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)