mirror of https://github.com/tdwg/dwc.git
Update documentation
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stijnvanhoey
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@ -118,15 +118,15 @@ class DwcDigester(object):
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return set(self.terms_config_data.keys())
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def _select_versions_term(self, term_iri):
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"""Select a specific term of the versions data, using term_iri match"""
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"""select a specific term of the versions data, using term_iri match"""
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return self.term_versions_data[term_iri]
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def _select_config_term(self, term_iri):
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"""Select a specific term of the config data, using term_iri match"""
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"""select a specific term of the config data, using term_iri match"""
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return self.terms_config_data[term_iri]
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def match_error_report(self):
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"""check if the prime dwc file and the humaninfo file provide corresponding terms"""
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"""check if the prime dwc file and the configurations file provide corresponding terms and inform user on the term differences in between both files"""
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overload_versionterms = self._version_terms - self._config_terms
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overload_configterms = self._config_terms - self._version_terms
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if len(overload_versionterms) > 0 or len(overload_configterms) > 0:
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@ -136,21 +136,25 @@ class DwcDigester(object):
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". Terms only in terms_config.csv: ", cf_terms]))
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@staticmethod
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def split_iri(term_iri):
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""""""
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"""split an iri field into the namespace url and the term itself"""
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prog = re.compile("(.*/)([^/]*$)")
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namespace, term = prog.findall(term_iri)[0]
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return namespace, term
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@staticmethod
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def resolve_namespace_abbrev(namespace):
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"""Using the NAMESPACE constant, get the namespace abbreviation"""
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"""Using the NAMESPACE constant, get the namespace abbreviation by providing the namespace link"""
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if namespace not in NAMESPACES.keys():
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raise DwcNamespaceError("The namespace url is currently not supported in NAMESPACES")
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return NAMESPACES[namespace]
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def get_term_definition(self, config_term):
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"""Extract the required information to show on the webpage of a single term
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requires configuration term
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def get_term_definition(self, term_iri):
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"""Extract the required information from both tables to show on the webpage of a single term
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by using the term_iri as the identifier
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Notes
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------
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Due to the current implementation, make sure to provide the same keys represented in the record-level specific version `process_terms` method (room for improvement)
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"""
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cf_term = self._select_config_term(term_iri)
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vs_term = self._select_versions_term(term_iri)
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@ -168,11 +172,28 @@ class DwcDigester(object):
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return term_data
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def process_terms(self):
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"""parse the config terms towards the structure required for the HTML template"""
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"""parse the config terms (sequence matters!), collect all required data from both the normative versions file and the config file and return the template ready data.
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Returns
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-------
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Data object that can be digested by the html-templatye file. Contains the term data formatted to create the indidivual outputs, each list element is a dictionary representing a class group. Hence, the data object is structured as follows:
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[
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{'name' : class_group_name_1, 'label': xxxx,...,
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'terms':
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[
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{'name' : term_1, 'label': xxxx,...},
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{'name' : term_2, 'label': xxxx,...},
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...
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]}
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{'name' : class_group_name_2,...
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...},
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...
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]
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"""
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template_data = []
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in_class = "Record-level"
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# sequence matters in config and it starts with Record-level
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# sequence matters in config and it starts with Record-level which we populate here ad-hoc
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class_group = {}
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class_group["name"] = "Record-level"
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class_group["iri"] = None
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@ -200,30 +221,12 @@ class DwcDigester(object):
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template_data.append(class_group)
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return template_data
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@staticmethod
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def create_html(template_data, html_template="./config/index.tmpl",
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def create_html(self, html_template="./config/index.tmpl",
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html_output="../guides/index.html"):
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"""build html with the processed term info, by filling in the tmpl-template
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Parameters
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-----------
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template_data : list of dict
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contains the term data formatted to create the indidivual outputs, each list element
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is a dictionary representing a class group. Hence, the data object is structured as
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follows
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[
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{'name' : class_group_name_1, 'label': xxxx,...,
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'terms':
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[
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{'name' : term_1, 'label': xxxx,...},
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{'name' : term_2, 'label': xxxx,...},
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...
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]}
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{'name' : class_group_name_2,...
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...},
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...
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]
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html_template : str
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relative path and filename to the [Cheetah3](http://cheetahtemplate.org/) compatible
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template
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@ -240,8 +243,7 @@ class DwcDigester(object):
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index_page.close()
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def simple_dwc_terms(self):
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"""only extract those terms that are simple dwc,
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defined as `simple` in the flags column of the config file of terms"""
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"""only extract those terms that are simple dwc, defined as `simple` in the flags column of the config file of terms"""
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properties = []
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for term in self.configs():
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term_data = self.get_term_definition(term['term_iri'])
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@ -251,13 +253,25 @@ class DwcDigester(object):
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return properties
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def create_dwc_list(self, file_output="../dist/simple_dwc_vertical.csv"):
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"""build a list of simple dwc terms"""
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"""build a list of simple dwc terms and write it to file
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Parameters
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-----------
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file_output : str
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relative path and filename to write the resulting list
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"""
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with codecs.open(file_output, 'w', 'utf-8') as dwc_list_file:
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for term in self.simple_dwc_terms():
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dwc_list_file.write(term + "\n")
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def create_dwc_header(self, file_output="../dist/simple_dwc_horizontal.csv"):
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"""build a header of simple dwc terms"""
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"""build a header of simple dwc terms and write it to file
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Parameters
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-----------
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file_output : str
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relative path and filename to write the resulting list
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"""
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with codecs.open(file_output, 'w', 'utf-8') as dwc_header_file:
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properties = self.simple_dwc_terms()
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dwc_header_file.write(",".join(properties))
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