class UpdateTermReadme():
def __init__(self, owl_file):
self.owl = OwlReader(owl_file)
# Write out Readme
def write_readme(self, readme_file, readme_txt):
readme_file_open = open(readme_file, 'w')
readme_file_open.write(readme_txt)
readme_file_open.close()
def create_term_row(self, term_name, definition, same_as, editor, note,
color, range_value=None, domain=None, indiv_type=None):
img_color = ""
if color:
img_color = '<img src="../../../doc/content/specs/img/'+color+'.png?raw=true"/> '
if same_as:
same_as = "(same as: <a href="+same_as+">"+same_as+"</a>)"
range_domain_type = ""
if range_value is not None:
range_domain_type = """
<td>"""+domain+"""</td>
<td>"""+range_value+"""</td>"""
if indiv_type is not None:
range_domain_type += """
<td>"""+indiv_type+"""</td>"""
# Github mardow-like links
nidm_repo = "https://github.com/incf-nidash/nidm/"
stato_repo = "https://github.com/ISA-tools/stato/"
nidm_pr_issue = re.compile(nidm_repo+r'[a-zA-Z]*/(\d+)')
note = nidm_pr_issue.sub(r'<a href="'+nidm_repo+r'pull/\1">'+r'#\1</a>', note)
stato_pr_issue = re.compile(stato_repo+r'[a-zA-Z]*/(\d+)')
note = stato_pr_issue.sub(r'<a href="'+stato_repo+r'pull/\1">'+r'ISA-tools/stato#\1</a>', note)
if note:
note = note+"<br/>"
# Add a search link (to check current state of the repo)
if "Under discussion" in note:
search_text = "more"
else:
search_text = "find issues/PR"
note = note+"<a href=\""+nidm_repo+"/issues?&q="+term_name.split(":")[1]+"\"> ["+search_text+"] </a>"
term_row = """
<tr>
<td>"""+img_color+"""</td>
<td>"""+note+"""</td>
<td><b>"""+term_name+""": </b>"""+definition+same_as+editor+"""</td>"""+range_domain_type+"""
</tr>"""
return term_row
def create_curation_legend(self, order):
curation_legend = "<b>Curation status</b>: \n"
curation_colors_sorted = [(key, CURATION_COLORS.get(key)) for key in order]
covered_colors = list()
for curation_color in curation_colors_sorted:
# curation_status = str(self.owl.qname(curation_color[0]))
# curation_status_labels = self.owl.objects(curation_color[0], RDFS['label'])
# curation_status = ", ".join(list(curation_status_labels))
color = curation_color[1]
if not color in covered_colors:
curation_legend = curation_legend+'<img src="../../../doc/content/specs/img/'+color+'.png?raw=true"/> '+\
CURATION_LEGEND[color]+";\n"
covered_colors.append(color)
return curation_legend
# Get README text according to owl file information
def update_readme(self, readme_file):
class_terms = dict()
prpty_terms = dict()
indiv_terms = dict()
definitions = dict()
editors = dict()
notes = dict()
ranges = dict()
domains = dict()
sameas = dict()
types = dict()
for owl_term in self.owl.classes.union(self.owl.properties).union(self.owl.individuals):
curation_status = self.owl.get_curation_status(owl_term)
definition = self.owl.get_definition(owl_term)
if definition == "":
definition = "<undefined>"
editor = self.owl.get_editor(owl_term)
note = self.owl.get_editor_note(owl_term)
range_value = self.owl.get_range(owl_term)
domain = self.owl.get_domain(owl_term)
same = self.owl.get_same_as(owl_term)
indiv_type = self.owl.get_individual_type(owl_term)
if curation_status:
curation_key = curation_status
term_key = self.owl.get_label(owl_term)
if term_key.startswith("nidm") or term_key.startswith("spm") or\
term_key.startswith("fsl") or term_key.startswith("afni"):
if owl_term in self.owl.classes:
class_terms.setdefault(curation_key, list()).append(term_key)
else:
if owl_term in self.owl.properties:
prpty_terms.setdefault(curation_key, list()).append(term_key)
else:
if owl_term in self.owl.individuals:
indiv_terms.setdefault(curation_key, list()).append(term_key)
definitions[term_key] = definition
editors[term_key] = editor
notes[term_key] = note
ranges[term_key] = range_value
domains[term_key] = domain
sameas[term_key] = same
types[term_key] = indiv_type
# Include missing keys and do not display ready for release terms
order=CURATION_ORDER+(list(set(class_terms.keys()).union(set(prpty_terms.keys())) - set(CURATION_ORDER+list([OBO_READY]))))
class_terms_sorted = [(key, class_terms.get(key)) for key in order]
prpty_terms_sorted = [(key, prpty_terms.get(key)) for key in order]
indiv_terms_sorted = [(key, indiv_terms.get(key)) for key in order]
class_table_txt = "<h2>Classes</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th></tr>"
for tuple_status_term in class_terms_sorted:
curation_status = tuple_status_term[0]
class_names = tuple_status_term[1]
if class_names:
for class_name in sorted(class_names):
class_table_txt += self.create_term_row(class_name, \
definitions[class_name], \
sameas[class_name], \
editors[class_name], \
notes[class_name], \
CURATION_COLORS.setdefault(curation_status, ""))
class_table_txt = class_table_txt+"\n</table>"
prpty_table_txt = "<h2>Properties</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th><th>Domain</th><th>Range</th></tr>"
for tuple_status_term in prpty_terms_sorted:
curation_status = tuple_status_term[0]
term_names = tuple_status_term[1]
if term_names:
for term_name in sorted(term_names):
prpty_table_txt += self.create_term_row(term_name, \
definitions[term_name], \
sameas[term_name], \
editors[term_name], \
notes[term_name], \
CURATION_COLORS.setdefault(curation_status, ""), \
ranges[term_name], \
domains[term_name])
prpty_table_txt = prpty_table_txt+"\n</table>"
indiv_table_txt = "<h2>Individuals</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th><th>Type</th></tr>"
for tuple_status_term in indiv_terms_sorted:
curation_status = tuple_status_term[0]
term_names = tuple_status_term[1]
if term_names:
for term_name in sorted(term_names):
indiv_table_txt += self.create_term_row(term_name, \
definitions[term_name], \
sameas[term_name], \
editors[term_name], \
notes[term_name], \
CURATION_COLORS.setdefault(curation_status, ""), \
None, None,
types[term_name])
indiv_table_txt = indiv_table_txt+"\n</table>"
curation_legend = self.create_curation_legend(order)
title = "<h1>NIDM-Results Terms curation status</h1>"
intro = """You will find below a listing of the NIDM-Results terms that \
need to be curated. If you would like **to help with the curation of a term, \
please follow those steps**:
1. Check if the terms is already under discussion in an issue.
2. If not, create a new issue including the current definition (available in\
the table below) and your proposed update.
If possible, priority should be given to uncurated terms (in red).
Thank you in advance for taking part in NIDM-Results term curation!\n\n"""
self.write_readme(readme_file, title+intro+\
curation_legend+class_table_txt+prpty_table_txt+indiv_table_txt)
class UpdateExpTermReadme():
def __init__(self, owl_file):
self.owl = OwlReader(owl_file)
# Write out Readme
def write_readme(self, readme_file, readme_txt):
readme_file_open = open(readme_file, 'w')
readme_file_open.write(readme_txt)
readme_file_open.close()
def create_term_row(self, term_name, definition, same_as, editor, note,
color, range_value=None, domain=None, indiv_type=None):
img_color = ""
if color:
img_color = '<img src="../../../doc/content/specs/img/'+color+'.png?raw=true"/> '
if same_as:
same_as = "(same as: <a href="+same_as+">"+same_as+"</a>)"
range_domain_type = ""
if range_value is not None:
range_domain_type = """
<td>"""+domain+"""</td>
<td>"""+range_value+"""</td>"""
if indiv_type is not None:
range_domain_type += """
<td>"""+indiv_type+"""</td>"""
# Github mardow-like links
nidm_repo = "https://github.com/incf-nidash/nidm/"
#stato_repo = "https://github.com/ISA-tools/stato/"
nidm_pr_issue = re.compile(nidm_repo+r'[a-zA-Z]*/(\d+)')
note = nidm_pr_issue.sub(r'<a href="'+nidm_repo+r'pull/\1">'+r'#\1</a>', note)
#stato_pr_issue = re.compile(stato_repo+r'[a-zA-Z]*/(\d+)')
#note = stato_pr_issue.sub(r'<a href="'+stato_repo+r'pull/\1">'+r'ISA-tools/stato#\1</a>', note)
if note:
note = note+"<br/>"
# Add a search link (to check current state of the repo)
if "Under discussion" in note:
search_text = "more"
else:
search_text = "find issues/PR"
note = note+"<a href=\""+nidm_repo+"/issues?&q="+term_name.split(":")[1]+"\"> ["+search_text+"] </a>"
term_row = """
<tr>
<td>"""+img_color+"""</td>
<td>"""+note+"""</td>
<td><b>"""+term_name+""": </b>"""+definition+same_as+editor+"""</td>"""+range_domain_type+"""
</tr>"""
return term_row
def create_curation_legend(self, order):
curation_legend = "<b>Curation status</b>: \n"
curation_colors_sorted = [(key, CURATION_COLORS.get(key)) for key in order]
covered_colors = list()
for curation_color in curation_colors_sorted:
# curation_status = str(self.owl.qname(curation_color[0]))
# curation_status_labels = self.owl.objects(curation_color[0], RDFS['label'])
# curation_status = ", ".join(list(curation_status_labels))
color = curation_color[1]
if not color in covered_colors:
curation_legend = curation_legend+\
'<img src="../../../doc/content/specs/img/'+color+\
'.png?raw=true"/> '+CURATION_LEGEND[color]+";\n"
covered_colors.append(color)
return curation_legend
# Get README text according to owl file information
def update_readme(self, readme_file):
class_terms = dict()
prpty_terms = dict()
indiv_terms = dict()
definitions = dict()
editors = dict()
notes = dict()
ranges = dict()
domains = dict()
sameas = dict()
types = dict()
for owl_term in self.owl.classes.union(self.owl.properties).union(self.owl.individuals):
curation_status = self.owl.get_curation_status(owl_term)
definition = self.owl.get_definition(owl_term)
if definition == "":
definition = "<undefined>"
editor = self.owl.get_editor(owl_term)
note = self.owl.get_editor_note(owl_term)
range_value = self.owl.get_range(owl_term)
domain = self.owl.get_domain(owl_term)
same = self.owl.get_same_as(owl_term)
indiv_type = self.owl.get_individual_type(owl_term)
if curation_status:
curation_key = curation_status
term_key = self.owl.get_label(owl_term)
if term_key.startswith("nidm"):
if owl_term in self.owl.classes:
class_terms.setdefault(curation_key, list()).append(term_key)
else:
if owl_term in self.owl.properties:
prpty_terms.setdefault(curation_key, list()).append(term_key)
else:
if owl_term in self.owl.individuals:
indiv_terms.setdefault(curation_key, list()).append(term_key)
definitions[term_key] = definition
editors[term_key] = editor
notes[term_key] = note
ranges[term_key] = range_value
domains[term_key] = domain
sameas[term_key] = same
types[term_key] = indiv_type
# Include missing keys and do not display ready for release terms
order=CURATION_ORDER+(list(set(class_terms.keys()).union(set(prpty_terms.keys())) - set(CURATION_ORDER+list([OBO_READY]))))
print 'order = ', order
class_terms_sorted = [(key, class_terms.get(key)) for key in order]
prpty_terms_sorted = [(key, prpty_terms.get(key)) for key in order]
indiv_terms_sorted = [(key, indiv_terms.get(key)) for key in order]
class_table_txt = "<h2>Classes</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th></tr>"
for tuple_status_term in class_terms_sorted:
curation_status = tuple_status_term[0]
class_names = tuple_status_term[1]
if class_names:
for class_name in sorted(class_names):
class_table_txt += self.create_term_row(class_name, \
definitions[class_name], \
sameas[class_name], \
editors[class_name], \
notes[class_name], \
CURATION_COLORS.setdefault(curation_status, ""))
class_table_txt = class_table_txt+"\n</table>"
prpty_table_txt = "<h2>Properties</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th><th>Domain</th><th>Range</th></tr>"
for tuple_status_term in prpty_terms_sorted:
curation_status = tuple_status_term[0]
term_names = tuple_status_term[1]
if term_names:
for term_name in sorted(term_names):
prpty_table_txt += self.create_term_row(term_name, \
definitions[term_name], \
sameas[term_name], \
editors[term_name], \
notes[term_name], \
CURATION_COLORS.setdefault(curation_status, ""), \
ranges[term_name], \
domains[term_name])
prpty_table_txt = prpty_table_txt+"\n</table>"
indiv_table_txt = "<h2>Individuals</h2>\n<table>\n<tr><th>Curation Status</th><th>Issue/PR</th><th>Term</th><th>Type</th></tr>"
for tuple_status_term in indiv_terms_sorted:
curation_status = tuple_status_term[0]
term_names = tuple_status_term[1]
if term_names:
for term_name in sorted(term_names):
indiv_table_txt += self.create_term_row(term_name, \
definitions[term_name], \
sameas[term_name], \
editors[term_name], \
notes[term_name], \
CURATION_COLORS.setdefault(curation_status, ""), \
None, None,
types[term_name])
indiv_table_txt = indiv_table_txt+"\n</table>"
curation_legend = self.create_curation_legend(order)
title = "<h1>NIDM-Experiment Terms curation status</h1>"
intro = """You will find below a listing of the NIDM-Experiment terms that \
need to be curated. If you would like to help with the curation of a term, \
please follow those steps: first, check if the term is already under discussion in an \
issue and if it is please contribute to the discussion there. If not, create a new issue, \
including the current definition (available in\
the table below) and your proposed update.
If possible, priority should be given to uncurated terms (in red).
Thank you in advance for taking part in NIDM-Experiment term curation!\n\n"""
self.write_readme(readme_file, title+intro+\
curation_legend+class_table_txt+prpty_table_txt+indiv_table_txt)
