Merge pull request #398 from Proteobench/proline-fix

Proline fix

proteobench/github/gh.py

@@ -72,22 +72,22 @@ def create_branch(self, branch_name):
         current_branch.checkout()
         return current_branch
 
-    def commit(self, commit_message):
+    def commit(self, commit_name, commit_message):
         # Stage all changes, commit, and push to the new branch
         self.repo.git.add(A=True)
-        self.repo.index.commit(commit_message)
+        self.repo.index.commit("\n".join([commit_name, commit_message]))
         self.repo.git.push("--set-upstream", "origin", self.repo.active_branch)
 
-    def create_pull_request(self, commit_message):
+    def create_pull_request(self, commit_name, commit_message):
         # Create a pull request using PyGithub
         g = Github(self.token)
         repo = g.get_repo(self.proteobot_repo_name)
         base = repo.get_branch("master")
         head = f"{self.username}:{self.repo.active_branch.name}"
 
         pr = repo.create_pull(
-            title=commit_message,
-            body="Pull request body",
+            title=commit_name,
+            body=commit_message,
             base=base.name,
             head=head,
         )

proteobench/io/params/proline.py

@@ -63,7 +63,7 @@ def extract_params(fname) -> ProteoBenchParameters:
     assert all(stats.loc["unique", cols] == 1), "Not all columns are unique"
     sheet = sheet[cols].drop_duplicates().reset_index(drop=True)
     # Extract
-    params.software_name = "Proline Studio"
+    params.software_name = "ProlineStudio"
     params.search_engine = sheet.loc[0, "software_name"]
     params.search_engine_version = sheet.loc[0, "software_version"]
     params.enzyme = sheet.loc[0, "enzymes"]

proteobench/modules/quant_base/quant_base_module.py

@@ -16,6 +16,16 @@
 )
 from proteobench.github.gh import GithubProteobotRepo
 from proteobench.io.params import ProteoBenchParameters
+from proteobench.io.params.alphadia import extract_params as extract_params_alphadia
+from proteobench.io.params.alphapept import extract_params as extract_params_alphapept
+from proteobench.io.params.diann import extract_params as extract_params_diann
+from proteobench.io.params.fragger import extract_params as extract_params_fragger
+from proteobench.io.params.i2masschroq import (
+    extract_params as extract_params_i2masschroq,
+)
+from proteobench.io.params.maxquant import extract_params as extract_params_maxquant
+from proteobench.io.params.proline import extract_params as extract_params_proline
+from proteobench.io.params.sage import extract_params as extract_params_sage
 from proteobench.io.parsing.parse_ion import load_input_file
 from proteobench.io.parsing.parse_settings_ion import ParseSettingsBuilder
 from proteobench.score.quant.quantscores import QuantScores
@@ -52,6 +62,18 @@ def __init__(self, token: str = None, proteobench_repo_name: str = "", proteobot
 
         self.precursor_name = ""
 
+    EXTRACT_PARAMS_DICT = {
+        "MaxQuant": extract_params_maxquant,
+        "ProlineStudio": extract_params_proline,
+        "AlphaPept": extract_params_alphapept,
+        "Sage": extract_params_sage,
+        "FragPipe": extract_params_fragger,
+        "i2MassChroQ": extract_params_i2masschroq,
+        "DIA-NN": extract_params_diann,
+        "AlphaDIA": extract_params_alphadia,
+        # "Spectronaut": extract_params_spectronaut
+    }
+
     def is_implemented(self) -> bool:
         """Returns whether the module is fully implemented."""
         return True
@@ -267,12 +289,13 @@ def clone_pr(
         all_datapoints.to_json(f, orient="records", indent=2)
 
         f.close()
-        commit_message = f"Added new run with id {branch_name} \n user comments: {submission_comments}"
+        commit_name = f"Added new run with id {branch_name}"
+        commit_message = f"User comments: {submission_comments}"
 
         try:
             self.github_repo.create_branch(branch_name)
-            self.github_repo.commit(commit_message)
-            pr_id = self.github_repo.create_pull_request(commit_message)
+            self.github_repo.commit(commit_name, commit_message)
+            pr_id = self.github_repo.create_pull_request(commit_name, commit_message)
         except Exception as e:
             logging.error(f"Error in PR: {e}")
             return "Unable to create PR. Please check the logs."
@@ -365,6 +388,6 @@ def load_params_file(self, input_file: list[str], input_format: str) -> ProteoBe
 
         # ! adapted to be able to parse more than one file.
         # ! how to ensure orrect order?
-        params = self.extract_params_dict[input_format](*input_file)
+        params = self.EXTRACT_PARAMS_DICT[input_format](*input_file)
         params.software_name = input_format
         return params

test/params/ProlineStudio_withMBR.csv

@@ -1,5 +1,5 @@
 ,0
-software_name,Proline Studio
+software_name,ProlineStudio
 software_version,
 search_engine,Mascot
 search_engine_version,2.8.3

test/params/Proline_example_2.csv

@@ -1,5 +1,5 @@
 ,0
-software_name,Proline Studio
+software_name,ProlineStudio
 software_version,
 search_engine,XTandem
 search_engine_version,X! Tandem Vengeance (2015.12.15.2)

test/params/Proline_example_w_Mascot_wo_proteinSets.csv

@@ -1,5 +1,5 @@
 ,0
-software_name,Proline Studio
+software_name,ProlineStudio
 software_version,
 search_engine,Mascot
 search_engine_version,2.8.0.1