orange-bioinformatics / orangecontrib / bio / widgets / OWDicty.py

"""
<name>dictyExpress</name>
<description>Access to data in dictyExpress database.</description>
<icon>icons/DictyExpress.svg</icon>
<priority>40</priority>
"""

from __future__ import absolute_import

from collections import defaultdict
import sys

import Orange
from Orange.orng import orngEnviron
from Orange.OrangeWidgets import OWGUI
from Orange.OrangeWidgets.OWWidget import *

from .. import obiDicty

NAME = "dictyExpress"
DESCRIPTION = "Access to data in dictyExpress database."
ICON = "icons/DictyExpress.svg"
PRIORITY = 40


INPUTS = []
OUTPUTS = [("Example table", Orange.data.Table)]

REPLACES = ["_bioinformatics.widgets.OWDicty.OWDicty"]


class MyTreeWidgetItem(QTreeWidgetItem):
    def __contains__(self, text):
        return any(text.upper() in str(self.text(i)).upper() for i in range(self.columnCount()))    

#set buffer file
bufferpath = os.path.join(orngEnviron.directoryNames["bufferDir"], "dicty")
try:
    os.makedirs(bufferpath)
except:
    pass
bufferfile = os.path.join(bufferpath, "database.sq3")

class OWDicty(OWWidget):
    settingsList = ["serverToken", "platform", "selectedExperiments", "server", "buffertime", "excludeconstant" ]
    def __init__(self, parent=None, signalManager=None, name="dictyExpress"):
        OWWidget.__init__(self, parent, signalManager, name)
        self.outputs = [("Example table", ExampleTable)]
        self.serverToken = ""
        self.server = obiDicty.defaddress

        self.platform = None

        self.selectedExperiments = []
        self.buffer = obiDicty.BufferSQLite(bufferfile)

        self.searchString = ""
        self.excludeconstant = False
        
        box = OWGUI.widgetBox(self.controlArea, "Cache")
        OWGUI.button(box, self, "Clear cache", callback=self.clear_buffer)

        OWGUI.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values" )

        OWGUI.button(self.controlArea, self, "&Commit", callback=self.Commit)
        box  = OWGUI.widgetBox(self.controlArea, "Server")
        OWGUI.lineEdit(box, self, "serverToken","Token", callback=self.Connect)
        OWGUI.rubber(self.controlArea)

        OWGUI.lineEdit(self.mainArea, self, "searchString", "Search", callbackOnType=True, callback=self.SearchUpdate)
        self.experimentsWidget = QTreeWidget()
        self.experimentsWidget.setHeaderLabels(["Strain", "Treatment", "Growth condition", "Platform", "N", "Chips"]) 
        self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
        self.experimentsWidget.setRootIsDecorated(False)
        self.experimentsWidget.setSortingEnabled(True)
##        self.experimentsWidget.setAlternatingRowColors(True)

        self.mainArea.layout().addWidget(self.experimentsWidget)

        self.loadSettings()
        self.dbc = None        

        QTimer.singleShot(0, self.UpdateExperiments)        

        self.resize(800, 600)

    def __updateSelectionList(self, oldList, oldSelection, newList):
        oldList = [oldList[i] for i in oldSelection]
        return [ i for i, new in enumerate(newList) if new in oldList]
    
    def Connect(self):

        address = self.server + "?"
        if self.serverToken:
            address += "token="+self.serverToken+"&"
        try:
            #obiDicty.verbose = 1
            self.dbc = obiDicty.DatabaseConnection(address, buffer=self.buffer)
        except Exception, ex:
            from traceback import print_exception
            print_exception(*sys.exc_info())
            self.error(0, "Error connecting to server" + str(ex))
            return
        self.error(0)

    def clear_buffer(self):
        self.buffer.clear()
        self.UpdateExperiments()

    def UpdateExperiments(self):
        self.chipsl = []
        self.experimentsWidget.clear()
        self.items = []

        if not self.dbc:
            self.Connect()

        """
        self.progressBarInit()

        strains = self.dbc.annotationOptions("sample")["sample"]

        for i, strain in enumerate(strains):
            chips = self.dbc.search("norms", sample=strain)
            annotations = self.dbc.annotations("norms", chips)

            elements = []

            for chip,annot in zip(chips,annotations):
                d = dict(annot)
                elements.append(((d.get("treatment", ""), d.get("growthCond", ""), d.get("platform", "")),chip))

            def different_chips(li):
                # Returns a map, where keys are different elements in li and values their chip ids
                dc = defaultdict(list)
                for a,chip in li:
                    dc[a].append(chip)
                return dc

            typeswchips = different_chips(elements) #types with counts

            for (treatment, cond, platforma),cchips in typeswchips.items():
                self.chipsl.append(cchips)
                num = len(cchips)
                experiment = [strain, treatment, cond, platform, str(num), ','.join(cchips)] 
                self.items.append(MyTreeWidgetItem(self.experimentsWidget, experiment))

            self.progressBarSet((100.0 * i) / len(strains))
        """

        annotations = self.dbc.annotations("norms", None)

        elements = []

        for chip,annot in annotations:
            d = dict(annot)
            elements.append(((d.get("treatment", ""), d.get("growthCond", ""), d.get("platform", ""), d.get("sample", "")),chip))

        def different_chips(li):
            # Returns a map, where keys are different elements in li and values their chip ids
            dc = defaultdict(list)
            for a,chip in li:
                dc[a].append(chip)
            return dc

        typeswchips = different_chips(elements) #types with counts

        for (treatment, cond, platform, strain),cchips in typeswchips.items():
            self.chipsl.append(cchips)
            num = len(cchips)
            experiment = [strain, treatment, cond, platform, str(num), ','.join(cchips)] 
            self.items.append(MyTreeWidgetItem(self.experimentsWidget, experiment))

        for i in range(5):
            self.experimentsWidget.resizeColumnToContents(i)

        self.progressBarFinished()

    def SearchUpdate(self, string=""):
        for item in self.items:
            item.setHidden(not all(s in item for s in self.searchString.split()))

    def Commit(self):
        if not self.dbc:
            self.Connect()
        allTables = []

        import time
        start = time.time()

        pb = OWGUI.ProgressBar(self, iterations=1000)

        table = None

        ids = []
        for item in self.experimentsWidget.selectedItems():
            ids += str(item.text(5)).split(",")

        table = self.dbc.get_single_data(ids=ids, callback=pb.advance, exclude_constant_labels=self.excludeconstant)

        end = int(time.time()-start)
        
        pb.finish()

        #self.send("Example table", None)
#        table.taxid = "352472"
#        table.genesinrows = False
        
        from Orange.orng.orngDataCaching import data_hints
        data_hints.set_hint(table, "taxid", "352472", 10.0)
        data_hints.set_hint(table, "genesinrows", False, 10.0)
        
        self.send("Example table", table)

if __name__ == "__main__":
    app  = QApplication(sys.argv)
##    from pywin.debugger import set_trace
##    set_trace()
    w = OWDicty()
    w.show()
    app.exec_()
    w.saveSettings()
            
        
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