly ?'display:flex; align-items: center;' : null">
<v-btn color="primary" :block="$vuetify.breakpoint.xsOnly" x-large v-on:click="search" :disabled="searchDisabled"><v-icon>{{ $MDI.Magnify }}</v-icon>&nbsp;Search</v-btn>
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Please restore previous changes

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done

<div :style="!$vuetify.breakpoint.xsOnly ? 'margin-left: 1em;' : 'margin-top: 1em;'">
<span><strong>Summary</strong></span><br>
Search <template v-if="taxFilter">
<strong>{{ taxFilter.text }}</strong> in
</template>
<template v-if="database.length == databases.length">
<strong>all available</strong> databases
</template>
<template v-else>
<strong>{{ database.length }}</strong>
<template v-if="database.length == 1">
database
</template>
<template v-else>
databases
</template>
({{
databases.filter(db => database.includes(db.path)).map(db => db.name).sort().join(", ")
}})
</template> with {{ $STRINGS.APP_NAME }} in <strong>{{ modes[mode] }}</strong> mode<span v-if="iterativeSearch"><strong> iterative</strong></span>.
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Please add iterative to beginning of sentence

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why?

<div v-if="errorMessage != ''" class="v-alert v-alert--outlined warning--text mt-2">
<span>{{ errorMessage }}</span>
</div>
</div>
</div>
</template>
<template v-else>
<strong>{{ database.length }}</strong>
<template v-if="database.length == 1">
database
</template>
<template v-else>
databases
</template>
({{
databases.filter(db => database.includes(db.path)).map(db => db.name).sort().join(", ")
}})
</template> with {{ $STRINGS.APP_NAME }} in <strong>{{ modes[mode] }}</strong> mode.
<div v-if="errorMessage != ''" class="v-alert v-alert--outlined warning--text mt-2">
<span>{{ errorMessage }}</span>
</div>
</div>
</div>
</template>
</panel>
</panel>
</v-flex>
</v-layout>
<v-layout wrap>
<v-flex xs12>
<v-card rounded="0">
<v-card-title primary-title class="pb-0 mb-0">
<div class="text-h5 mb-0">Reference</div>
</v-card-title>
<v-card-title primary-title class="pt-0 mt-0">
<p class="text-subtitle-2 mb-0" v-html="$STRINGS.CITATION"></p>
</v-card-title>
</v-card>
</v-flex>
</v-layout>
<reference :reference="$STRINGS.CITATION"></reference>
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Please restore the previous version

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done

</v-container>
</v-container>
</template>

<script>
Expand Down Expand Up @@ -168,14 +213,16 @@ export default {
return {
inSearch: false,
errorMessage: "",
mode: storage.getItem('mode') || this.$STRINGS.MODE_DEFAULT_KEY,
showCurl: false,
mode: this.$STRINGS.MODE_DEFAULT_KEY,
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Please restore the previous version

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done

modes: Array.from({length: this.$STRINGS.MODE_COUNT - 0}, (_, i) => i + 1)
.reduce((dict, i, _) => { dict[this.$STRINGS['MODE_KEY_' + i]] = this.$STRINGS['MODE_TITLE_' + i]; return dict; }, {}),
email: storage.getItem('email') || "",
hideEmail: true,
query: "",
database: JSON.parse(storage.getItem('database') || '[]'),
databases: JSON.parse(storage.getItem('databases') || '[]'),
iterativeSearch: JSON.parse(storage.getItem('iterativeSearch') || false),
taxFilter: JSON.parse(storage.getItem('taxFilter') || 'null'),
predictable: false,
accessionLoading: false,
Expand All @@ -193,6 +240,18 @@ export default {
} else {
this.query = this.$STRINGS.QUERY_DEFAULT;
}
if (localStorageEnabled && localStorage.database) {
this.database = JSON.parse(localStorage.database);
}
if (localStorageEnabled && localStorage.databases) {
this.databases = JSON.parse(localStorage.databases);
}
if (localStorageEnabled && localStorage.iterativeSearch) {
this.iterativeSearch = JSON.parse(localStorage.iterativeSearch);
}
if (localStorageEnabled && localStorage.taxFilter) {
this.taxFilter = JSON.parse(localStorage.taxFilter);
}
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These should be set somewhere else, they were removed in the last refactoring

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done

},
computed: {
searchDisabled() {
Expand Down Expand Up @@ -235,6 +294,9 @@ export default {
databases(value) {
storage.setItem('databases', JSON.stringify(value));
},
iterativeSearch(value) {
storage.setItem('iterativeSearch', JSON.stringify(value));
},
taxFilter(value) {
storage.setItem('taxFilter', JSON.stringify(value));
},
Expand All @@ -245,7 +307,8 @@ export default {
q: this.query,
database: this.database,
mode: this.mode,
email: this.email
email: this.email,
iterativesearch: this.iterativeSearch
};
if (__APP__ == "foldseek" && typeof(request.q) === 'string' && request.q != '') {
if (request.q[request.q.length - 1] != '\n') {
Expand Down