erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / experiments / __init__.py

diff --git a/cistematic/experiments/__init__.py b/cistematic/experiments/__init__.py
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+###########################################################################
+#                                                                         #
+# C O P Y R I G H T   N O T I C E                                         #
+#  Copyright (c) 2003-10 by:                                              #
+#    * California Institute of Technology                                 #
+#                                                                         #
+#    All Rights Reserved.                                                 #
+#                                                                         #
+# Permission is hereby granted, free of charge, to any person             #
+# obtaining a copy of this software and associated documentation files    #
+# (the "Software"), to deal in the Software without restriction,          #
+# including without limitation the rights to use, copy, modify, merge,    #
+# publish, distribute, sublicense, and/or sell copies of the Software,    #
+# and to permit persons to whom the Software is furnished to do so,       #
+# subject to the following conditions:                                    #
+#                                                                         #
+# The above copyright notice and this permission notice shall be          #
+# included in all copies or substantial portions of the Software.         #
+#                                                                         #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
+# SOFTWARE.                                                               #
+###########################################################################
+#
+try:
+    from pysqlite2 import dbapi2 as sqlite
+except:
+    from sqlite3 import dbapi2 as sqlite
+
+__all__ = ["analyzeMotifs", "experiment", "locate",  "phyloFoot", "phyloTest",
+           "randomset", "simple", "varyLength",  "orthology"]
+
+experimentTypes = [("simple", "Simple"), ("fasta", "Fasta"), ("locate", "Locate"),
+                   ("varyLength", "VaryLength"), ("phyloFoot", "PhyloFoot"),
+                   ("phyloTest", "PhyloTest"), ("orthology", "Orthology"),
+                   ("experiment", "generic")]
+
+webExperimentTypes = [("simple", "Simple"), ("orthology", "Orthology")]
+
+
+def loadExperiment(expID, expFilePath, analysisID="default", conservationID="default", consDB=""):
+    newExp = ""
+    try:
+        db = sqlite.connect(expFilePath)
+        sql = db.cursor()
+        sql.execute('select data from settings where expID = :expID and settingName = "experimentType"', locals())
+        expType = str(sql.fetchone()[0])
+        sql.close()
+        db.close()
+        expClass = ""
+        for etype in experimentTypes:
+            if etype[0] == expType:
+                expClass = etype[1]
+
+        if expClass != "":
+            importString = "from %s import %s" % (expType, expClass)
+            exec importString
+            expString = 'newExp = %s("%s","%s")' % (expClass, expID, expFilePath)
+            exec expString
+        else:
+            print "Could not find associated class for %s" % expType
+    except:
+        print "Could not load experiment %s from database %s " % (expID, expFilePath)
+
+    if consDB == "":
+        consDB = expFilePath
+    try:
+        expString = 'newExp.loadAnalysis("%s")' % analysisID
+        exec expString
+        print "loaded analysis %s" % analysisID
+        expString = "newExp.loadConservation('%s', '%s')" % (conservationID, consDB)   
+        exec expString
+        print "loaded conservation %s" % conservationID
+    except:
+        pass
+
+    return newExp
+
+
+def listExperiments(expFilePath):
+    result = []
+    try:
+        db = sqlite.connect(expFilePath)
+        sql = db.cursor()
+        sql.execute('select distinct expID, data from settings where settingName = "experimentType" ')
+        data = sql.fetchall()
+        sql.close()
+        db.close()
+        for (expID, expType) in data:
+            result.append((str(expID), str(expType)))
+    except:
+        print "Could not list experiments in database %s " % (expFilePath)             
+
+    return result
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