def test_partial_taxonomic_with_synonymy(self):
"exporting one genus which is not an accepted name."
f = self.session.query(
Family).filter(
Family.family == u'Orchidaceae').one()
bu = Genus(family=f, genus=u'Bulbophyllum') # accepted
zy = Genus(family=f, genus=u'Zygoglossum') # synonym
bu.synonyms.append(zy)
self.session.add_all([f, bu, zy])
self.session.commit()
selection = self.session.query(Genus).filter(
Genus.genus == u'Zygoglossum').all()
mock_view.set_selection(selection)
exporter = JSONExporter(mock_view)
exporter.start(self.temp_path, selection)
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Zygoglossum')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
accepted = result[0].get('accepted')
self.assertTrue(isinstance(accepted, dict))
self.assertEquals(accepted['rank'], 'genus')
self.assertEquals(accepted['epithet'], 'Bulbophyllum')
self.assertEquals(accepted['ht-rank'], 'familia')
self.assertEquals(accepted['ht-epithet'], 'Orchidaceae')
def test_partial_taxonomic_with_synonymy(self):
"exporting one genus which is not an accepted name."
f = self.session.query(
Family).filter(
Family.family == u'Orchidaceae').one()
bu = Genus(family=f, genus=u'Bulbophyllum') # accepted
zy = Genus(family=f, genus=u'Zygoglossum') # synonym
bu.synonyms.append(zy)
self.session.add_all([f, bu, zy])
self.session.commit()
selection = self.session.query(Genus).filter(
Genus.genus == u'Zygoglossum').all()
exporter = JSONExporter(MockView())
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = True
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Zygoglossum')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
accepted = result[0].get('accepted')
self.assertTrue(isinstance(accepted, dict))
self.assertEquals(accepted['rank'], 'genus')
self.assertEquals(accepted['epithet'], 'Bulbophyllum')
self.assertEquals(accepted['ht-rank'], 'familia')
self.assertEquals(accepted['ht-epithet'], 'Orchidaceae')
def test_writes_complete_database(self):
"exporting without specifying what: export complete database"
mock_view.set_selection([])
exporter = JSONExporter(mock_view)
exporter.start(self.temp_path)
## must still check content of generated file!
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 5)
families = [i for i in result if i['rank'] == 'familia']
self.assertEquals(len(families), 2)
genera = [i for i in result if i['rank'] == 'genus']
self.assertEquals(len(genera), 2)
species = [i for i in result if i['rank'] == 'species']
self.assertEquals(len(species), 1)
self.assertEquals(open(self.temp_path).read(),
"""\
[{"epithet": "Orchidaceae", "object": "taxon", "rank": "familia"},
{"epithet": "Myrtaceae", "object": "taxon", "rank": "familia"},
{"author": "R. Br.", "epithet": "Calopogon", "ht-epithet": "Orchidaceae", \
"ht-rank": "familia", "object": "taxon", "rank": "genus"},
{"author": "", "epithet": "Panisea", "ht-epithet": "Orchidaceae", \
"ht-rank": "familia", "object": "taxon", "rank": "genus"},
{"epithet": "tuberosus", "ht-epithet": "Calopogon", "ht-rank": "genus", \
"hybrid": false, "object": "taxon", "rank": "species"}]""")
def test_when_selection_huge_ask(self):
view = MockView()
exporter = JSONExporter(view)
exporter.selection_based_on == 'sbo_selection'
view.selection = range(5000)
view.reply_yes_no_dialog = [False]
exporter.run()
self.assertTrue('run_yes_no_dialog' in view.invoked)
self.assertEquals(view.reply_yes_no_dialog, [])
def test_writes_complete_database(self):
"exporting without specifying what: export complete database"
exporter = JSONExporter(MockView())
exporter.view.selection = None
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
## must still check content of generated file!
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 11)
families = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'familia']
self.assertEquals(len(families), 2)
genera = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'genus']
self.assertEquals(len(genera), 2)
species = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'species']
self.assertEquals(len(species), 1)
target = [
{"epithet": u"Orchidaceae", u"object": u"taxon", 'aggregate': u'',
"rank": u"familia", u"author": u"", u"hybrid_marker": u""},
{u"epithet": u"Myrtaceae", u"object": u"taxon", 'aggregate': u'',
u"rank": u"familia", u"author": u"", u"hybrid_marker": u""},
{u"author": u"R. Br.", u"epithet": u"Calopogon",
u"ht-epithet": u"Orchidaceae", u"ht-rank": u"familia",
u"object": u"taxon", u"rank": u"genus", 'aggregate': u'',
u"hybrid_marker": u""},
{u"object": u"taxon", u"author": u"", u"epithet": u"Panisea",
u"ht-epithet": u"Orchidaceae", u"ht-rank": u"familia",
'aggregate': u'', u"rank": u"genus", u"hybrid_marker": u''},
{u"epithet": u"tuberosus", u"ht-epithet": u"Calopogon",
u"ht-rank": u"genus", u"hybrid_marker": u"", u"object": u"taxon",
u"rank": u"species", u'aggregate': u'', 'author': u''},
{u"code": u"2015.0001", u"object": u"accession", u"private": False,
u"species": u"Calopogon tuberosus"},
{u"code": u"2015.0002", u"object": u"accession", u"private": False,
u"species": u"Calopogon tuberosus"},
{u"code": u"2015.0003", u"object": u"accession", u"private": True,
u"species": u"Calopogon tuberosus"},
{u"code": u"1", u"object": u"location"},
{u"accession": u"2015.0001", u"code": u"1", u"location": u"1",
u"memorial": False, u"object": u"plant", u"quantity": 1},
{u"accession": u"2015.0003", u"code": u"1", u"location": u"1",
u"memorial": False, u"object": u"plant", u"quantity": 1}]
print sorted(result)
print sorted(target)
#self.assertEquals(sorted(result), sorted(target))
for o1 in result:
self.assertTrue(o1 in target, o1)
for o2 in target:
self.assertTrue(o1 in result, o2)
def test_writes_full_taxonomic_info(self):
"exporting one family: export full taxonomic information below family"
selection = self.session.query(Family).filter(
Family.family == u'Orchidaceae').all()
mock_view.set_selection(selection)
exporter = JSONExporter(mock_view)
exporter.start(self.temp_path, selection)
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'familia')
self.assertEquals(result[0]['epithet'], 'Orchidaceae')
def test_writes_partial_taxonomic_info(self):
"exporting one genus: all species below genus"
selection = self.session.query(Genus).filter(
Genus.genus == u'Calopogon').all()
mock_view.set_selection(selection)
exporter = JSONExporter(mock_view)
exporter.start(self.temp_path, selection)
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Calopogon')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
self.assertEquals(result[0]['author'], 'R. Br.')
def test_writes_partial_taxonomic_info_species(self):
"exporting one species: all species below species"
selection = self.session.query(
Species).filter(Species.sp == u'tuberosus').join(
Genus).filter(Genus.genus == u"Calopogon").all()
mock_view.set_selection(selection)
exporter = JSONExporter(mock_view)
exporter.start(self.temp_path, selection)
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'species')
self.assertEquals(result[0]['epithet'], 'tuberosus')
self.assertEquals(result[0]['ht-rank'], 'genus')
self.assertEquals(result[0]['ht-epithet'], 'Calopogon')
self.assertEquals(result[0]['hybrid'], False)
def test_export_with_vernacular(self):
"exporting one genus which is not an accepted name."
## precondition
sola = Family(family='Solanaceae')
brug = Genus(family=sola, genus=u'Brugmansia')
arbo = Species(genus=brug, sp=u'arborea')
vern = VernacularName(species=arbo,
language=u"es", name=u"Floripondio")
self.session.add_all([sola, brug, arbo, vern])
self.session.commit()
## action
exporter = JSONExporter(MockView())
exporter.view.selection = None
exporter.selection_based_on = 'sbo_taxa'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
## check
result = json.load(open(self.temp_path))
vern_from_json = [i for i in result
if i['object'] == 'vernacular_name']
self.assertEquals(len(vern_from_json), 1)
self.assertEquals(vern_from_json[0]['language'], 'es')
def test_export_private_if_sbo_plants(self):
exporter = JSONExporter(MockView())
exporter.view.selection = None
exporter.selection_based_on = 'sbo_plants'
exporter.include_private = True
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 8)
def test_partial_taxonomic_with_synonymy(self):
"exporting one genus which is not an accepted name."
f = self.session.query(Family).filter(
Family.epithet == u'Orchidaceae').one()
bu = Genus(family=f, epithet=u'Bulbophyllum') # accepted
zy = Genus(family=f, epithet=u'Zygoglossum') # synonym
bu.synonyms.append(zy)
self.session.add_all([f, bu, zy])
self.session.commit()
selection = self.session.query(Genus).filter(
Genus.epithet == u'Zygoglossum').all()
exporter = JSONExporter(MockView())
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = True
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Zygoglossum')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
accepted = result[0].get('accepted')
self.assertTrue(isinstance(accepted, dict))
self.assertEquals(accepted['rank'], 'genus')
self.assertEquals(accepted['epithet'], 'Bulbophyllum')
self.assertEquals(accepted['ht-rank'], 'familia')
self.assertEquals(accepted['ht-epithet'], 'Orchidaceae')
def test_on_btnbrowse_clicked(self):
view = MockView()
exporter = JSONExporter(view)
view.reply_file_chooser_dialog = ['/tmp/test.json']
exporter.on_btnbrowse_clicked('button')
exporter.on_text_entry_changed('filename')
self.assertEquals(exporter.filename, '/tmp/test.json')
self.assertEquals(JSONExporter.last_folder, '/tmp')
def test_export_ignores_private_if_sbo_selection(self):
exporter = JSONExporter(MockView())
selection = [o for o in self.objects if isinstance(o, Accession)]
non_private = [a for a in selection if a.private is False]
self.assertEquals(len(selection), 3)
self.assertEquals(len(non_private), 2)
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 3)
def test_writes_full_taxonomic_info(self):
"exporting one family: export full taxonomic information below family"
selection = self.session.query(Family).filter(
Family.family == u'Orchidaceae').all()
exporter = JSONExporter(MockView())
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.view.selection = selection
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'familia')
self.assertEquals(result[0]['epithet'], 'Orchidaceae')
def test_writes_complete_database(self):
"exporting without specifying what: export complete database"
exporter = JSONExporter(MockView())
exporter.view.selection = None
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
## must still check content of generated file!
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 11)
families = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'familia']
self.assertEquals(len(families), 2)
genera = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'genus']
self.assertEquals(len(genera), 2)
species = [i for i in result
if i['object'] == 'taxon' and i['rank'] == 'species']
self.assertEquals(len(species), 1)
target = [
{"epithet": "Orchidaceae", "object": "taxon", "rank": "familia"},
{"epithet": "Myrtaceae", "object": "taxon", "rank": "familia"},
{"author": "R. Br.", "epithet": "Calopogon",
"ht-epithet": "Orchidaceae", "ht-rank": "familia",
"object": "taxon", "rank": "genus"},
{"author": "", "epithet": "Panisea", "ht-epithet": "Orchidaceae",
"ht-rank": "familia", "object": "taxon", "rank": "genus"},
{"epithet": "tuberosus", "ht-epithet": "Calopogon",
"ht-rank": "genus", "hybrid": False, "object": "taxon",
"rank": "species"},
{"code": "2015.0001", "object": "accession", "private": False,
"species": "Calopogon tuberosus"},
{"code": "2015.0002", "object": "accession", "private": False,
"species": "Calopogon tuberosus"},
{"code": "2015.0003", "object": "accession", "private": True,
"species": "Calopogon tuberosus"},
{"code": "1", "object": "location"},
{"accession": "2015.0001", "code": "1", "location": "1",
"memorial": False, "object": "plant", "quantity": 1},
{"accession": "2015.0003", "code": "1", "location": "1",
"memorial": False, "object": "plant", "quantity": 1}]
for o1 in result:
self.assertTrue(o1 in target)
for o2 in target:
self.assertTrue(o1 in result)
def test_writes_partial_taxonomic_info(self):
"exporting one genus: all species below genus"
selection = self.session.query(Genus).filter(
Genus.genus == u'Calopogon').all()
exporter = JSONExporter(MockView())
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Calopogon')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
self.assertEquals(result[0]['author'], 'R. Br.')
def test_writes_partial_taxonomic_info_species(self):
"exporting one species: all species below species"
selection = self.session.query(
Species).filter(Species.sp == u'tuberosus').join(
Genus).filter(Genus.genus == u"Calopogon").all()
exporter = JSONExporter(MockView())
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'species')
self.assertEquals(result[0]['epithet'], 'tuberosus')
self.assertEquals(result[0]['ht-rank'], 'genus')
self.assertEquals(result[0]['ht-epithet'], 'Calopogon')
self.assertEquals(result[0]['hybrid'], False)