import sys
sys.path.append("../")
from autecology_xml import AutecologyXML
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Birds/Phalacrocorax carbo.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Molluscs/Dreissena_polymorpha.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Macrophytes/Nitellopsis obtusa.xml")
xmltest = AutecologyXML(
filename=
"../../../_knowledgerules/species/Macrophytes/Myriophyllum_spicatum.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
print(xmltest.topic_name)
print(xmltest.EoL_ID)
print(xmltest.EoL_Link)
print(xmltest.latinname)
print(xmltest.commonnames)
xmltest._scan_modeltype("HSI")
print(xmltest.modeltypename)
print(xmltest.systems)
xmltest._scan_knowledgerules(modeltypename=xmltest.modeltypename,
systemname=xmltest.systems[0])
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
print(xmltest.knowledgeRulesNames)
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
import sys
from matplotlib import pyplot as plt
sys.path.append("../")
from autecology_xml import AutecologyXML
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/parameters/water_quality/Light_extinction.xml")
xmltest = AutecologyXML(
filename="../../../_knowledgerules/parameters/hydrodynamics/Fetch.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/parameters/hydrodynamics/Watersurface.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
print(xmltest.topic_name)
print(xmltest.commonnames)
xmltest._scan_modeltype("HSI")
print(xmltest.modeltypename)
print(xmltest.systems)
xmltest._scan_knowledgerules(modeltypename="HSI",
systemname="ijsselmeergebied")
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
print(xmltest.knowledgeRulesNames)
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
import sys
from matplotlib import pyplot as plt
sys.path.append("../")
from autecology_xml import AutecologyXML
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/WFD_indicators/ecological_status/Macrofauna_in_beken_en_kleine_rivieren.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/WFD_indicators/ecological_indicators/Aquatic_plants_total_coverage.xml")
xmltest = AutecologyXML(filename = "../../../_knowledgerules/WFD_indicators/ecological_indicators/Filamentous_algae.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
print(xmltest.topic_name)
print(xmltest.commonnames)
xmltest._scan_modeltype("HSI")
print(xmltest.modeltypename)
print(xmltest.systems)
xmltest._scan_knowledgerules(modeltypename = xmltest.modeltypename, systemname = xmltest.systems[0])
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
print(xmltest.knowledgeRulesNames)
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print("Done.")
import sys
sys.path.append("../")
from autecology_xml import AutecologyXML
xmltest = AutecologyXML(
filename="../../../_knowledgerules/species/Macrophytes/Chara_spp.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
testext = xmltest._read_topicdescription()
print(type(testext))
xmltest._scan_modeltype("HSI")
xmltest._scan_knowledgerules(modeltypename="HSI", systemname="Markermeer")
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print(xmltest.knowledgeRulesNames)
print(xmltest.knowledgeRulesCategories)
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
fb_tag = xmltest.get_element_formula_based(modeltypename="HSI",
systemname="Markermeer",
fbname="P_Chara_visibility")
fb_data = xmltest.get_data_formula_based_data(fb_tag)
print(fb_data)
print(fb_data['parameters'])
print(fb_data['parameters'][0]['data'])
print(type(fb_data))
fb_settings = {
import sys
from matplotlib import pyplot as plt
sys.path.append("../")
from autecology_xml import AutecologyXML
xmltest = AutecologyXML(
filename=
"../../../_knowledgerules/Habitats/Vegetation_associations/Vegetationtypes_Northern_Delta.xml"
)
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
print(xmltest.topic_name)
print(xmltest.commonnames)
xmltest._scan_modeltype("HSI")
print(xmltest.modeltypename)
print(xmltest.systems)
xmltest._scan_knowledgerules(modeltypename=xmltest.modeltypename,
systemname=xmltest.systems[0])
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
print(xmltest.knowledgeRulesNames)
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print("Done.")
#validate the xml file and log if incorrect try: val_res = validate(path_xml_file, path_xsd) #check validation if(val_res): pass else: validation_log.append(["Not valid : " + path_xml_file]) except: validation_log.append(["Not valid : " + path_xml_file]) continue #load the xml file try: xmltest = AutecologyXML(filename = path_xml_file) xmltest._readxml() xmltest._scan() except: validation_log.append(["XML could not be read with AutecologyXML : " + path_xml_file]) continue #CHECK languages Names and descriptions cur_species_commonnames = xmltest.commonnames cur_species_commonname_LANG = sorted([line["language"] for line in cur_species_commonnames]) cur_species_descriptions = xmltest._read_topicdescription() cur_species_description_LANG = sorted([line["language"] for line in cur_species_descriptions]) if(cur_species_commonname_LANG != cur_species_description_LANG): miss_common_name = (set(cur_species_description_LANG).difference(cur_species_commonname_LANG)) miss_species_description = (set(cur_species_commonname_LANG).difference(cur_species_description_LANG))
import sys
sys.path.append("../")
from autecology_xml import AutecologyXML
import os #for dir creation
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Birds/Phalacrocorax carbo.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Molluscs/Dreissena_polymorpha.xml")
xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Birds/Alcedo_atthis.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
xmltest._scan_modeltype(modeltypename = "HSI")
xmltest._scan_system(modeltypename = "HSI", systemname = "adult")
xmltest._scan_systemflowdiagrams(modeltypename = "HSI", systemname = "adult")
print(xmltest.flowdiagrams)
print(xmltest.flowdiagrams_list)
#Create a specific flow diagram
#flowdiagram = xmltest._read_systemflowdiagram(modeltypename = "HSI", systemname = "adult", diagramname ="livingarea_stagnant_waters" )
flowdiagram = xmltest._read_systemflowdiagram(modeltypename = "HSI", systemname = "adult", diagramname ="breeding_area" )
svg_str = xmltest.create_flowdiagram_image(flowdiagram, output = None)
print(svg_str)
# #Write to file
# directory = "test"
# if(not os.path.exists(directory)):
# os.makedirs(directory)
import sys
from matplotlib import pyplot as plt
sys.path.append("../")
from autecology_xml import AutecologyXML
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Birds/Phalacrocorax carbo.xml")
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Molluscs/Dreissena_polymorpha.xml")
xmltest = AutecologyXML(
filename="../../../_knowledgerules/species/Birds/Gallinago_gallinago.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
testext = xmltest._read_topicdescription()
print(type(testext))
xmltest._scan_modeltype("HSI")
#xmltest._scan_knowledgerules(systemname = "adult")
xmltest._scan_knowledgerules(modeltypename="HSI", systemname="adult")
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print(xmltest.knowledgeRulesNames)
print(xmltest.knowledgeRulesCategories)
#rc_tag = xmltest.get_element_response_curve(modeltypename = "HSI", systemname = "adult", rcname = "afstand_tot_moeras")
#rc_tag = xmltest.get_element_response_curve(modeltypename = "HSI", systemname = "adult", rcname = "substrate_type")
rc_tag = xmltest.get_element_response_curve(modeltypename="HSI",
systemname="adult",
rcname="water_storage_capacity")
print(rc_tag)
rc_data = xmltest.get_data_response_curve_data(rc_tag)
print(rc_data)
import sys
from matplotlib import pyplot as plt
sys.path.append("../")
from autecology_xml import AutecologyXML
#xmltest = AutecologyXML(filename = "../../../_knowledgerules/species/Birds/Phalacrocorax carbo.xml")
xmltest = AutecologyXML(filename = "../../../tool_adapters/Deltares_Habitat/examples/Plecoglossus_altivelis.xml")
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
testext = xmltest._read_topicdescription()
print(type(testext))
xmltest._scan_modeltype("HSI")
#xmltest._scan_knowledgerules(systemname = "adult")
xmltest._scan_knowledgerules(modeltypename = "HSI", systemname = "adult")
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print(xmltest.knowledgeRulesCategorie)
print(xmltest.XMLconvention["allowed_knowledgeRulesCategories"])
flowdiagram = xmltest._read_systemflowdiagrams(modeltypename = "HSI", systemname = "adult")
print(flowdiagram)
print(flowdiagram[0]["name"])
print(flowdiagram[0]["Links"])
import sys
import pandas
sys.path.append("../")
from autecology_xml import AutecologyXML
xmltest = AutecologyXML(
filename=
"../../../_knowledgerules/Habitats/Vegetation_associations/Vegetationtypes_Northen_Delta.xml"
)
xmltest._readxml()
print(type(xmltest.xmlroot))
xmltest._scan()
testext = xmltest._read_topicdescription()
print(type(testext))
xmltest._scan_modeltype("HSI")
xmltest._scan_knowledgerules(modeltypename="HSI", systemname="biesbosch_area")
print(all(elem in xmltest.XMLconvention["allowed_knowledgeRulesCategories"] for elem \
in xmltest.knowledgeRulesCategories))
print(xmltest.systemname)
print(xmltest.knowledgeRulesNr)
print(xmltest.knowledgeRulesCategorie)
print(xmltest.knowledgeRulesNames)
print(xmltest.XMLconvention["allowed_knowledgeRulesNames"])
#TO DO: CREATE TABLE OUT OF MultipleReclassification
mr_element = xmltest.get_element_multiple_reclassification(
modeltypename="HSI",
systemname="biesbosch_area",
mrname="vegetationtypes_without_grazing")
mr_data = xmltest.get_data_multiple_reclassification_data(mr_element)
#add data to the log and count xmls
path_xml_file = os.path.join(path_l2_dir, xml_file)
if (xml_file in list_skip):
shutil.copyfile(
path_xml_file,
os.path.join(path_newkr_dir, level1_dir, level2_dir,
xml_file))
continue
log.append([" /" + xml_file])
nr_xmls = nr_xmls + 1
#load the xml file
try:
xmltest = AutecologyXML(filename=path_xml_file)
xmltest._readxml()
except:
log.append([
"XML could not be read with AutecologyXML : " +
path_xml_file
])
continue
#Replace text ContentDescription -> TopicDescription
for element in xmltest.xmlroot.iter(
xmltest.make_find(['ContentDescription'])):
element.tag = 'TopicDescription'
#update response curve elements
#LOOP OVER ALL RESPONSE CURVES THEN SPECIFY FOR TYPE OF KNOWLEDGE RULE (CONTENT DIFFERENT)