Merge branch 'main' into add-module-proposal-DOM-ABC

proteobench/io/params/diann.py

@@ -257,9 +257,12 @@ def extract_params(fname: str) -> ProteoBenchParameters:
         "protein_inference": "Heuristic protein inference",
     }
 
-    # Read in the log file
-    with open(fname) as f:
-        lines = f.readlines()
+    try:
+        # Read in the log file
+        with open(fname) as f:
+            lines = f.readlines()
+    except:
+        lines = [l for l in fname.read().decode("utf-8").splitlines()]
 
     # Extract software versions from the log file.
     software_version = search_engine_version = extract_with_regex(lines, software_version_regex)

proteobench/modules/quant_base/quant_base_module.py

@@ -287,7 +287,7 @@ def clone_pr(
             logging.error("The run was previously submitted. Will not submit.")
             return False
 
-        branch_name = current_datapoint["id"]
+        branch_name = current_datapoint["id"].replace(" ", "_").replace("(", "").replace(")", "")
 
         path_write = os.path.join(self.t_dir_pr, "results.json")
         logging.info(f"Writing the json to: {path_write}")

webinterface/.streamlit/config.toml

@@ -1,6 +1,9 @@
 [theme]
 base="light"
 
+[global]
+disableWidgetStateDuplicationWarning = true
+
 [server]
 enableStaticServing = true
 maxUploadSize = 1000

webinterface/pages/DDA_Quant_ion.py

@@ -39,30 +39,33 @@ def _main_page(self) -> None:
         """
         # Create tabs
         (
-            tab_description,
+            # tab_description,
             tab_results_all,
             tab_submission_details,
             tab_indepth_plots,
             tab_results_new,
             tab_public_submission,
         ) = st.tabs(
             [
-                "Module description",
-                "Results (All Data)",
-                "Submission form",
-                "In-depth submission",
-                "Results (New Submissions)",
+                # "Module description",
+                "Public Benchmark Runs",
+                "Submit New Data",
+                "Results In-Depth",
+                "Results New Data",
                 "Public Submission",
             ]
         )
 
         # Tab 0: Description
-        with tab_description:
-            self.quant_uiobjects.create_text_header()
+        # with tab_description:
+        #    self.quant_uiobjects.create_text_header()
 
         # Tab 1: Results (All Data)
         with tab_results_all:
             st.title(self.variables_dda_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dda_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dda_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
@@ -71,13 +74,24 @@ def _main_page(self) -> None:
 
         # Tab 2: Submission Details
         with tab_submission_details:
-            self.quant_uiobjects.create_text_header()
+            # self.quant_uiobjects.create_text_header_submit()
+            st.title(self.variables_dda_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dda_quant.texts.ShortMessages.doc_url})"
+            )
+            if self.variables_dda_quant.beta_warning:
+                st.warning(
+                    "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
+                )
             self.quant_uiobjects.create_main_submission_form()
             # self.quant_uiobjects.display_submission_details()
 
         # Tab 2.5: in-depth plots current data
         with tab_indepth_plots:
             st.title(self.variables_dda_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dda_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dda_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
@@ -87,16 +101,23 @@ def _main_page(self) -> None:
         # Tab 3: Results (New Submissions)
         with tab_results_new:
             st.title(self.variables_dda_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dda_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dda_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
                 )
+
             self.quant_uiobjects.display_results_all_data_submitted()
             # self.quant_uiobjects.display_results_new_submissions()
 
         # Tab 4: Public Submission
         with tab_public_submission:
             st.title(self.variables_dda_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dda_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dda_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."

webinterface/pages/DIA_Quant_ion.py

@@ -39,30 +39,33 @@ def _main_page(self) -> None:
         """
         # Create tabs
         (
-            tab_description,
+            # tab_description,
             tab_results_all,
             tab_submission_details,
             tab_indepth_plots,
             tab_results_new,
             tab_public_submission,
         ) = st.tabs(
             [
-                "Module description",
-                "Results (All Data)",
-                "Submission form",
-                "In-depth submission",
-                "Results (New Submissions)",
+                # "Module description",
+                "Public Benchmark Runs",
+                "Submit New Data",
+                "Results In-Depth",
+                "Results New Data",
                 "Public Submission",
             ]
         )
 
         # Tab 0: Description
-        with tab_description:
-            self.quant_uiobjects.create_text_header()
+        # with tab_description:
+        #    self.quant_uiobjects.create_text_header()
 
         # Tab 1: Results (All Data)
         with tab_results_all:
             st.title(self.variables_dia_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dia_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dia_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
@@ -71,13 +74,24 @@ def _main_page(self) -> None:
 
         # Tab 2: Submission Details
         with tab_submission_details:
-            self.quant_uiobjects.create_text_header()
+            # self.quant_uiobjects.create_text_header_submit()
+            st.title(self.variables_dia_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dia_quant.texts.ShortMessages.doc_url})"
+            )
+            if self.variables_dia_quant.beta_warning:
+                st.warning(
+                    "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
+                )
             self.quant_uiobjects.create_main_submission_form()
             # self.quant_uiobjects.display_submission_details()
 
         # Tab 2.5: in-depth plots current data
         with tab_indepth_plots:
             st.title(self.variables_dia_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dia_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dia_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
@@ -87,16 +101,23 @@ def _main_page(self) -> None:
         # Tab 3: Results (New Submissions)
         with tab_results_new:
             st.title(self.variables_dia_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dia_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dia_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."
                 )
+
             self.quant_uiobjects.display_results_all_data_submitted()
             # self.quant_uiobjects.display_results_new_submissions()
 
         # Tab 4: Public Submission
         with tab_public_submission:
             st.title(self.variables_dia_quant.texts.ShortMessages.title)
+            st.write(
+                f"The full description of the module is available [here]({self.variables_dia_quant.texts.ShortMessages.doc_url})"
+            )
             if self.variables_dia_quant.beta_warning:
                 st.warning(
                     "This module is in BETA phase. The figure presented below and the metrics calculation may change in the near future."