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Fix GH #351

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merged 3 commits into from
Sep 2, 2024
Merged

Fix GH #351

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dcc9c62
Instructions new module
RobbinBouwmeester Aug 30, 2024
28c3c79
Update module.py
RobbinBouwmeester Sep 2, 2024
f434c4b
Merge branch 'main' into peptidoform
RobbinBouwmeester Sep 2, 2024
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11 changes: 5 additions & 6 deletions proteobench/modules/dda_quant_base/module.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ def clone_pr(

branch_name = current_datapoint["id"]

path_write = os.path.join(self.t_dir, "results.json")
path_write = os.path.join(self.t_dir_pr, "results.json")
logging.info(f"Writing the json to: {path_write}")
f = open(path_write, "w")

Expand All @@ -189,8 +189,7 @@ def clone_pr(
return "https://" + remote_git.replace(".git", "") + "/pull/" + str(pr_id)

def write_json_local_development(self, temporary_datapoints, datapoint_params):
t_dir = TemporaryDirectory().name
os.mkdir(t_dir)
os.mkdir(self.t_dir_pr)

current_datapoint = temporary_datapoints.iloc[-1]

Expand All @@ -202,14 +201,14 @@ def write_json_local_development(self, temporary_datapoints, datapoint_params):
all_datapoints = self.add_current_data_point(None, current_datapoint)

# TODO write below to logger instead of std.out
fname = os.path.join(t_dir, "results.json")
fname = os.path.join(self.t_dir_pr, "results.json")
logging.info(f"Writing the json to: {fname}")

f = open(os.path.join(t_dir, "results.json"), "w")
f = open(os.path.join(self.t_dir_pr, "results.json"), "w")

all_datapoints.to_json(f, orient="records", indent=2)

return os.path.join(t_dir, "results.json")
return os.path.join(self.t_dir_pr, "results.json")

def write_intermediate_raw(self, dir, ident, input_df, result_performance, param_loc):
path_write = os.path.join(dir, ident)
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