def admin_edithomemessage():
g.headcenter = "Edit home page message<br><a href='/admin/'>Back to admin home</a>"
txt = "<script src='//cdn.ckeditor.com/4.6.0/full/ckeditor.js'></script>"
message = ""
NomFichier = 'appli/static/home/appmanagermsg.html'
if gvp("msg", None) is not None:
with open(NomFichier, 'w', encoding='utf-8', newline="\n") as f:
f.write(gvp("msg"))
if os.path.exists(NomFichier):
with open(NomFichier, 'r', encoding='utf-8') as f:
message = f.read()
txt += """<form action=? method=post>
Enter bellow the message you want display :
<button type=button class='btn btn-default btn-sm' onclick='EnableCK()'>Enable HTML Editor</button><br>
<textarea name=msg style='width:1000px;height:200px;'>{0}</textarea>
<br><button type=submit class='btn btn-primary'>Save</button>
</form>
<script>
function EnableCK() {{
CKEDITOR.replace( 'msg' );
}}
</script>
""".format(message)
return PrintInCharte(txt)
def QuestionProcess(self):
txt = "<h1>Test Task</h1>"
if self.task.taskstep == 0:
txt += "<h3>Task Creation</h3>"
if gvp('starttask') == "Y":
for k, v in self.param.__dict__.items():
setattr(self.param, k, gvp(k))
# Verifier la coherence des données
if (len(self.param.InData) < 5):
flash("Champ In Data trop court", "error")
else:
return self.StartTask(self.param)
return render_template('task/testcreate.html',
header=txt,
data=self.param)
if self.task.taskstep == 1:
txt += "<h3>Task Question 1</h3>"
if gvp('starttask') == "Y":
self.param.InData2 = gvp("InData2")
# Verifier la coherence des données
if (len(self.param.InData2) < 5):
flash("Champ In Data 2 trop court", "error")
else:
return self.StartTask(self.param, step=2)
return render_template('task/testquestion1.html',
header=txt,
data=self.param)
return PrintInCharte(txt)
def QuestionProcessScreenSelectSourceTaxo(self,Prj):
# Second écran de configuration, choix des taxon utilisés dans la source
# recupere les categories et le nombre d'occurence dans les projet de base/learning
# sql = """select n.classif_id,t.name||case when p1.name is not null and t.name not like '%% %%' then ' ('||p1.name||')' else ' ' end as name
sql = """select n.classif_id,t.display_name as name
,n.nbr
from (select o.classif_id,count(*) nbr
from obj_head o where projid in ({0}) and classif_qual='V'
group by classif_id) n
JOIN taxonomy t on n.classif_id=t.id
left join taxonomy p1 on t.parent_id=p1.id
order by nbr desc,name""".format(database.CSVIntStringToInClause(gvp('src', gvg('src'))))
g.TaxoList = GetAll(sql, None, cursor_factory=None)
s = sum([r[2] for r in g.TaxoList]) # Nbr total d'objet par categorie
d = DecodeEqualList(Prj.classifsettings)
TaxoCSV=d.get('seltaxo')
if TaxoCSV:
TaxoList={int(x) for x in TaxoCSV.split(',')}
else: TaxoList = {}
g.TaxoList = [[r[0], r[1], r[2], round(100 * r[2] / s, 1), 'checked' if len(TaxoList)==0 or r[0] in TaxoList else ''] for r in
g.TaxoList] # Ajout du % d'objet par categorie
ExtraHeader="<input type='hidden' name='src' value='{}'>".format(gvp('src', gvg('src')))
ExtraHeader += self.GetFilterText()
return render_template('task/classifauto2_create_lsttaxo.html'
,url=request.query_string.decode('utf-8')
,ExtraHeader=ExtraHeader,prj=Prj)
def routesettaxon():
"""
Update a taxon or create a new one if 'id' parameter is not supplied.
"""
CheckInstanceSecurity()
taxotype = gvp('taxotype')
name = gvp('name')
parent = gvp('parent_id')
taxonid = gvp('id', '')
with TaxoOperationLocker():
app.logger.info('In Locker')
msg = checktaxon(taxotype, name, parent=parent, updatetarget=taxonid)
if msg != 'ok':
return jsonify(msg=msg)
if taxonid != '':
Taxon = database.Taxonomy.query.filter_by(id=int(taxonid)).first()
CheckTaxonUpdateRight(Taxon)
else:
Taxon = database.Taxonomy()
db.session.add(Taxon)
UpdateObjectFromForm(Taxon)
db.session.commit()
ComputeDisplayName([Taxon.id])
return jsonify(msg='ok', id=Taxon.id)
def part_sampleedit(psampleid):
model = partdatabase.part_samples.query.filter_by(
psampleid=psampleid).first()
form = UvpSampleForm(request.form, model)
if gvp('delete') == 'Y':
delete_sample(psampleid)
return redirect("/part/prj/" + str(model.pprojid))
if request.method == 'POST' and form.validate():
for k, v in form.data.items():
setattr(model, k, v)
db.session.commit()
if gvp('forcerecalc') == 'Y':
appli.part.prj.ComputeHistoDet(model.psampleid,
model.project.instrumtype)
appli.part.prj.ComputeHistoRed(model.psampleid,
model.project.instrumtype)
appli.part.prj.ComputeZooMatch(model.psampleid,
model.project.projid)
flash("Histograms have been recomputed", "success")
return redirect("/part/prj/" + str(model.pprojid))
return PrintInCharte(
render_template("part/sampleedit.html",
form=form,
prjid=model.pprojid,
psampleid=model.psampleid))
def CheckInstanceSecurity():
id_instance = gvp('id_instance', '')
if not id_instance.isdigit():
abort(jsonify(msg="invalid instance id format"))
Instance = database.GetAll(
"select sharedsecret from ecotaxainst WHERE id=%s", [int(id_instance)])
if len(Instance) != 1:
abort(jsonify(msg="invalid instance"))
if Instance[0]['sharedsecret'] != gvp('sharedsecret'):
time.sleep(random.random())
abort(jsonify(msg="invalid instance secret"))
g.ecotaxa_version = gvp('ecotaxa_version')
g.ecotaxa_version_int = 0
re_match = re.match(r"(\d+).(\d+).(\d+)", g.ecotaxa_version)
if re_match:
g.ecotaxa_version_int = int(re_match.group(1)) * 10000 + int(
re_match.group(2)) * 100 + int(re_match.group(3))
else:
abort(jsonify(msg='invalid version'))
g.MsgVersion = "ok"
if g.ecotaxa_version_int < 20000:
g.MsgVersion = "Current Ecotaxa version is 2.0.0 it's recommanded to upgrade your version (%s.%s.%s) ." % (
re_match.group(1), re_match.group(2), re_match.group(3))
if g.ecotaxa_version_int < 20000:
abort(jsonify(msg='Your Ecotaxa version is too old, you must upgrade'))
def routegettaxon():
sql = """select t.id,t.parent_id,t.name,t.taxotype,t.display_name,t.id_source,t.source_url,t.source_desc
,t.creator_email
,to_char(t.creation_datetime,'YYYY-MM-DD HH24:MI:SS') creation_datetime
,to_char(t.lastupdate_datetime,'YYYY-MM-DD HH24:MI:SS') lastupdate_datetime,t.id_instance,t.taxostatus,t.rename_to
from taxonomy t where 1=1 """
sqlparam = {}
filtertype = gvp('filtertype')
if filtertype == 'id':
sql += " and id=%(id)s "
sqlparam['id'] = int(gvp('id'))
elif filtertype == 'since':
sql += """ and lastupdate_datetime>=to_timestamp(%(startdate)s,'YYYY-MM-DD HH24:MI:SS')
"""
# and (taxostatus!='N' or id_instance=%(id_instance)s) ==> Désactivé dans un premier temps
sqlparam['startdate'] = gvp('startdate')
# sqlparam['id_instance']=gvp('id_instance')
else:
return jsonify(msg='filtertype required')
sql += " order by lastupdate_datetime "
res = database.GetAll(sql,
sqlparam,
cursor_factory=psycopg2.extras.RealDictCursor)
if len(res) == 0 and filtertype == 'id':
return jsonify(msg='no data found')
return jsonify(res)
def PrjEdit(PrjId):
g.useselect4 = True
Prj = database.Projects.query.filter_by(projid=PrjId).first()
g.headcenter = "<h4><a href='/prj/{0}'>{1}</a></h4>".format(
Prj.projid, XSSEscape(Prj.title))
if Prj is None:
flash("Project doesn't exists", 'error')
return PrintInCharte("<a href=/prj/>Select another project</a>")
if not Prj.CheckRight(2): # Level 0 = Read, 1 = Annotate, 2 = Admin
flash('You cannot edit settings for this project', 'error')
return PrintInCharte("<a href=/prj/>Select another project</a>")
if gvp('save') == "Y":
PreviousCNN = Prj.cnn_network_id
for f in request.form:
if f in dir(Prj):
setattr(Prj, f, gvp(f))
if PreviousCNN != Prj.cnn_network_id:
database.ExecSQL(
"delete from obj_cnn_features where objcnnid in (select objid from obj_head where projid=%s)",
[PrjId])
flash("SCN features erased", "success")
Prj.visible = True if gvp('visible') == 'Y' else False
# print(request.form)
for m in Prj.projmembers:
if gvp('priv_%s_delete' % m.id) == 'Y':
db.session.delete(m)
elif gvp('priv_%s_member' %
m.id) != '': # si pas delete c'est update
m.member = int(gvp('priv_%s_member' % m.id))
m.privilege = gvp('priv_%s_privilege' % m.id)
if gvp('priv_new_member') != '':
new = database.ProjectsPriv(member=int(gvp('priv_new_member')),
privilege=gvp('priv_new_privilege'),
projid=PrjId)
db.session.add(new)
try:
db.session.commit()
flash("Project settings Saved successfuly", "success")
except Exception as E:
flash("Database exception : %s" % E, "error")
db.session.rollback()
if Prj.initclassiflist is None:
lst = []
else:
lst = [int(x) for x in Prj.initclassiflist.split(",") if x.isdigit()]
g.predeftaxo = GetAll(
"""select t.id,t.display_name as name
from taxonomy t
left join taxonomy t2 on t.parent_id=t2.id
where t.id= any(%s) order by upper(t.display_name) """, (lst, ))
g.users = GetAssoc2Col("select id,name from users order by lower(name)",
dicttype=collections.OrderedDict)
g.maplist = [
'objtime', 'objdate', 'latitude', 'longitude', 'depth_min', 'depth_max'
] + sorted(DecodeEqualList(Prj.mappingobj).values())
g.scn = GetSCNNetworks()
return render_template('project/editproject.html', data=Prj)
def TaskCreateRouter(ClassName):
gvp(
'dummy'
) # Protection bug flask connection reset si on fait post sans lire les champs
AddTaskSummaryForTemplate()
t = TaskFactory(ClassName)
t.task.owner_id = current_user.get_id()
return t.QuestionProcess()
def routechecktaxonHTML():
# CheckInstanceSecurity()
taxotype = gvp('taxotype')
name = gvp('name')
parent = gvp('parent_id')
updatetarget = gvp('updatetarget')
msg = checktaxon(taxotype, name, parent=parent, updatetarget=updatetarget)
if msg == 'ok':
return FormatSuccess("Naming rules OK")
else:
return FormatError(msg)
def routechecktaxon():
CheckInstanceSecurity()
taxotype = gvp('taxotype')
name = gvp('name')
parent = gvp('parent_id')
updatetarget = gvp('updatetarget')
res = {
"msg": checktaxon(taxotype,
name,
parent=parent,
updatetarget=updatetarget)
}
return json.dumps(res)
def PrjEditPriv(PrjId):
Prj=database.Projects.query.filter_by(projid=PrjId).first()
g.headcenter="<h4><a href='/prj/{0}'>{1}</a></h4>".format(Prj.projid,XSSEscape(Prj.title))
if Prj is None:
flash("Project doesn't exists",'error')
return PrintInCharte("<a href=/prj/>Select another project</a>")
if not Prj.CheckRight(2): # Level 0 = Read, 1 = Annotate, 2 = Admin
flash('You cannot edit settings for this project','error')
return PrintInCharte("<a href=/prj/>Select another project</a>")
if gvp('save')=="Y":
# print(request.form)
for m in Prj.projmembers:
if gvp('priv_%s_delete'%m.id)=='Y':
db.session.delete(m)
elif gvp('priv_%s_member'%m.id)!='': # si pas delete c'est update
m.member=int(gvp('priv_%s_member'%m.id))
m.privilege=gvp('priv_%s_privilege'%m.id)
if gvp('priv_new_member')!='':
new=database.ProjectsPriv(member=int(gvp('priv_new_member')),privilege=gvp('priv_new_privilege'),projid=PrjId)
db.session.add(new)
try:
db.session.commit()
flash("Project settings Saved successfuly","success")
except Exception as E:
flash("Database exception : %s"%E,"error")
db.session.rollback()
g.users=GetAssoc2Col("select id,name from users order by lower(name)",dicttype=collections.OrderedDict)
return render_template('project/editprojectpriv.html',data=Prj)
def routetaxodel():
txt = ""
try:
taxoid = int(gvp('id'))
params = dict(id=taxoid)
UsedTaxon = database.GetAll(
"""select 1 from taxonomy t where id=(%s)
and (
exists(select 1 from taxonomy p where p.parent_id=t.id)
or exists(select 1 from obj_head where classif_id=t.id) )
""", [taxoid])
if len(UsedTaxon) > 0:
return appli.ErrorFormat(
"This Taxon is used locally, you cannot remove it")
database.ExecSQL("delete from taxonomy t where id=%s", [taxoid])
j = request_withinstanceinfo("/deltaxon/", params)
if j['msg'] != 'ok':
return appli.ErrorFormat("deltaxon Error :" + j['msg'])
txt = """<script> DoSync(); At2PopupClose(0); </script>"""
return txt
except Exception as e:
import traceback
tb_list = traceback.format_tb(e.__traceback__)
return appli.FormatError("Saving Error : {}\n{}", e,
"__BR__".join(tb_list[::-1]))
def CheckTaxonUpdateRight(Taxon):
if Taxon is None:
abort(jsonify(msg="unable to update a non existing id"))
if Taxon.taxostatus != 'N':
abort(jsonify(msg="unable to update a validated taxon"))
if Taxon.id_instance != int(gvp('id_instance')):
abort(jsonify(msg="Only instance author of a taxon can update it"))
def dbadmin_console():
sql = gvp("sql")
if len(
request.form
) > 0 and request.referrer != request.url: # si post doit venir de cette page
return PrintInCharte("Invalid referer")
g.headcenter = "<font color=red style='font-size:18px;'>Warning : This screen must be used only by experts</font><br><a href=/admin/>Back to admin home</a>"
txt = "<form method=post>SQL : <textarea name=sql rows=15 cols=100>%s</textarea><br>" % escape(
sql)
txt += """<input type=submit class='btn btn-primary' name=doselect value='Execute Select'>
<input type=submit class='btn btn-primary' name=dodml value='Execute DML'>
Note : For DML ; can be used, but only the result of the last query displayed
</form>"""
if gvp("doselect"):
txt += "<br>Select Result :"
cur = db.engine.raw_connection().cursor()
try:
cur.execute(sql)
txt += "<table class='table table-condensed table-bordered'>"
for c in cur.description:
txt += "<td>%s</td>" % c[0]
for r in cur:
s = "<tr>"
for c in r:
s += "<td>%s</td>" % c
txt += s + "</tr>"
txt += "</table>"
except Exception as e:
txt += "<br>Error = %s" % e
cur.connection.rollback()
finally:
cur.close()
if gvp("dodml"):
txt += "<br>DML Result :"
cur = db.engine.raw_connection().cursor()
try:
cur.execute(sql)
txt += "%s rows impacted" % cur.rowcount
cur.connection.commit()
except Exception as e:
txt += "<br>Error = %s" % e
cur.connection.rollback()
finally:
cur.close()
return PrintInCharte(txt)
def routedeltaxon():
CheckInstanceSecurity()
with TaxoOperationLocker():
Taxon = database.Taxonomy.query.filter_by(id=int(gvp('id'))).first()
CheckTaxonUpdateRight(Taxon)
db.session.delete(Taxon)
db.session.commit()
return jsonify(msg='ok')
def routesetstat():
CheckInstanceSecurity()
id_instance = int(gvp('id_instance'))
database.ExecSQL("delete from ecotaxainststat WHERE id_instance=%s" %
id_instance)
# sql="insert into ecotaxainststat(id_instance, id_taxon, nbr) VALUES ({},%s,%s)".format(id_instance)
sql = "insert into ecotaxainststat(id_instance, id_taxon, nbr) VALUES "
stat = json.loads(gvp('data'))
if len(stat) > 0: # to avoid error on empty DB
sql += ",".join("({},{},{})".format(id_instance, int(k), int(v))
for (k, v) in stat.items())
database.ExecSQL(sql)
database.ExecSQL(
"update ecotaxainst set laststatupdate_datetime=timezone('utc',now()),ecotaxa_version=%s WHERE id=%s",
[g.ecotaxa_version, id_instance])
PurgeDeprecatedTaxon()
return jsonify(msg='ok', msgversion=g.MsgVersion)
def objectdetailsupdate(objid):
request.form # Force la lecture des données POST sinon il y a une erreur 504
obj = database.Objects.query.filter_by(objid=objid).first()
Prj = obj.project
if not Prj.CheckRight(2): # Level 0 = Read, 1 = Annotate, 2 = Admin
return '<span class="label label-danger">You cannot edit data on this project</span>'
table = gvp("table")
field = gvp("field")
if table == "object":
if hasattr(obj, field):
target = obj
elif hasattr(obj.objfrel, field):
target = obj.objfrel
else:
return '<span class="label label-danger">Invalid field %s.%s</span>' % (
table, field)
elif table == "sample":
target = obj.sample
elif table == "acquis":
target = obj.acquis
elif table == "processrel":
target = obj.processrel
else:
return '<span class="label label-danger">Invalid table %s</span>' % (
table, )
oldval = getattr(target, field)
newval = gvp("newval")
try:
dbval = newval
if field == "objdate":
dbval = datetime.date(int(newval[0:4]), int(newval[5:7]),
int(newval[8:10]))
if dbval == "": dbval = None
setattr(target, field, dbval)
db.session.commit()
except Exception as E:
return '<span class="label label-danger">Data update error %s</span>' % (
str(E)[0:100], )
return "<span class='label label-success'>changed value '%s' by '%s'" % (
oldval, newval)
def QuestionProcessScreenSelectModel(self, Prj):
Models=self.ReadModels()
# app.logger.info("Modèles = %s",Models)
# Premier écran de configuration pour prédiction depuis un modèle, choix du projet du modèle
PreviousTxt = self.GetFilterText()
d = DecodeEqualList(Prj.classifsettings)
g.posttaxomapping=d.get('posttaxomapping',"")
# TargetFeatures = set(DecodeEqualList(Prj.mappingobj).values())
TargetFeatures =set(self.GetReverseObjMap(Prj).keys())
TblBody = ""
sortedmodellist=sorted(Models.keys(),key=str.lower)
for modeldir in sortedmodellist:
r=Models[modeldir]
# bug sur les fichiers initiaux qui avaient : en trop dans le nom de cette entrée
ModelFeatures=set(r.get('zooprocess_fields',r.get('zooprocess_fields:')))
MatchingFeatures = len(ModelFeatures & TargetFeatures)
if MatchingFeatures < int(gvp("filt_featurenbr") if gvp("filt_featurenbr") else 10):
continue
if gvp('filt_title'):
if r['name'].lower().find(gvp('filt_title').lower())<0 and modeldir.lower().find(gvp('filt_title').lower())<0:
continue
Radio = ""
# Pour être compatible foit utiliser le même SCN que le projet ou ne pas en utiliser
if (r['scn_model']==Prj.cnn_network_id) or (r['scn_model']==''):
Radio="<input name=selmodel type='radio' class='selmodel ' data-modeldir='{0}' {1}>".format(modeldir
,"checked" if modeldir == d.get('usemodel_foldername') else "")
if len(ModelFeatures)!=MatchingFeatures:
MatchingFeatures='Missing'
Radio = ""
TaxoDetails=" <span class='showcat'>Show categories</span><span style='display: none'><br>"\
+TaxoNameAddSpaces(', '.join(sorted(r.get('categories',{}).values(),key=lambda v: v.upper())))+"</span>"
TblBody += """<tr><td> {6}</td>
<td>{0} - {1}{7}{5}</td><td>{2:0.0f}</td><td>{3}</td><td>{4}</td>
</tr>""".format(modeldir, r['name'],r['n_objects'],MatchingFeatures, r['scn_model']
,"<br>Comments : "+JinjaNl2BR(r.get('comments')) if r.get('comments') else ""
,Radio,TaxoDetails)
return render_template('task/classifauto2_create_selectmodel.html'
, url=request.query_string.decode('utf-8')
, TblBody=TblBody
, PreviousTxt=PreviousTxt)
def QuestionProcess(self):
txt = "<h1>Taxonomy Import Task</h1>"
if self.task.taskstep == 0:
txt += "<h3>Task Creation</h3>"
if gvp('starttask') == "Y":
for k, v in self.param.__dict__.items():
setattr(self.param, k, gvp(k))
if len(self.param.host) < 7:
flash("Host Field Too short", "error")
elif len(self.param.port) < 2:
flash("Port Field Too short", "error")
elif len(self.param.database) < 2:
flash("database Field Too short", "error")
else:
return self.StartTask(self.param)
return render_template('task/taxosynccreate.html',
header=txt,
data=self.param)
return PrintInCharte(txt)
def QuestionProcessScreenSelectModelTaxo(self,Prj):
# Second écran de configuration, mapping des taxon utilisés dans le modele
PreviousTxt = self.GetFilterText()
g.modeldir=gvp('modeldir')
ModelFolder = Path("RF_models") / g.modeldir
Meta = json.load((ModelFolder / "meta.json").open("r"))
categories=Meta.get("categories","")
g.TaxoList = database.GetTaxoNameFromIdList([int(x) for x in categories])
return render_template('task/classifauto2_create_lsttaxo_frommodel.html'
,url=request.query_string.decode('utf-8')
,prj=Prj, PreviousTxt=PreviousTxt)
def PrjUpdateComment(ObjId):
Obj=database.Objects.query.filter_by(objid=ObjId).first()
if Obj is None:
return "Object doesnt exists"
Prj=database.Projects.query.filter_by(projid=Obj.projid).first()
if not Prj.CheckRight(1): # Level 0 = Read, 1 = Annotate, 2 = Admin
return "You cannot Annotate this project"
Obj.complement_info=gvp('comment')
db.session.commit()
return '<span class="label label-success">Database update Successfull</span>'
def browseinstancesavepopup():
try:
# txt = json.dumps(request.form)
instance_id = gvp('id')
if instance_id != 'new':
instance = database.EcotaxaInst.query.filter_by(
id=instance_id).first()
if instance is None:
raise Exception("Instance not found in Database")
else:
instance = database.EcotaxaInst()
db.session.add(instance)
instance.url = gvp('url')
instance.name = gvp('name')
instance.sharedsecret = gvp('sharedsecret')
db.session.commit()
return "<script>location.reload(true);</script>"
except Exception as e:
tb_list = traceback.format_tb(e.__traceback__)
return FormatError("Saving Error : {}\n{}", e,
"__BR__".join(tb_list[::-1]))
def routetaxosave():
txt = ""
try:
params = {}
for c in [
'parent_id', 'name', 'taxotype', 'source_desc', 'source_url',
'creation_datetime', 'creator_email'
]:
params[c] = gvp(c)
if int(gvp('id')) > 0:
params['id'] = int(gvp('id'))
params['taxostatus'] = 'N'
j = request_withinstanceinfo("/settaxon/", params)
if j['msg'] != 'ok':
return appli.ErrorFormat("settaxon Error :" + j['msg'])
txt = """<script> DoSync(); At2PopupClose(0); </script>"""
return txt
except Exception as e:
import traceback
tb_list = traceback.format_tb(e.__traceback__)
return appli.FormatError("Saving Error : {}\n{}", e,
"__BR__".join(tb_list[::-1]))
def routetaxobrowse():
BackProjectBtn = ''
if gvp('updatestat') == 'Y':
# DoSyncStatUpdate()
DoFullSync()
if gvg('fromprj'):
BackProjectBtn = "<a href='/prj/{}' class='btn btn-default btn-primary'>{} Back to project</a> ".format(
int(gvg('fromprj')), FAIcon('arrow-left'))
if gvg('fromtask'):
BackProjectBtn = "<a href='/Task/Question/{}' class='btn btn-default btn-primary'>{} Back to importation task</a> ".format(
int(gvg('fromtask')), FAIcon('arrow-left'))
if not (current_user.has_role(database.AdministratorLabel)
or current_user.has_role(database.ProjectCreatorLabel)):
# /prj/653
txt = "You cannot create tanonomy category, you must request to your project manager (check project page)"
if gvg('fromprj'):
txt += "<br>" + BackProjectBtn
return PrintInCharte(FormatError(txt, DoNotEscape=True))
g.taxoserver_url = app.config.get('TAXOSERVER_URL')
if current_user.has_role(database.AdministratorLabel):
ExtraWehereClause = ""
else:
ExtraWehereClause = "and t.creator_email='{}'".format(
current_user.email)
lst = GetAll(
"""select t.id,t.parent_id,t.display_name as name,case t.taxotype when 'M' then 'Morpho' when 'P' then 'Phylo' else t.taxotype end taxotype,t.taxostatus,t.creator_email,t.id_source
,to_char(t.creation_datetime,'yyyy-mm-dd hh24:mi') creation_datetime,to_char(t.lastupdate_datetime,'yyyy-mm-dd hh24:mi') lastupdate_datetime,{}
from taxonomy t
{}
where t.id_instance ={} {}
order by case t.taxostatus when 'N' then 1 else 2 end,t.id
LIMIT 400
""".format(SQLTreeSelect, SQLTreeJoin,
app.config.get('TAXOSERVER_INSTANCE_ID'), ExtraWehereClause))
for lstitem in lst:
# lstitem['tree']=PackTreeTxt(lstitem['tree']) #evite les problèmes de safe
if lstitem['parent_id'] is None:
lstitem['parent_id'] = ""
# nbrtaxon=GetAll("select count(*) from taxonomy")[0][0]
# return render_template('browsetaxo.html',lst=lst,nbrtaxon=nbrtaxon)
return PrintInCharte(
render_template('taxonomy/browse.html',
lst=lst,
BackProjectBtn=BackProjectBtn))
def QuestionProcess(self):
g.headcenter = "<h3>TAXONOMY IMPORTATION</h3><a href='/admin'/>Back to admin home</a>"
txt = "<h1>Taxonomy Text File Importation Task</h1>"
errors = []
if self.task.taskstep == 0:
# txt+="<h3>Task Creation</h3>"
if not current_user.has_role(database.AdministratorLabel):
return PrintInCharte(
"ACCESS DENIED reserved to administrators")
if gvp('starttask') == "Y":
FileToSave = None
FileToSaveFileName = None
# Verifier la coherence des données
uploadfile = request.files.get("uploadfile")
if uploadfile is not None and uploadfile.filename != '': # import d'un fichier par HTTP
FileToSave = uploadfile # La copie est faite plus tard, car à ce moment là, le repertoire de la tache n'est pas encore créé
FileToSaveFileName = "uploaded.txt"
self.param.InData = "uploaded.txt"
else:
errors.append("txt file is missing")
if len(errors) > 0:
for e in errors:
flash(e, "error")
else:
return self.StartTask(
self.param,
FileToSave=FileToSave,
FileToSaveFileName=FileToSaveFileName)
else: # valeurs par default
pass
return render_template('task/taxoimport_create.html',
header=txt,
data=self.param,
ServerPath=gvp("ServerPath"),
TxtTaxoMap=gvp("TxtTaxoMap"))
return PrintInCharte(txt)
def browseinstancedelpopup():
try:
instance_id = gvp('id')
instance = database.EcotaxaInst.query.filter_by(id=instance_id).first()
if instance is None:
raise Exception("Instance not found in Database")
database.ExecSQL("delete from ecotaxainststat where id_instance=%s",
[instance.id])
db.session.delete(instance)
db.session.commit()
return "<script>location.reload(true);</script>"
except Exception as e:
tb_list = traceback.format_tb(e.__traceback__)
return FormatError("Saving Error : {}\n{}", e,
"__BR__".join(tb_list[::-1]))
def part_prjcalc(PrjId):
Prj = partdatabase.part_projects.query.filter_by(pprojid=PrjId).first()
if Prj.ownerid!=current_user.id and not current_user.has_role(database.AdministratorLabel):
return PrintInCharte(ErrorFormat("Access Denied"))
txt=""
CheckedSampleList=[]
for f in request.form:
if f[0:2] == "s_" and request.form.get(f)=='Y':
CheckedSampleList.append(int(f[2:]))
app.logger.info("request.form=%s", request.form)
app.logger.info("CheckedSampleList=%s", CheckedSampleList)
app.logger.info("dohistodet=%s,domatchecotaxa=%s,dohistotaxo=%s", gvp('dohistodet'), gvp('domatchecotaxa'), gvp('dohistotaxo'))
dbsample = database.GetAll("""select profileid,psampleid,filename,sampleid,histobrutavailable
,(select count(*) from part_histopart_det where psampleid=s.psampleid) nbrlinedet
from part_samples s
where pprojid=%s and psampleid = any (%s)""" , (PrjId,CheckedSampleList))
for S in dbsample:
prefix="<br>{profileid} :".format(**S)
if gvp('delete') == 'Y':
sampleedit.delete_sample(S['psampleid'])
txt += prefix + " deleted"
continue
if gvp('dohistodet')=='Y':
txt += prefix + ComputeHistoDet(S['psampleid'], Prj.instrumtype)
if gvp('dohistored')=='Y':
txt += prefix + ComputeHistoRed(S['psampleid'], Prj.instrumtype)
if gvp('domatchecotaxa') == 'Y':
txt += prefix +ComputeZooMatch(S['psampleid'],Prj.projid)
if gvp('dohistotaxo') == 'Y':
txt += prefix + ComputeZooHisto(S['psampleid'])
# try:
# uvp_sample_import.GenerateTaxonomyHistogram(S['psampleid'])
# txt += prefix + " Taxonomy Histogram computed"
# except Exception as E:
# txt += prefix + " <span style='color: red;'>Taxonomy Histogram can't be computed : %s </span>"%(E)
if gvp('doctdimport') == 'Y':
if common_import.ImportCTD(S['psampleid'],current_user.name,current_user.email):
txt += prefix + " CTD imported"
else:
txt += prefix + " <span style='color: red;'>CTD No file</span>"
#
# txt+="CheckedSampleList=%s"%(CheckedSampleList)
# txt+="<br>dbsample = %s"%(dbsample)
txt += "<br><br><a href=/part/prj/%s class='btn btn-primary'><span class='glyphicon glyphicon-arrow-left'></span> Back to project samples list</a>"%PrjId
return PrintInCharte(txt)
def QuestionProcessScreenSelectSource(self,Prj):
# Premier écran de configuration, choix du projet de base
PreviousTxt = self.GetFilterText()
d = DecodeEqualList(Prj.classifsettings)
TargetFeatures = set(DecodeEqualList(Prj.mappingobj).values())
PreviousLS=d.get("baseproject", "")
if PreviousLS != "":
BasePrj = GetAll("select projid,title from projects where projid in ({0})".format(PreviousLS))
if len(BasePrj):
PreviousTxt += """<a class='btn btn-primary' href='?{0}&src={1}'>
USE previous Learning Set : {2}</a><br><br>OR USE another project<br><br>""".format(
request.query_string.decode("utf-8"),PreviousLS, " + ".join(["#{0} - {1}".format(*r) for r in BasePrj]) )
from flask_login import current_user
sql = """select projid,title,round(coalesce(objcount,0)*coalesce(pctvalidated,0)/100) objvalid
,mappingobj,coalesce(cnn_network_id,'') cnn_network_id
from projects where 1=1 """
sqlparam=[]
if gvp('filt_title'):
sql += " and title ilike (%s) "
sqlparam.append(("%"+gvp('filt_title')+"%"))
if gvp('filt_instrum', '') != '':
sql += " and projid in (select distinct projid from acquisitions where instrument ilike '%%'||(%s) ||'%%' ) "
sqlparam.append(gvp('filt_instrum'))
sql += " order by title"
ProjList = database.GetAll(sql,sqlparam,doXSSEscape=True)
TblBody=""
for r in ProjList:
MatchingFeatures = len(set(DecodeEqualList(r['mappingobj']).values()) & TargetFeatures)
if MatchingFeatures<int(gvp("filt_featurenbr") if gvp("filt_featurenbr") else 10):
continue
TblBody += """<tr><td><input type='checkbox' class='selproj' data-prjid='{projid}'></td>
<td>#{projid} - {title}</td><td>{objvalid:0.0f}</td><td>{MatchingFeatures}</td><td>{cnn_network_id}</td>
</tr>""".format(MatchingFeatures=MatchingFeatures, **r)
return render_template('task/classifauto2_create_lstproj.html'
,url=request.query_string.decode('utf-8')
,TblBody=TblBody
,PreviousTxt=PreviousTxt)
def QuestionProcess(self):
ServerRoot = Path(app.config['SERVERLOADAREA'])
txt = "<h1>Text File Importation Task</h1>"
errors = []
if self.task.taskstep == 0:
txt += "<h3>Task Creation</h3>"
Prj = database.Projects.query.filter_by(projid=gvg("p")).first()
g.prjtitle = Prj.title
g.prjprojid = Prj.projid
g.prjmanagermailto = Prj.GetFirstManagerMailto()
txt = ""
if Prj.CheckRight(2) == False:
return PrintInCharte("ACCESS DENIED for this project")
if gvp('starttask') == "Y":
FileToSave = None
FileToSaveFileName = None
self.param.ProjectId = gvg("p")
self.param.updateclassif = gvp("updateclassif")
TaxoMap = {}
for l in gvp('TxtTaxoMap').splitlines():
ls = l.split('=', 1)
if len(ls) != 2:
errors.append(
"Taxonomy Mapping : Invalid format for line %s" %
(l))
else:
TaxoMap[ls[0].strip().lower()] = ls[1].strip().lower()
# Verifier la coherence des données
uploadfile = request.files.get("uploadfile")
if uploadfile is not None and uploadfile.filename != '': # import d'un fichier par HTTP
FileToSave = uploadfile # La copie est faite plus tard, car à ce moment là, le repertoire de la tache n'est pas encore créé
FileToSaveFileName = "uploaded.zip"
self.param.InData = "uploaded.zip"
elif len(gvp("ServerPath")) < 2:
errors.append("Input Folder/File Too Short")
else:
sp = ServerRoot.joinpath(Path(gvp("ServerPath")))
if not sp.exists(): #verifie que le repertoire existe
errors.append("Input Folder/File Invalid")
else:
self.param.InData = sp.as_posix()
if len(errors) > 0:
for e in errors:
flash(e, "error")
else:
self.param.TaxoMap = TaxoMap # on stocke le dictionnaire et pas la chaine
return self.StartTask(
self.param,
FileToSave=FileToSave,
FileToSaveFileName=FileToSaveFileName)
else: # valeurs par default
self.param.ProjectId = gvg("p")
return render_template('task/importupdate_create.html',
header=txt,
data=self.param,
ServerPath=gvp("ServerPath"),
TxtTaxoMap=gvp("TxtTaxoMap"))
if self.task.taskstep == 1:
PrjId = self.param.ProjectId
Prj = database.Projects.query.filter_by(projid=PrjId).first()
g.prjtitle = Prj.title
g.appmanagermailto = GetAppManagerMailto()
# self.param.TaxoFound['agreia pratensis']=None #Pour TEST A EFFACER
NotFoundTaxo = [
k for k, v in self.param.TaxoFound.items() if v == None
]
NotFoundUsers = [
k for k, v in self.param.UserFound.items()
if v.get('id') == None
]
app.logger.info("Pending Taxo Not Found = %s", NotFoundTaxo)
app.logger.info("Pending Users Not Found = %s", NotFoundUsers)
if gvp('starttask') == "Y":
app.logger.info("Form Data = %s", request.form)
for i in range(1, 1 + len(NotFoundTaxo)):
orig = gvp(
"orig%d" % (i)
) #Le nom original est dans origXX et la nouvelle valeur dans taxolbXX
newvalue = gvp("taxolb%d" % (i))
if orig in NotFoundTaxo and newvalue != "":
t = database.Taxonomy.query.filter(
database.Taxonomy.id == int(newvalue)).first()
app.logger.info(orig + " associated to " + t.name)
self.param.TaxoFound[orig] = t.id
else:
errors.append(
"Taxonomy Manual Mapping : Invalid value '%s' for '%s'"
% (newvalue, orig))
for i in range(1, 1 + len(NotFoundUsers)):
orig = gvp(
"origuser%d" % (i)
) #Le nom original est dans origXX et la nouvelle valeur dans taxolbXX
newvalue = gvp("userlb%d" % (i))
if orig in NotFoundUsers and newvalue != "":
t = database.users.query.filter(
database.users.id == int(newvalue)).first()
app.logger.info("User " + orig + " associated to " +
t.name)
self.param.UserFound[orig]['id'] = t.id
else:
errors.append(
"User Manual Mapping : Invalid value '%s' for '%s'"
% (newvalue, orig))
app.logger.info("Final Taxofound = %s", self.param.TaxoFound)
self.UpdateParam() # On met à jour ce qui à été accepté
# Verifier la coherence des données
if len(errors) == 0:
return self.StartTask(self.param, step=2)
for e in errors:
flash(e, "error")
NotFoundTaxo = [
k for k, v in self.param.TaxoFound.items() if v == None
]
NotFoundUsers = [
k for k, v in self.param.UserFound.items()
if v.get('id') == None
]
return render_template('task/import_question1.html',
header=txt,
taxo=NotFoundTaxo,
users=NotFoundUsers,
task=self.task)
return PrintInCharte(txt)
