set and save query type

rwst · Oct 26, 2023 · 4a37ce7 · 4a37ce7
1 parent 66d13e0
commit 4a37ce7
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Showing 6 changed files with 69 additions and 20 deletions.
diff --git a/src/main/kotlin/org/reactome/lit_ball/common/LitBallQuery.kt b/src/main/kotlin/org/reactome/lit_ball/common/LitBallQuery.kt
@@ -4,6 +4,7 @@ import kotlinx.coroutines.Dispatchers
 import kotlinx.coroutines.sync.Mutex
 import kotlinx.coroutines.withContext
 import kotlinx.serialization.ExperimentalSerializationApi
+import kotlinx.serialization.Serializable
 import kotlinx.serialization.encodeToString
 import kotlinx.serialization.json.decodeFromStream
 import org.reactome.lit_ball.model.AnnotatingRootStore
@@ -24,6 +25,12 @@ import java.util.*
 import kotlin.io.path.Path
 
 enum class QueryStatus { UNINITIALIZED, FILTERED2, EXPANDED, FILTERED1 }
+@Serializable
+enum class Qtype(val pretty: String) {
+    EXPRESSION_SEARCH("Expression Search"),
+    SNOWBALLING("Snowballing"),
+    SUPERVISED_SNOWBALLING("Supervised Snowballing"),
+}
 
 fun getQueryDir(name: String): File {
     val queryPath = Settings.map["path-to-queries"] ?: ""
@@ -47,6 +54,7 @@ fun getDOIs(dir: File, fileName: String): MutableSet<String> {
 data class LitBallQuery(
     var id: Int,
     val name: String = "",
+    var type: Qtype = Qtype.SUPERVISED_SNOWBALLING,
     var status: QueryStatus = QueryStatus.UNINITIALIZED,
     var setting: QuerySetting? = null,
     var acceptedSet: MutableSet<String> = mutableSetOf(),

diff --git a/src/main/kotlin/org/reactome/lit_ball/common/QueryList.kt b/src/main/kotlin/org/reactome/lit_ball/common/QueryList.kt
@@ -42,6 +42,7 @@ object QueryList {
                         newQuery.noNewAccepted = false
                     }
                 }
+                newQuery.type = newQuery.setting?.type ?: Qtype.SUPERVISED_SNOWBALLING
                 newQuery
             }
         }
@@ -50,7 +51,7 @@ object QueryList {
     }
 
     fun itemFromId(id: Int?): LitBallQuery? = id?.let { list.find { id == it.id } }
-    fun addNewItem(name: String, dois: Set<String>) {
+    fun addNewItem(type: Int, name: String, dois: Set<String>) {
         val queryDir = getQueryDir(name)
         if (queryDir.exists()) {
             handleException(IOException("Directory ${queryDir.absolutePath} already exists. Query not created."))
@@ -71,6 +72,7 @@ object QueryList {
         list = list.plus(
             LitBallQuery(
                 id = list.size,
+                type = Qtype.entries[type],
                 name = name,
                 acceptedSet = dois.toMutableSet()
             )

diff --git a/src/main/kotlin/org/reactome/lit_ball/common/QuerySetting.kt b/src/main/kotlin/org/reactome/lit_ball/common/QuerySetting.kt
@@ -8,13 +8,14 @@ import java.io.File
 
 @Serializable
 data class QuerySetting(
+    var type: Qtype = Qtype.SUPERVISED_SNOWBALLING,
     var mandatoryKeyWords: MutableSet<String> = mutableSetOf(),
     var forbiddenKeyWords: MutableSet<String> = mutableSetOf(),
     var classifier: String = "virus-EXP",
     var annotationClasses: MutableSet<String> = mutableSetOf(),
 ) {
     override fun toString(): String {
-        return "QuerySetting(posKeyWords=$mandatoryKeyWords, negKeyWords=$forbiddenKeyWords, classifier=$classifier), annotationClasses=$annotationClasses"
+        return "QuerySetting(type=${type.name} posKeyWords=$mandatoryKeyWords, negKeyWords=$forbiddenKeyWords, classifier=$classifier), annotationClasses=$annotationClasses"
     }
 
     companion object {

diff --git a/src/main/kotlin/org/reactome/lit_ball/dialog/NewItemDialog.kt b/src/main/kotlin/org/reactome/lit_ball/dialog/NewItemDialog.kt
@@ -16,6 +16,7 @@ import androidx.compose.ui.unit.dp
 import kotlinx.coroutines.CoroutineScope
 import kotlinx.coroutines.Dispatchers
 import kotlinx.coroutines.launch
+import org.reactome.lit_ball.common.Qtype
 import org.reactome.lit_ball.common.QueryList
 import org.reactome.lit_ball.common.Settings
 import org.reactome.lit_ball.window.components.Icons
@@ -32,6 +33,7 @@ fun NewItemDialog(
     rootScope: CoroutineScope,
     onCloseClicked: () -> Unit,
 ) {
+    val typeValue = rememberSaveable { mutableStateOf(2) }
     val fieldValue = rememberSaveable { mutableStateOf("") }
     val nameValue = rememberSaveable { mutableStateOf("") }
     val checkValue = rememberSaveable { mutableStateOf(true) }
@@ -55,7 +57,7 @@ fun NewItemDialog(
                     checkValue.value = dois.isNotEmpty() && name.isNotEmpty()
                     if (checkValue.value) {
                         rootScope.launch(Dispatchers.IO) {
-                            QueryList.addNewItem(name, dois)
+                            QueryList.addNewItem(typeValue.value, name, dois)
                         }
                         (onCloseClicked)()
                     }
@@ -78,6 +80,36 @@ fun NewItemDialog(
         },
         text = {
             Column(horizontalAlignment = Alignment.Start) {
+                Row {
+                    Tooltip(text = """
+                        Available query types are:
+                        1. Simple expression search: your positive and negative
+                           keyphrases/expressions are sent to Semantic Scholar
+                           for a search over the whole graph. Starting DOIs are
+                           ignored.
+                        2. Snowballing with automated keyphrase/expression
+                           filtering. No supervised filtering (all matches are
+                           accepted).
+                        3. (default) Snowballing with automated and supervised
+                           filtering.
+                    """.trimIndent(),
+                        Modifier.align(Alignment.CenterVertically)) {
+                        Icon(
+                            painterResource(Icons.Help),
+                            contentDescription = "Query Settings",
+                            tint = Color.Gray,
+                            modifier = Modifier.size(20.dp)
+                                .align(Alignment.CenterVertically),
+                        )
+                    }
+                    Spacer(modifier = Modifier.width(14.dp))
+                    RadioButtonOptions(
+                        Qtype.entries.map { it.pretty },
+                        typeValue.value,
+                        onOptionSelected = { btn -> typeValue.value = btn}
+                    )
+                }
+                Spacer(modifier = Modifier.height(8.dp))
                 Row {
                     Tooltip(text = """
                         Enter name of query. The string is cut off

diff --git a/src/main/kotlin/org/reactome/lit_ball/dialog/QuerySettingsDialog.kt b/src/main/kotlin/org/reactome/lit_ball/dialog/QuerySettingsDialog.kt
@@ -62,6 +62,7 @@ fun QuerySettingsDialog(
                     item.setting!!.forbiddenKeyWords = StringPatternMatcher.patternSettingFrom(field2Value.value)
                     item.setting!!.classifier = field3Value.value.trim()
                     item.setting!!.annotationClasses = field4Value.value.splitToSet(",")
+                    item.setting!!.type = item.type
                     rootScope.launch(Dispatchers.IO) {
                         item.saveSettings()
                     }

diff --git a/src/main/kotlin/org/reactome/lit_ball/window/components/QueryCard.kt b/src/main/kotlin/org/reactome/lit_ball/window/components/QueryCard.kt
@@ -9,10 +9,7 @@ import androidx.compose.material.IconButton
 import androidx.compose.material.Text
 import androidx.compose.material.icons.Icons
 import androidx.compose.material.icons.filled.Settings
-import androidx.compose.material3.ButtonDefaults
-import androidx.compose.material3.ElevatedButton
-import androidx.compose.material3.ElevatedCard
-import androidx.compose.material3.SuggestionChip
+import androidx.compose.material3.*
 import androidx.compose.runtime.Composable
 import androidx.compose.ui.Alignment
 import androidx.compose.ui.Modifier
@@ -35,6 +32,11 @@ fun QueryCard(
     onGoClicked: (status: QueryStatus, id: Int) -> Unit,
     onAnnotateClicked: () -> Unit,
 ) {
+    val chipColors = listOf(
+        Color.hsv(186F, 1F, 1F),
+        Color.hsv(163f, 1f, 1f),
+        Color.hsv(0f, 0f, .9f),
+    )
     ElevatedCard {
         Row(modifier = Modifier.clickable(onClick = onClicked)) {
             Tooltip("Query-specific settings", Modifier.align(Alignment.CenterVertically)) {
@@ -53,19 +55,22 @@ fun QueryCard(
             }
             Spacer(modifier = Modifier.width(14.dp))
             Column {
-                SuggestionChip(
-                    onClick = {},
-                    label = {
-                        Text(
-                            text = AnnotatedString(item.name),
-                            fontWeight = FontWeight.Bold,
-                            maxLines = 1,
-                            overflow = TextOverflow.Ellipsis,
-                        )
-                    },
-                    modifier = Modifier
-                        .align(Alignment.Start),
-                )
+                Tooltip("Query Type ${item.type.ordinal+1}", Modifier) {
+                    SuggestionChip(
+                        onClick = {},
+                        label = {
+                            Text(
+                                text = AnnotatedString(item.name),
+                                fontWeight = FontWeight.Bold,
+                                maxLines = 1,
+                                overflow = TextOverflow.Ellipsis,
+                            )
+                        },
+                        modifier = Modifier
+                            .align(Alignment.Start),
+                        colors = SuggestionChipDefaults.suggestionChipColors(containerColor = chipColors[item.type.ordinal]),
+                    )
+                }
                 Text(
                     text = "Accepted: ${item.nrAccepted()}",
                     fontSize = 14.sp,