def garun_plot(self, **kwargs):
dbPath = SNDBDict[kwargs["name"]]
cherrypy.response.headers["Content-Type"] = "image/png"
snName = kwargs["name"]
# prepare string for sn site
conn = dalekDB.getDBConnection(dbPath)
curs = conn.cursor()
gaRunID = int(kwargs["garunid"])
dbSelectStmt = (
"""select GA_GENERATION.ID,avg(GA_INDIVIDUAL.FITNESS), max(GA_INDIVIDUAL.FITNESS) from GA_GENERATION
join GA_INDIVIDUAL on GA_GENERATION.ID=GA_INDIVIDUAL.GENERATION_ID where
GA_GENERATION.GA_RUN_ID=%d
group by GA_INDIVIDUAL.GENERATION_ID"""
% gaRunID
)
generation, fitAvg, fitMax = zip(*curs.execute(dbSelectStmt).fetchall())
fh = StringIO.StringIO()
fig = Figure()
canvas = FigureCanvas(fig)
ax = canvas.figure.add_subplot(111)
ax.plot(generation, fitAvg, "b-", label="Fitness average")
ax.plot(generation, fitMax, "r-", label="Fitness max")
ax.legend()
canvas.print_figure(fh, fmt="png")
fh.seek(0)
conn.close()
return fh.read()
def model_site(kwargs):
dbPath = SNDBDict[kwargs["name"]]
snName = kwargs["name"]
gaRunID = int(kwargs["garunid"])
genID = int(kwargs["genid"])
# prepare string for sn site
conn = dalekDB.getDBConnection(dbPath)
curs = conn.cursor()
def garun_site(kwargs):
dbPath = SNDBDict[kwargs["name"]]
snName = kwargs["name"]
gaRunID = int(kwargs["garunid"])
# prepare string for sn site
conn = dalekDB.getDBConnection(dbPath)
curs = conn.cursor()
siteString = htmlHeader + collapseScript
siteString += "<img src=garun_plot?name=%s&garunid=%d><p>" % (snName, gaRunID)
gaConfDict = pp.pformat(
dalekDB.convertZipPickle(curs.execute("select GA_CONF_DICT from GA_RUN where ID=%d" % gaRunID).fetchone()[0])
)
gaConfDictTuple = ("GA_CONF_DICT code", "gaconfdict", "gaconfdict", gaConfDict, "gaconfdict", "gaconfdict")
siteString += collapseSection % gaConfDictTuple
gaBreedFunc = dalekDB.convertZipPickle(
curs.execute("select GA_BREED_FUNC from GA_RUN where ID=%d" % gaRunID).fetchone()[0]
)
gaBreedTuple = ("breed code", "gabreed", "gabreed", gaBreedFunc, "gabreed", "gabreed")
siteString += collapseSection % gaBreedTuple
gaCrossFunc = dalekDB.convertZipPickle(
curs.execute("select GA_CROSS_FUNC from GA_RUN where ID=%d" % gaRunID).fetchone()[0]
)
gaCrossTuple = ("cross code", "gacross", "gacross", gaCrossFunc, "gacross", "gacross")
siteString += collapseSection % gaCrossTuple
gaSelectFunc = dalekDB.convertZipPickle(
curs.execute("select GA_SELECT_FUNC from GA_RUN where ID=%d" % gaRunID).fetchone()[0]
)
gaSelectTuple = ("select code", "gaselect", "gaselect", gaSelectFunc, "gaselect", "gaselect")
siteString += collapseSection % gaSelectTuple
siteString += "<table>\n"
tmpString = "<tr>" + tableColumnElement * 2 + "</tr>\n"
siteString += tmpString % ("ID", "FITNESS")
dbSelectStmt = (
"""select GA_GENERATION.ID, max(GA_INDIVIDUAL.FITNESS) from GA_GENERATION
join GA_INDIVIDUAL on GA_GENERATION.ID=GA_INDIVIDUAL.GENERATION_ID where
GA_GENERATION.GA_RUN_ID=%d
group by GA_INDIVIDUAL.GENERATION_ID"""
% gaRunID
)
for item in curs.execute(dbSelectStmt):
siteString += "<tr><td><a href=/gaexplore?name=%s&garunid=%d&genid=%d>%s</a></td>" % (
snName,
gaRunID,
item[0],
item[0],
)
tmpString = tableColumnElement + "</tr>\n"
siteString += tmpString % item[1]
siteString += "</table>" + htmlFooter
conn.close()
return siteString
def generation_site(kwargs):
dbPath = SNDBDict[kwargs["name"]]
snName = kwargs["name"]
gaRunID = int(kwargs["garunid"])
genID = int(kwargs["genid"])
# prepare string for sn site
conn = dalekDB.getDBConnection(dbPath)
curs = conn.cursor()
siteString = htmlHeader + "<table>\n"
siteString += "<tr>" + tableColumnElement * 16 + "</tr>\n"
siteString = siteString % (
"INDIVIDUAL ID",
"LUM",
"VPH",
"C",
"O",
"NA",
"MG",
"SI",
"S",
"CA",
"TI",
"CR",
"MN",
"FE0",
"NI0",
"FITNESS",
)
dbSelectStmt = """select GA_INDIVIDUAL.ID, FICA_MODEL.ID, FICA_LUMVPH.LUM, FICA_LUMVPH.VPH, FICA_ABUNDANCE.C,
FICA_ABUNDANCE.O, FICA_ABUNDANCE.NA, FICA_ABUNDANCE.MG, FICA_ABUNDANCE.SI,
FICA_ABUNDANCE.S, FICA_ABUNDANCE.CA, FICA_ABUNDANCE.TI, FICA_ABUNDANCE.CR,
FICA_ABUNDANCE.MN, FICA_ABUNDANCE.FE0, FICA_ABUNDANCE.NI0, GA_INDIVIDUAL.FITNESS
from FICA_DICA, FICA_ABUNDANCE, FICA_LUMVPH, FICA_MODEL, GA_INDIVIDUAL
where GA_INDIVIDUAL.GENERATION_ID=%d and GA_INDIVIDUAL.MODEL_ID=FICA_MODEL.ID
and FICA_ABUNDANCE.ID=FICA_MODEL.ABUNDANCE_ID
and FICA_DICA.ID=FICA_MODEL.DICA_ID
and FICA_LUMVPH.ID=FICA_MODEL.LUMVPH_ID
ORDER BY GA_INDIVIDUAL.FITNESS DESC
""" % (
genID
)
for item in curs.execute(dbSelectStmt):
# siteString += "<tr><td><a href=/gaexplore?name=%s&garunid=%d&genid=%d&modelid=%d>%s</a></td>" \
# % (snName, gaRunID, genID, item[0], item[0])
siteString += "<tr><td><a href=/model_plot?name=%s&modelid=%d&garunid=%d>%s</a></td>" % (
snName,
item[1],
gaRunID,
item[0],
)
siteString += tableColumnElement * 15 + "</tr>\n"
siteString = siteString % item[2:]
siteString += "</table>" + htmlFooter
conn.close()
return siteString
def model_plot(self, **kwargs):
cherrypy.response.headers["Content-Type"] = "image/png"
snName = kwargs["name"]
modelID = int(kwargs["modelid"])
gaRunID = int(kwargs["garunid"])
dbPath = SNDBDict[kwargs["name"]]
conn = dalekDB.getDBConnection(dbName)
curs = conn.cursor()
fh = StringIO.StringIO()
modelind = model.model.fromDB(conn, modelID, gaRunID)
fig = Figure()
canvas = FigureCanvas(fig)
ax = canvas.figure.add_subplot(111)
ax.plot(modelind.origSpec.x, modelind.origSpec.y, "k-", label="observed")
ax.plot(modelind.aSpec.x, modelind.aSpec.y, label="model")
ax.legend()
canvas.print_figure(fh, fmt="png")
fh.seek(0)
conn.close()
return fh.read()
def sn_site(kwargs):
dbPath = SNDBDict[kwargs["name"]]
snName = kwargs["name"]
# prepare string for sn site
conn = dalekDB.getDBConnection(dbPath)
curs = conn.cursor()
siteString = htmlHeader + "<table>"
siteString += "<tr>" + tableColumnElement * 4 + "</tr>\n"
siteString = siteString % ("GA_RUN_ID", "START DATE", "current gen", "SN DATE")
dbSelectStmt = """select GA_RUN.ID, GA_RUN.START_TIME,
GA_RUN.GA_CUR_GEN, SN_SPECTRA.DATE from
GA_RUN, SN_SPECTRA where GA_RUN.SN_ID=SN_SPECTRA.ID
"""
for item in curs.execute(dbSelectStmt):
siteString += "<tr><td><a href=/gaexplore?name=%s&garunid=%d>%s</a></td>" % (snName, item[0], item[0])
siteString += tableColumnElement * 3 + "</tr>"
siteString = siteString % item[1:]
siteString += "</table>" + htmlFooter
conn.close()
return siteString
