Skip to content

Commit

Permalink
conditional batch options. modal notice for malformed markers.
Browse files Browse the repository at this point in the history
  • Loading branch information
@MikeWLloyd
MikeWLloyd committed May 16, 2024
1 parent 771c133 commit 815036f
Show file tree
Hide file tree
Showing 2 changed files with 80 additions and 50 deletions.
4 changes: 1 addition & 3 deletions strprofiler/shiny_app/clastr_api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def _valid_marker_check(markers):
'SE33']

# remove extra fields, if present as keys may come from _clastr_query or other.
query_markers = [marker for marker in markers if marker not in ['algorithm', 'includeAmelogenin', 'scoreFilter']]
query_markers = [marker for marker in markers if marker not in ['algorithm', 'includeAmelogenin', 'scoreFilter', 'description']]

missing_markers = list(set(query_markers) - set(valid_api_markers))

Expand Down Expand Up @@ -143,8 +143,6 @@ def _clastr_query(query, query_filter, include_amelogenin, score_filter):
query_added = pd.concat([query_df, merged]).reset_index(drop=True)
query_added["bestScore"] = query_added['bestScore'].map("{0:.2f}".format).replace("nan", "")

# print(query_added.columns)

if 'problem' in query_added.columns:
query_added = query_added[['accession', 'name', 'species', 'bestScore', 'accession_link', 'problem'] +
[c for c in query_added if c not in
Expand Down
126 changes: 79 additions & 47 deletions strprofiler/shiny_app/shiny_app.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,25 @@ def _link_wrap(name, link, problem):
return ui.tags.a(name, href=str(link), target="_blank")


def notify_modal(marker_list):
ui.modal_show(
ui.modal(
"Marker(s): {} are incompatible with the CLASTR query."
.format(str(marker_list)[1:-1]),
ui.tags.br(),
ui.tags.br(),
"The marker(s) will not be used in the query.",
ui.tags.br(),
ui.tags.br(),
"See: ", ui.tags.a('CLASTR', href=str("https://www.cellosaurus.org/str-search/"), target="_blank"),
" for a complete list of compatible marker names",
title="Inompatible CLASTR Markers",
easy_close=True,
footer=ui.modal_button('Understood')
)
)


# App Generation ###
def create_app(db=None):

Expand Down Expand Up @@ -236,33 +255,61 @@ def create_app(db=None):
{"id": "batch_sidebar"},
ui.tags.h3("Options"),
ui.tags.hr(),
ui.input_select(
"search_type_batch",
"Search Type",
["STRprofiler Database", "Cellosaurus Database (CLASTR)"],
width="100%"
),
ui.card(
ui.input_switch(
"score_amel_batch", "Score Amelogenin", value=False
),
ui.input_numeric(
"mix_threshold_batch",
"'Mixed' Sample Threshold",
value=3,
width="100%",
),
ui.input_numeric(
"tan_threshold_batch",
"Tanabe Filter Threshold",
value=80,
width="100%",
),
ui.input_numeric(
"mas_q_threshold_batch",
"Masters (vs. query) Filter Threshold",
value=80,
width="100%",
ui.panel_conditional(
"input.search_type_batch === 'STRprofiler Database'",
ui.input_numeric(
"mix_threshold_batch",
"'Mixed' Sample Threshold",
value=3,
width="100%",
),
ui.input_numeric(
"tan_threshold_batch",
"Tanabe Filter Threshold",
value=80,
width="100%",
),
ui.input_numeric(
"mas_q_threshold_batch",
"Masters (vs. query) Filter Threshold",
value=80,
width="100%",
),
ui.input_numeric(
"mas_r_threshold_batch",
"Masters (vs. reference) Filter Threshold",
value=80,
width="100%",
),
),
ui.input_numeric(
"mas_r_threshold_batch",
"Masters (vs. reference) Filter Threshold",
value=80,
width="100%",
ui.panel_conditional(
"input.search_type_batch === 'Cellosaurus Database (CLASTR)'",
ui.input_select(
"batch_query_filter",
"Similarity Score Filter",
choices=[
"Tanabe",
"Masters Query",
"Masters Reference",
],
width="100%",
),
ui.input_numeric(
"batch_query_filter_threshold",
"Similarity Score Filter Threshold",
value=80,
width="100%",
),
),
),
ui.input_file(
Expand All @@ -272,12 +319,6 @@ def create_app(db=None):
multiple=False,
width="100%",
),
ui.input_select(
"search_type_batch",
"Search Type",
["STRprofiler Database", "Cellosaurus Database (CLASTR)"],
width="100%"
),
ui.input_action_button(
"csv_query",
"CSV Query",
Expand Down Expand Up @@ -645,23 +686,11 @@ def loaded_example_text():
input.query_filter_threshold(),
)
elif input.search_type() == 'Cellosaurus Database (CLASTR)':

malformed_markers = _valid_marker_check(query.keys())
if malformed_markers:
notify_m = ui.modal(
"Markers: {} are incompatible with the CLASTR query."
.format(str(malformed_markers)[1:-1]),
ui.tags.br(),
ui.tags.br(),
"These markers will not be used in the query.",
ui.tags.br(),
ui.tags.br(),
"See: ", ui.tags.a('CLASTR', href=str("https://www.cellosaurus.org/str-search/"), target="_blank"),
" for a complete list of compatible marker names",
title="Inompatible CLASTR Markers",
easy_close=True,
footer=ui.modal_button('Understood')
)
ui.modal_show(notify_m)
notify_modal(malformed_markers)

results = _clastr_query(
query,
input.query_filter(),
Expand Down Expand Up @@ -741,7 +770,6 @@ def download():
@render.data_frame
def out_batch_df():
output_df.set(batch_query_results())
print(output_df)
with reactive.isolate():
if input.search_type_batch() == 'STRprofiler Database':
try:
Expand Down Expand Up @@ -842,13 +870,17 @@ def batch_query_results():
)
elif input.search_type_batch() == 'Cellosaurus Database (CLASTR)':
clastr_query = [(lambda d: d.update(description=key) or d)(val) for (key, val) in query_df.items()]

malformed_markers = _valid_marker_check(query_df[next(iter(query_df))].keys())
if malformed_markers:
notify_modal(malformed_markers)

results = _clastr_batch_query(
clastr_query,
input.query_filter(),
input.batch_query_filter(),
input.score_amel_batch(),
input.query_filter_threshold()
input.batch_query_filter_threshold()
)
# TO DO: Change to a batch filter option set.
return results

# File input loading
Expand Down

0 comments on commit 815036f

Please sign in to comment.