SummaryDb.scala 9.05 KB
Newer Older
1
2
package nl.lumc.sasc.biopet.utils.summary

Peter van 't Hof's avatar
Peter van 't Hof committed
3
import nl.lumc.sasc.biopet.utils.ConfigUtils
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
import slick.driver.H2Driver.api._

import scala.concurrent.{Await, Future}
import scala.concurrent.duration.Duration
import nl.lumc.sasc.biopet.utils.summary.db.Schema._

import scala.concurrent.ExecutionContext.Implicits.global

/**
  * Created by pjvanthof on 05/02/2017.
  */
class SummaryDb(db: Database) {
  /** This method will create all table */
  def createTables(): Unit = {
    try {
      val setup = DBIO.seq(
        (runs.schema ++ samples.schema ++
21
22
          libraries.schema ++ pipelines.schema ++
          modules.schema ++ stats.schema ++ settings.schema ++
23
24
25
26
27
28
29
30
31
          files.schema ++ executables.schema).create
      )
      val setupFuture = db.run(setup)
      Await.result(setupFuture, Duration.Inf)
    }
  }

  def createRun(runName: String, outputDir: String): Future[Int] = {
    val id = Await.result(db.run(runs.size.result), Duration.Inf)
32
    db.run(runs.forceInsert(Run(id, runName, outputDir))).map(_ => id)
33
34
35
36
37
38
39
  }

  def getRuns(runId: Option[Int] = None, runName: Option[String] = None, outputDir: Option[String] = None) = {
    val q = runs.filter { run =>
      List(
        runId.map(run.id === _),
        runName.map(run.runName === _),
40
        outputDir.map(run.outputDir === _)
41
42
43
44
45
      ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
    }
    db.run(q.result)
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
46
  def createSample(name: String, runId: Int, tags: Option[String] = None): Future[Int] = {
47
    val id = Await.result(db.run(samples.size.result), Duration.Inf)
48
    db.run(samples.forceInsert(Sample(id, name, runId, tags))).map(_ => id)
49
50
51
52
53
54
55
  }

  def getSamples(sampleId: Option[Int] = None, runId: Option[Int] = None, name: Option[String] = None) = {
    val q = samples.filter { sample =>
      List(
        sampleId.map(sample.id === _),
        runId.map(sample.runId === _),
56
        name.map(sample.name === _)
57
58
59
60
61
      ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
    }
    db.run(q.map(x => (x.id, x.runId, x.name)).result)
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
62
63
64
65
66
67
68
  def getSampleTags(sampleId: Int): Future[Option[Map[String, Any]]] = {
    db.run(samples.filter(_.id === sampleId).map(_.tags).result)
      .map(_.headOption.flatten.map(ConfigUtils.jsonTextToMap))
  }

  def createLibrary(name: String, runId: Int, sampleId: Int, tags: Option[String] = None): Future[Int] = {
    val id = Await.result(db.run(libraries.size.result), Duration.Inf)
69
    db.run(libraries.forceInsert(Library(id, name, runId, sampleId, tags))).map(_ => id)
Peter van 't Hof's avatar
Peter van 't Hof committed
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
  }

  def getLibraries(libId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None, sampleId: Option[Int] = None) = {
    val q = libraries.filter { lib =>
      List(
        libId.map(lib.id === _),
        sampleId.map(lib.sampleId === _),
        runId.map(lib.runId === _),
        name.map(lib.name === _) // not a condition as `criteriaRoast` evaluates to `None`
      ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
    }
    db.run(q.map(x => (x.id, x.name, x.runId, x.sampleId)).result)
  }

  def getLibraryTags(libId: Int): Future[Option[Map[String, Any]]] = {
    db.run(libraries.filter(_.id === libId).map(_.tags).result)
      .map(_.headOption.flatten.map(ConfigUtils.jsonTextToMap))
87
88
  }

89
90
91
92
93
94
95
96
97
98
  def createPipeline(name: String, runId: Int): Future[Int] = {
    val id = Await.result(db.run(pipelines.size.result), Duration.Inf)
    db.run(pipelines.forceInsert(Pipeline(id, name, runId))).map(_ => id)
  }

  def getPipelines(pipelineId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None) = {
    val q = pipelines.filter { lib =>
      List(
        pipelineId.map(lib.id === _),
        runId.map(lib.runId === _),
99
        name.map(lib.name === _)
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
      ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
    }
    db.run(q.map(x => (x.id, x.name, x.runId)).result)
  }

  def createModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
    val id = Await.result(db.run(modules.size.result), Duration.Inf)
    db.run(modules.forceInsert(Module(id, name, runId, pipelineId))).map(_ => id)
  }

  def getModules(moduleId: Option[Int] = None, name: Option[String] = None, runId: Option[Int] = None, pipelineId: Option[Int] = None) = {
    val q = modules.filter { lib =>
      List(
        moduleId.map(lib.id === _),
        runId.map(lib.runId === _),
        pipelineId.map(lib.pipelineId === _),
116
        name.map(lib.name === _)
117
118
119
120
121
      ).collect({ case Some(criteria) => criteria }).reduceLeftOption(_ && _).getOrElse(true: Rep[Boolean])
    }
    db.run(q.map(x => (x.id, x.name, x.runId)).result)
  }

122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
  def createStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
                 sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
    db.run(stats.forceInsert(Stat(runId, pipelineId, moduleId, sampleId, libId, content)))
  }

  def getStats(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
               sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
    val q = List(
      runId.map(x => (y:Query[Stats, Stats#TableElementType, Seq]) => y.filter(_.runId === x)),
      pipelineId.map(x => (y:Query[Stats, Stats#TableElementType, Seq]) => y.filter(_.pipelineId === x)),
      moduleId.map(x => (y:Query[Stats, Stats#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.moduleId === x) else y.filter(_.moduleId.isEmpty))),
      sampleId.map(x => (y:Query[Stats, Stats#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.sampleId === x) else y.filter(_.sampleId.isEmpty))),
      libId.map(x => (y:Query[Stats, Stats#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.libraryId === x) else y.filter(_.libraryId.isEmpty)))
    ).flatten.foldLeft(stats.subquery)((a,b) => b(a))

    db.run(q.result)
  }

  def getStat(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
              sampleId: Option[Int] = None, libId: Option[Int] = None): Future[Option[Map[String, Any]]] = {
    val q = List(
      (y:Query[Stats, Stats#TableElementType, Seq]) => y.filter(_.runId === runId),
      (y:Query[Stats, Stats#TableElementType, Seq]) => y.filter(_.pipelineId === pipelineId),
      (y:Query[Stats, Stats#TableElementType, Seq]) => (if (moduleId.isDefined) y.filter(_.moduleId === moduleId) else y.filter(_.moduleId.isEmpty)),
      (y:Query[Stats, Stats#TableElementType, Seq]) => (if (sampleId.isDefined) y.filter(_.sampleId === sampleId) else y.filter(_.sampleId.isEmpty)),
      (y:Query[Stats, Stats#TableElementType, Seq]) => (if (libId.isDefined) y.filter(_.libraryId === libId) else y.filter(_.libraryId.isEmpty))
    ).foldLeft(stats.subquery)((a,b) => b(a))

    db.run(q.map(_.content).result).map(_.headOption.map(ConfigUtils.jsonTextToMap))
  }

  def createSetting(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
                 sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
    db.run(settings.forceInsert(Setting(runId, pipelineId, moduleId, sampleId, libId, content)))
  }

  def getSettings(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
               sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
    val q = List(
      runId.map(x => (y:Query[Settings, Settings#TableElementType, Seq]) => y.filter(_.runId === x)),
      pipelineId.map(x => (y:Query[Settings, Settings#TableElementType, Seq]) => y.filter(_.pipelineId === x)),
      moduleId.map(x => (y:Query[Settings, Settings#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.moduleId === x) else y.filter(_.moduleId.isEmpty))),
      sampleId.map(x => (y:Query[Settings, Settings#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.sampleId === x) else y.filter(_.sampleId.isEmpty))),
      libId.map(x => (y:Query[Settings, Settings#TableElementType, Seq]) => (if (x.isDefined) y.filter(_.libraryId === x) else y.filter(_.libraryId.isEmpty)))
    ).flatten.foldLeft(settings.subquery)((a,b) => b(a))

    db.run(q.result)
  }

  def getSetting(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
              sampleId: Option[Int] = None, libId: Option[Int] = None): Future[Option[Map[String, Any]]] = {
    val q = List(
      (y:Query[Settings, Settings#TableElementType, Seq]) => y.filter(_.runId === runId),
      (y:Query[Settings, Settings#TableElementType, Seq]) => y.filter(_.pipelineId === pipelineId),
      (y:Query[Settings, Settings#TableElementType, Seq]) => (if (moduleId.isDefined) y.filter(_.moduleId === moduleId) else y.filter(_.moduleId.isEmpty)),
      (y:Query[Settings, Settings#TableElementType, Seq]) => (if (sampleId.isDefined) y.filter(_.sampleId === sampleId) else y.filter(_.sampleId.isEmpty)),
      (y:Query[Settings, Settings#TableElementType, Seq]) => (if (libId.isDefined) y.filter(_.libraryId === libId) else y.filter(_.libraryId.isEmpty))
    ).foldLeft(settings.subquery)((a,b) => b(a))

    db.run(q.map(_.content).result).map(_.headOption.map(ConfigUtils.jsonTextToMap))
  }

184
}