def optimal_substemma_csv ():
"""Do an exhaustive search for the combination among a given set of ancestors
that best explains a given manuscript.
"""
if current_app.config.val is None:
current_app.config.val = init (current_app.config.dba)
val = current_app.config.val
with current_app.config.dba.engine.begin () as conn:
# the manuscript to explain
ms = Manuscript (conn, request.args.get ('ms'))
# get the selected set of ancestors and build all combinations of that set
selected = [ Manuscript (conn, anc_id)
for anc_id in (request.args.get ('selection') or '').split () ]
combinations = []
i = 0
for l in range (len (selected)):
for c in itertools.combinations (selected, l + 1):
combinations.append (Combination (c, i))
i += 1
explain_matrix = build_explain_matrix (conn, val, ms.ms_id)
_optimal_substemma (ms.ms_id, explain_matrix, combinations, mode = 'search')
res = [c.to_csv () for c in combinations]
return csvify (_OptimalSubstemmaRow._fields,
list (map (_OptimalSubstemmaRow._make, res)))
def attesting_csv (passage_or_id, labez):
""" Serve all relatives of all mss. attesting labez at passage. """
auth ()
with current_app.config.dba.engine.begin () as conn:
passage = Passage (conn, passage_or_id)
res = execute (conn, """
SELECT ms_id, hs, hsnr
FROM apparatus_view
WHERE pass_id = :pass_id AND labez = :labez
ORDER BY hsnr
""", dict (parameters, pass_id = passage.pass_id, labez = labez))
Attesting = collections.namedtuple ('Attesting', 'ms_id hs hsnr')
return csvify (Attesting._fields, list (map (Attesting._make, res)))
def optimal_substemma_detail_csv():
"""Report details about one combination of ancestors.
"""
if current_app.config.val is None:
current_app.config.val = init(current_app.config.dba)
val = current_app.config.val
with current_app.config.dba.engine.begin() as conn:
# the manuscript to explain
ms = Manuscript(conn, request.args.get('ms'))
# get the selected set of ancestors
selected = [
Manuscript(conn, anc_id)
for anc_id in (request.args.get('selection') or '').split()
]
combinations = [Combination(selected, 0)]
explain_matrix = build_explain_matrix(conn, val, ms.ms_id)
_optimal_substemma(ms.ms_id,
explain_matrix,
combinations,
mode='detail')
res = execute(
conn, """
SELECT 'unknown' as type, p.pass_id, p.begadr, p.endadr, v.labez_clique, v.lesart
FROM passages p
JOIN apparatus_cliques_view v USING (pass_id)
WHERE v.ms_id = :ms_id AND pass_id IN :unknown_pass_ids
UNION
SELECT 'open' as type, p.pass_id, p.begadr, p.endadr, v.labez_clique, v.lesart
FROM passages p
JOIN apparatus_cliques_view v USING (pass_id)
WHERE v.ms_id = :ms_id AND pass_id IN :open_pass_ids
""",
dict(ms_id=ms.ms_id,
unknown_pass_ids=combinations[0].unknown_indices or (-1, ),
open_pass_ids=combinations[0].open_indices or (-1, )))
return csvify(
_OptimalSubstemmaDetailRowCalcFields._fields,
list(map(_OptimalSubstemmaDetailRowCalcFields._make, res)))
def attesting_csv(passage_or_id, labez):
""" Serve all relatives of all mss. attesting labez at passage. """
auth()
with current_app.config.dba.engine.begin() as conn:
passage = Passage(conn, passage_or_id)
res = execute(
conn, """
SELECT ms_id, hs, hsnr
FROM apparatus_view
WHERE pass_id = :pass_id AND labez = :labez
ORDER BY hsnr
""", dict(parameters, pass_id=passage.pass_id, labez=labez))
Attesting = collections.namedtuple('Attesting', 'ms_id hs hsnr')
return csvify(Attesting._fields, list(map(Attesting._make, res)))
def optimal_substemma_detail_csv ():
"""Report details about one combination of ancestors.
"""
if current_app.config.val is None:
current_app.config.val = init (current_app.config.dba)
val = current_app.config.val
with current_app.config.dba.engine.begin () as conn:
# the manuscript to explain
ms = Manuscript (conn, request.args.get ('ms'))
# get the selected set of ancestors
selected = [ Manuscript (conn, anc_id)
for anc_id in (request.args.get ('selection') or '').split () ]
combinations = [Combination (selected, 0)]
explain_matrix = build_explain_matrix (conn, val, ms.ms_id)
_optimal_substemma (ms.ms_id, explain_matrix, combinations, mode = 'detail')
res = execute (conn, """
SELECT 'unknown' as type, p.pass_id, p.begadr, p.endadr, v.labez_clique, v.lesart
FROM passages p
JOIN apparatus_cliques_view v USING (pass_id)
WHERE v.ms_id = :ms_id AND pass_id IN :unknown_pass_ids
UNION
SELECT 'open' as type, p.pass_id, p.begadr, p.endadr, v.labez_clique, v.lesart
FROM passages p
JOIN apparatus_cliques_view v USING (pass_id)
WHERE v.ms_id = :ms_id AND pass_id IN :open_pass_ids
""", dict (
ms_id = ms.ms_id,
unknown_pass_ids = combinations[0].unknown_indices,
open_pass_ids = combinations[0].open_indices
))
return csvify (_OptimalSubstemmaDetailRowCalcFields._fields,
list (map (_OptimalSubstemmaDetailRowCalcFields._make, res)))
def optimal_substemma_csv():
"""Do an exhaustive search for the combination among a given set of ancestors
that best explains a given manuscript.
"""
if current_app.config.val is None:
current_app.config.val = init(current_app.config.dba)
val = current_app.config.val
with current_app.config.dba.engine.begin() as conn:
# the manuscript to explain
ms = Manuscript(conn, request.args.get('ms'))
# get the selected set of ancestors and build all combinations of that set
selected = [
Manuscript(conn, anc_id)
for anc_id in (request.args.get('selection') or '').split()
]
combinations = []
i = 0
for l in range(len(selected)):
for c in itertools.combinations(selected, l + 1):
combinations.append(Combination(c, i))
i += 1
explain_matrix = build_explain_matrix(conn, val, ms.ms_id)
_optimal_substemma(ms.ms_id,
explain_matrix,
combinations,
mode='search')
res = [c.to_csv() for c in combinations]
return csvify(_OptimalSubstemmaRow._fields,
list(map(_OptimalSubstemmaRow._make, res)))
def relatives_csv (passage_or_id, hs_hsnr_id):
"""Output a table of the nearest relatives of a manuscript.
Output a table of the nearest relatives/ancestors/descendants of a
manuscript and what they attest.
"""
auth ()
type_ = request.args.get ('type') or 'rel'
chapter = request.args.get ('range') or 'All'
limit = int (request.args.get ('limit') or 0)
labez = request.args.get ('labez') or 'all'
mode = request.args.get ('mode') or 'sim'
include = request.args.getlist ('include[]') or []
fragments = request.args.getlist ('fragments[]') or []
view = 'affinity_view' if mode == 'rec' else 'affinity_p_view'
where = ''
if type_ == 'anc':
where = ' AND older < newer'
if type_ == 'des':
where = ' AND older >= newer'
if labez == 'all':
where += " AND labez !~ '^z'"
elif labez == 'all+lac':
pass
else:
where += " AND labez = '%s'" % labez
if 'fragments' in fragments:
frag_where = ''
else:
frag_where = 'AND aff.common > aff.ms1_length / 2'
limit = '' if limit == 0 else ' LIMIT %d' % limit
with current_app.config.dba.engine.begin () as conn:
passage = Passage (conn, passage_or_id)
ms = Manuscript (conn, hs_hsnr_id)
rg_id = passage.range_id (chapter)
exclude = get_excluded_ms_ids (conn, include)
# Get the X most similar manuscripts and their attestations
res = execute (conn, """
/* get the LIMIT closest ancestors for this node */
WITH ranks AS (
SELECT ms_id1, ms_id2,
rank () OVER (ORDER BY affinity DESC, common, older, newer DESC, ms_id2) AS rank,
affinity
FROM {view} aff
WHERE ms_id1 = :ms_id1 AND aff.rg_id = :rg_id AND ms_id2 NOT IN :exclude
AND newer > older {frag_where}
ORDER BY affinity DESC
)
SELECT r.rank,
aff.ms_id2 as ms_id,
ms.hs,
ms.hsnr,
aff.ms2_length,
aff.common,
aff.equal,
aff.older,
aff.newer,
aff.unclear,
aff.common - aff.equal - aff.older - aff.newer - aff.unclear as norel,
CASE WHEN aff.newer < aff.older THEN ''
WHEN aff.newer = aff.older THEN '-'
ELSE '>'
END as direction,
aff.affinity,
a.labez
FROM
{view} aff
JOIN apparatus_view_agg a
ON aff.ms_id2 = a.ms_id
JOIN manuscripts ms
ON aff.ms_id2 = ms.ms_id
LEFT JOIN ranks r
ON r.ms_id2 = aff.ms_id2
WHERE aff.ms_id2 NOT IN :exclude AND aff.ms_id1 = :ms_id1
AND aff.rg_id = :rg_id AND aff.common > 0
AND a.pass_id = :pass_id {where} {frag_where}
ORDER BY affinity DESC, r.rank, newer DESC, older DESC, hsnr
{limit}
""", dict (parameters, where = where, frag_where = frag_where,
ms_id1 = ms.ms_id, hsnr = ms.hsnr,
pass_id = passage.pass_id, rg_id = rg_id, limit = limit,
view = view, exclude = exclude))
Relatives = collections.namedtuple (
'Relatives',
'rank ms_id hs hsnr length common equal older newer unclear norel direction affinity labez'
)
return csvify (Relatives._fields, list (map (Relatives._make, res)))
def relatives_csv(passage_or_id, hs_hsnr_id):
"""Output a table of the nearest relatives of a manuscript.
Output a table of the nearest relatives/ancestors/descendants of a
manuscript and what they attest.
"""
auth()
type_ = request.args.get('type') or 'rel'
limit = int(request.args.get('limit') or 0)
labez = request.args.get('labez') or 'all'
mode = request.args.get('mode') or 'sim'
include = request.args.getlist('include[]') or []
fragments = request.args.getlist('fragments[]') or []
view = 'affinity_view' if mode == 'rec' else 'affinity_p_view'
where = ''
if type_ == 'anc':
where = ' AND older < newer'
if type_ == 'des':
where = ' AND older >= newer'
if labez == 'all':
where += " AND labez !~ '^z'"
elif labez == 'all+lac':
pass
else:
where += " AND labez = '%s'" % labez
if 'fragments' in fragments:
frag_where = ''
else:
frag_where = 'AND aff.common > aff.ms1_length / 2'
limit = '' if limit == 0 else ' LIMIT %d' % limit
with current_app.config.dba.engine.begin() as conn:
passage = Passage(conn, passage_or_id)
ms = Manuscript(conn, hs_hsnr_id)
rg_id = passage.request_rg_id(request)
exclude = get_excluded_ms_ids(conn, include)
# Get the X most similar manuscripts and their attestations
res = execute(
conn, """
/* get the LIMIT closest ancestors for this node */
WITH ranks AS (
SELECT ms_id1, ms_id2,
rank () OVER (ORDER BY affinity DESC, common, older, newer DESC, ms_id2) AS rank,
affinity
FROM {view} aff
WHERE ms_id1 = :ms_id1 AND aff.rg_id = :rg_id AND ms_id2 NOT IN :exclude
AND newer > older {frag_where}
ORDER BY affinity DESC
)
SELECT r.rank,
aff.ms_id2 as ms_id,
ms.hs,
ms.hsnr,
aff.ms2_length,
aff.common,
aff.equal,
aff.older,
aff.newer,
aff.unclear,
aff.common - aff.equal - aff.older - aff.newer - aff.unclear as norel,
CASE WHEN aff.newer < aff.older THEN ''
WHEN aff.newer = aff.older THEN '-'
ELSE '>'
END as direction,
aff.affinity,
a.labez,
a.certainty
FROM
{view} aff
JOIN apparatus_view_agg a
ON aff.ms_id2 = a.ms_id
JOIN manuscripts ms
ON aff.ms_id2 = ms.ms_id
LEFT JOIN ranks r
ON r.ms_id2 = aff.ms_id2
WHERE aff.ms_id2 NOT IN :exclude AND aff.ms_id1 = :ms_id1
AND aff.rg_id = :rg_id AND aff.common > 0
AND a.pass_id = :pass_id {where} {frag_where}
ORDER BY affinity DESC, r.rank, newer DESC, older DESC, hsnr
{limit}
""",
dict(parameters,
where=where,
frag_where=frag_where,
ms_id1=ms.ms_id,
hsnr=ms.hsnr,
pass_id=passage.pass_id,
rg_id=rg_id,
limit=limit,
view=view,
exclude=exclude))
Relatives = collections.namedtuple(
'Relatives',
'rank ms_id hs hsnr length common equal older newer unclear norel direction affinity labez certainty'
)
return csvify(Relatives._fields, list(map(Relatives._make, res)))
def comparison_detail_csv ():
"""Endpoint. Serve a CSV table. (see also :func:`comparison_detail`)"""
auth ()
return csvify (_ComparisonDetailRowCalcFields._fields, comparison_detail ())
def comparison_summary_csv ():
"""Endpoint. Serve a CSV table. (see also :func:`comparison_summary`)"""
auth ()
return csvify (_ComparisonRowCalcFields._fields, comparison_summary ())
def comparison_detail_csv ():
"""Endpoint. Serve a CSV table. (see also :func:`comparison_detail`)"""
auth ()
return csvify (_ComparisonDetailRowCalcFields._fields, comparison_detail ())
def comparison_summary_csv ():
"""Endpoint. Serve a CSV table. (see also :func:`comparison_summary`)"""
auth ()
return csvify (_ComparisonRowCalcFields._fields, comparison_summary ())