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fix: check for length of rel path before splitting
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@bilalshaikh42
bilalshaikh42 committed Jun 24, 2021
1 parent fdd0597 commit fba4b3f
Showing 1 changed file with 65 additions and 44 deletions.
109 changes: 65 additions & 44 deletions vcell_cli_utils/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,16 @@
# Create temp directory
tmp_dir = tempfile.mkdtemp()


def gen_sedml_2d_3d(omex_file_path, base_out_path):

temp_path = os.path.join(base_out_path, "temp")
if not os.path.exists(temp_path):
os.mkdir(temp_path, stat.S_IRWXU|stat.S_IRWXG|stat.S_IRWXO)
os.mkdir(temp_path, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)

# defining archive
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=temp_path, try_reading_as_plain_zip_archive=False)
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=temp_path,
try_reading_as_plain_zip_archive=False)

# determine files to execute
sedml_contents = get_sedml_contents(archive)
Expand Down Expand Up @@ -61,7 +63,8 @@ def gen_sedml_2d_3d(omex_file_path, base_out_path):

for data_generator in data_generators.values():
report.data_sets.append(DataSet(
id='__data_set__{}_{}'.format(output.id, data_generator.id),
id='__data_set__{}_{}'.format(
output.id, data_generator.id),
name=data_generator.name,
label=data_generator.id,
data_generator=data_generator,
Expand All @@ -70,12 +73,15 @@ def gen_sedml_2d_3d(omex_file_path, base_out_path):
report.data_sets.sort(key=lambda data_set: data_set.id)
doc.outputs.append(report)

filename_with_reports_for_plots = os.path.join(temp_path, f'simulation_{sedml_name}.sedml')
SedmlSimulationWriter().run(doc, filename_with_reports_for_plots, validate_models_with_languages=False)
filename_with_reports_for_plots = os.path.join(
temp_path, f'simulation_{sedml_name}.sedml')
SedmlSimulationWriter().run(doc, filename_with_reports_for_plots,
validate_models_with_languages=False)


def exec_plot_output_sed_doc(omex_file_path, base_out_path):
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=tmp_dir, try_reading_as_plain_zip_archive=True)
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=tmp_dir,
try_reading_as_plain_zip_archive=True)

# determine files to execute
sedml_contents = get_sedml_contents(archive)
Expand All @@ -84,17 +90,17 @@ def exec_plot_output_sed_doc(omex_file_path, base_out_path):
for i_content, content in enumerate(sedml_contents):
content_filename = os.path.join(tmp_dir, content.location)


for report_filename in glob.glob(os.path.join(base_out_path, content.location,'*.csv')):
for report_filename in glob.glob(os.path.join(base_out_path, content.location, '*.csv')):
if report_filename.find('__plot__') != -1:
report_id = os.path.splitext(os.path.basename(report_filename))[0]
report_id = os.path.splitext(
os.path.basename(report_filename))[0]

# read report from CSV file produced by tellurium
# data_set_df = pd.read_csv(report_filename).transpose()

data_set_df = pd.read_csv(report_filename,header=None).T
data_set_df = pd.read_csv(report_filename, header=None).T
data_set_df.columns = data_set_df.iloc[0]
data_set_df.drop(0,inplace=True)
data_set_df.drop(0, inplace=True)
data_set_df.reset_index(inplace=True)
data_set_df.drop('index', axis=1, inplace=True)

Expand All @@ -103,8 +109,8 @@ def exec_plot_output_sed_doc(omex_file_path, base_out_path):
for col in list(data_set_df.columns):
datasets.append(DataSet(id=col, label=col, name=col))
#report.data_sets = datasets
report = Report(id=report_id, name=report_id, data_sets=datasets)

report = Report(id=report_id, name=report_id,
data_sets=datasets)

data_set_results = DataSetResults()

Expand All @@ -116,18 +122,23 @@ def exec_plot_output_sed_doc(omex_file_path, base_out_path):
# save file in desired BioSimulators format(s)
export_id = report_id.replace('__plot__', '')
report.id = export_id
rel_path=os.path.join(content.location, report.id).split("./")[1]
rel_path = os.path.join(
content.location, report.id)
if len(rel_path.split("./")) > 1:
rel_path = rel_path.split("./")[1]
ReportWriter().run(report,
data_set_results,
base_out_path,
rel_path,
format='h5')
os.rename(report_filename, report_filename.replace('__plot__', ''))
os.rename(report_filename,
report_filename.replace('__plot__', ''))


def exec_sed_doc(omex_file_path, base_out_path):
# defining archive
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=tmp_dir, try_reading_as_plain_zip_archive=True)
archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=tmp_dir,
try_reading_as_plain_zip_archive=True)

# determine files to execute
sedml_contents = get_sedml_contents(archive)
Expand Down Expand Up @@ -162,13 +173,14 @@ def exec_sed_doc(omex_file_path, base_out_path):
if type(report) != Plot2D and type(report) != Plot3D:
# Considering the scenario where it has the datasets in sedml
for data_set in report.data_sets:
data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')
data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(
dtype='float64')
# print("DF for report: ", data_set_results[data_set.id], file=sys.stderr)
# print("df.types: ", data_set_results[data_set.id].dtype, file=sys.stderr)
else:
data_set_df = pd.read_csv(report_filename,header=None).T
data_set_df = pd.read_csv(report_filename, header=None).T
data_set_df.columns = data_set_df.iloc[0]
data_set_df.drop(0,inplace=True)
data_set_df.drop(0, inplace=True)
data_set_df.reset_index(inplace=True)
data_set_df.drop('index', axis=1, inplace=True)
# print("DF for plot: ", data_set_df, file=sys.stderr)
Expand All @@ -186,8 +198,11 @@ def exec_sed_doc(omex_file_path, base_out_path):
# print("HDF base_out_path: ", base_out_path,file=sys.stderr)
# print("HDF path: ", os.path.join(content.location, report.id), file=sys.stderr)

rel_path=os.path.join(content.location, report.id).split("./")[1]
print(rel_path)
rel_path = os.path.join(content.location, report.id)

if len(rel_path.split("./")) > 1:
rel_path = rel_path.split("./")[1]

if type(report) != Plot2D and type(report) != Plot3D:
ReportWriter().run(report,
data_set_results,
Expand All @@ -205,7 +220,7 @@ def exec_sed_doc(omex_file_path, base_out_path):
rel_path,
format='h5')

## Remove temp directory
# Remove temp directory
shutil.rmtree(tmp_dir)


Expand Down Expand Up @@ -248,44 +263,46 @@ def get_all_dataref_and_curves(sedml_path):
'data_label': dataset.getLabel()
})


return all_report_dataref, all_plot_curves



def get_report_label_from_data_ref(dataref: str, all_report_dataref):
for report in all_report_dataref.keys():
for data_ref in all_report_dataref[report]:
if dataref == data_ref['data_reference']:
return report, data_ref['data_label']


### Update plots dict
# Update plots dict

def update_dataref_with_report_label(all_report_dataref, all_plot_curves):

for plot,curves in all_plot_curves.items():
for curve_name,datarefs in curves.items():
for plot, curves in all_plot_curves.items():
for curve_name, datarefs in curves.items():
new_ref = dict(datarefs)
new_ref['x'] = get_report_label_from_data_ref(datarefs['x'], all_report_dataref)[1]
new_ref['y'] = get_report_label_from_data_ref(datarefs['y'], all_report_dataref)[1]
new_ref['report'] = get_report_label_from_data_ref(datarefs['y'], all_report_dataref)[0]
new_ref['x'] = get_report_label_from_data_ref(
datarefs['x'], all_report_dataref)[1]
new_ref['y'] = get_report_label_from_data_ref(
datarefs['y'], all_report_dataref)[1]
new_ref['report'] = get_report_label_from_data_ref(
datarefs['y'], all_report_dataref)[0]
curves[curve_name] = new_ref

return all_report_dataref, all_plot_curves



def get_report_dataframes(all_report_dataref, result_out_dir):
report_frames = {}
reports_list = list(set(all_report_dataref.keys()))
for report in reports_list:
report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()
report_frames[report] = pd.read_csv(os.path.join(
result_out_dir, report + ".csv")).T.reset_index()
report_frames[report].columns = report_frames[report].iloc[0].values
report_frames[report].drop(index = 0, inplace=True)
report_frames[report].drop(index=0, inplace=True)
return report_frames

## PLOTTING
# PLOTTING


def plot_and_save_curves(all_plot_curves, report_frames, result_out_dir):
all_plots = dict(all_plot_curves)
Expand All @@ -294,16 +311,21 @@ def plot_and_save_curves(all_plot_curves, report_frames, result_out_dir):
fig, ax = plt.subplots(figsize=dims)
for curve, data in curve_dat.items():
df = report_frames[data['report']]
df.to_csv(os.path.join(result_out_dir, plot + '.csv'), index = False, header=True)
df.to_csv(os.path.join(result_out_dir, plot + '.csv'),
index=False, header=True)
transpose_vcml_csv(os.path.join(result_out_dir, plot + '.csv'))
sns.lineplot(x=df[data['x']].astype(np.float64), y=df[data['y']].astype(np.float64), ax=ax, label=curve)
sns.lineplot(x=df[data['x']].astype(
np.float64), y=df[data['y']].astype(np.float64), ax=ax, label=curve)
ax.set_ylabel('')
# plt.show()
plt.savefig(os.path.join(result_out_dir, plot + '.pdf'), dpi=300)


def gen_plot_pdfs(sedml_path, result_out_dir):
all_report_dataref, all_plot_curves = get_all_dataref_and_curves(sedml_path)
all_report_dataref, all_plot_curves = update_dataref_with_report_label(all_report_dataref, all_plot_curves)
all_report_dataref, all_plot_curves = get_all_dataref_and_curves(
sedml_path)
all_report_dataref, all_plot_curves = update_dataref_with_report_label(
all_report_dataref, all_plot_curves)
report_frames = get_report_dataframes(all_report_dataref, result_out_dir)
plot_and_save_curves(all_plot_curves, report_frames, result_out_dir)

Expand Down Expand Up @@ -332,21 +354,20 @@ def gen_plots_for_sed2d_only(sedml_path, result_out_dir):
dims = (12, 8)
fig, ax = plt.subplots(figsize=dims)
for curve, data in curve_dat.items():
df = pd.read_csv(os.path.join(result_out_dir, plot + '.csv'), header=None).T
df = pd.read_csv(os.path.join(
result_out_dir, plot + '.csv'), header=None).T
df.columns = df.iloc[0]
df.drop(0,inplace=True)
df.drop(0, inplace=True)
df.reset_index(inplace=True)
df.drop('index', axis=1, inplace=True)



sns.lineplot(x=df[data['x']].astype(np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
sns.lineplot(x=df[data['x']].astype(
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
ax.set_ylabel('')
# plt.show()
plt.savefig(os.path.join(result_out_dir, plot + '.pdf'), dpi=300)



if __name__ == "__main__":
fire.Fire({
'genSedml2d3d': gen_sedml_2d_3d,
Expand Down

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