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Now handling dictionaries with one key

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This commit is contained in:
Celine Mercier
2021-03-10 16:50:30 +13:00
parent fbf0f7dfb6
commit ad1fd3c341
25 changed files with 115 additions and 64 deletions
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2
python/obitools3/commands/cat.pyx
View File

@ -115,7 +115,7 @@ def run(config):
v.close()
for coln in dict_cols:
Column.new_column(o_view, coln, dict_cols[coln]['obitype'],
nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']), dict_column=True)
# Initialize the progress bar
if not config['obi']['noprogressbar']:

10
python/obitools3/commands/import.pyx
View File

@ -257,7 +257,8 @@ def run(config):
for tag in dict_dict:
dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
nb_elements_per_line=len(dict_dict[tag][0]), \
elements_names=list(dict_dict[tag][0])), \
elements_names=list(dict_dict[tag][0]), \
dict_column=True), \
dict_dict[tag][1])
@ -328,10 +329,13 @@ def run(config):
value_type = type(value)
nb_elts = 1
value_obitype = OBI_VOID
dict_col = False
if value_type == dict or value_type == list :
nb_elts = len(value)
elt_names = list(value)
if value_type == dict :
dict_col = True
else :
nb_elts = 1
elt_names = None
@ -339,11 +343,9 @@ def run(config):
value_obitype = get_obitype(value)
if value_obitype != OBI_VOID :
dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names), value_obitype)
dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col), value_obitype)
# Fill value
if value_type == dict and nb_elts == 1: # special case that makes the OBI3 create a 1 elt/line column which won't read a dict value
value = value[list(value.keys())[0]] # The solution is to transform the value in a simple atomic one acceptable by the column
dcols[tag][0][i] = value
# TODO else log error?

5
python/obitools3/commands/test.pyx
View File

@ -302,12 +302,16 @@ def create_random_column(config, infos) :
alias = random.choice([b'', random_unique_name(infos)])
tuples = random.choice([True, False])
if not tuples :
dict_column = random.choice([True, False])
nb_elements_per_line=random.randint(1, config['test']['maxelts'])
if nb_elements_per_line > 1:
dict_column = True
elements_names = []
for i in range(nb_elements_per_line) :
elements_names.append(random_unique_element_name(config, infos))
elements_names = random.choice([None, elements_names])
else :
dict_column = False
nb_elements_per_line = 1
elements_names = None
name = random_unique_name(infos)
@ -318,6 +322,7 @@ def create_random_column(config, infos) :
data_type,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
dict_column=dict_column,
tuples=tuples,
comments=random_comments(config),
alias=alias

2
python/obitools3/commands/uniq.pyx
View File

@ -378,6 +378,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
OBI_INT,
nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'],
elements_names=list(merged_infos[merged_col_name]['elt_names']),
dict_column=True,
comments=i_col.comments,
alias=merged_col_name
)
@ -400,6 +401,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
OBI_INT,
nb_elements_per_line=len(view),
elements_names=[id for id in i_id_col],
dict_column=True,
alias=TAXID_DIST_COLUMN
)