removed default parameters

webinterface/configuration/dda_quant.json

@@ -1 +1 @@
-{"version": {"type": "text_input", "label": "Search engine version", "value": {"MaxQuant": 1.0, "AlphaPept": 1.0, "MSFragger": 1.0, "Proline": 1.0, "WOMBAT": 1.0}}, "software_name": {"type": "text_input", "label": "Search engine name", "value": {"MaxQuant": "MaxQuant", "AlphaPept": "AlphaPept", "MSFragger": "MSFragger", "Proline": "Proline", "WOMBAT": "WOMBAT"}}, "fdr_psm": {"type": "number_input", "label": "FDR psm", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_peptide": {"type": "number_input", "label": "FDR peptide", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_protein": {"type": "number_input", "label": "FDR protein", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "precursor_mass_tolerance": {"type": "number_input", "label": "Precursor mass tolerance", "value": {"MaxQuant": 10.0, "AlphaPept": 10.0, "MSFragger": 10.0, "Proline": 10.0, "WOMBAT": 10.0}, "min_value": 0.0, "max_value": 5.0, "format": "%.4f"}, "precursor_mass_tolerance_unit": {"type": "selectbox", "label": "Precursor tolerance unit", "value": {"MaxQuant": "PPM", "AlphaPept": "PPM", "MSFragger": "PPM", "Proline": "PPM", "WOMBAT": "PPM"}, "options": ["PPM", "Da"]}, "fragment_mass_tolerance": {"type": "number_input", "label": "Fragment mass tolerance", "value": {"MaxQuant": 10.0, "AlphaPept": 10.0, "MSFragger": 10.0, "Proline": 10.0, "WOMBAT": 10.0}, "min_value": 0.0, "max_value": 5.0, "format": "%.4f"}, "fragment_mass_tolerance_unit": {"type": "selectbox", "label": "Fragment mass tolerance unit", "value": {"MaxQuant": "PPM", "AlphaPept": "PPM", "MSFragger": "PPM", "Proline": "PPM", "WOMBAT": "PPM"}, "options": ["PPM", "Da"]}, "search_enzyme_name": {"type": "selectbox", "label": "Enzyme", "value": {"MaxQuant": "Trypsin", "AlphaPept": "Trypsin", "MSFragger": "Trypsin", "Proline": "Trypsin", "WOMBAT": "Trypsin"}, "options": ["Trypsin", "Chemotrypsin"]}, "allowed_missed_cleavage": {"type": "number_input", "label": "Maximum allowed number of missed cleavage", "value": {"MaxQuant": 2, "AlphaPept": 2, "MSFragger": 2, "Proline": 2, "WOMBAT": 2}, "format": "%d"}, "fixed_mods": {"type": "text_input", "label": "Specify the fixed mods that were set", "value": {"MaxQuant": "CAM", "AlphaPept": "CAM", "MSFragger": "CAM", "Proline": "CAM", "WOMBAT": "CAM"}}, "variable_mods": {"type": "text_input", "label": "Specify the variable mods that were set (separated by a comma)", "value": {"MaxQuant": "MOxid, 'N-term Acetyl'", "AlphaPept": "MOxid, 'N-term Acetyl'", "MSFragger": "MOxid, 'N-term Acetyl'", "Proline": "MOxid, 'N-term Acetyl'", "WOMBAT": "MOxid, 'N-term Acetyl'"}}, "precursor_charge": {"type": "text_input", "label": "Possible charge states (separated by a comma)", "value": {"MaxQuant": "2,3,4,5,6", "AlphaPept": "2,3,4,5,6", "MSFragger": "2,3,4,5,6", "Proline": "2,3,4,5,6", "WOMBAT": "2,3,4,5,6"}}, "max_num_mods_on_peptide": {"type": "number_input", "label": "Maximum number of modifications on peptides", "value": {"MaxQuant": 2, "AlphaPept": 2, "MSFragger": 2, "Proline": 2, "WOMBAT": 2}, "format": "%d"}, "min_peptide_length": {"type": "number_input", "label": "Minimum peptide length", "value": {"MaxQuant": 6, "AlphaPept": 6, "MSFragger": 6, "Proline": 6, "WOMBAT": 6}, "format": "%d"}, "max_peptide_length": {"type": "number_input", "label": "max_peptide_length", "value": {"MaxQuant": 25, "AlphaPept": 25, "MSFragger": 25, "Proline": 25, "WOMBAT": 25}, "format": "%d"}, "mbr": {"type": "checkbox", "label": "Quantified with MBR", "value": {"MaxQuant": true, "AlphaPept": true, "MSFragger": true, "Proline": true, "WOMBAT": true}}, "workflow_description": {"type": "text_area", "label": "Fill in details not specified above, such as:", "value": {"MaxQuant": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "AlphaPept": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "MSFragger": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "Proline": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "WOMBAT": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ..."}, "height": 275}}
+{"version": {"type": "text_input", "label": "Search engine version", "placeholder" : "1.0"}, "software_name": {"type": "text_input", "label": "Search engine name", "value": {"MaxQuant": "MaxQuant", "AlphaPept": "AlphaPept", "MSFragger": "MSFragger", "Proline": "Proline", "WOMBAT": "WOMBAT"}}, "fdr_psm": {"type": "number_input", "label": "FDR psm", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_peptide": {"type": "number_input", "label": "FDR peptide", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_protein": {"type": "number_input", "label": "FDR protein", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "precursor_mass_tolerance": {"type": "number_input", "label": "Precursor mass tolerance", "min_value": 0.0, "max_value": 200.0, "format": "%.4f"}, "precursor_mass_tolerance_unit": {"type": "selectbox", "label": "Precursor tolerance unit", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "PPM", "Da"]}, "fragment_mass_tolerance": {"type": "number_input", "label": "Fragment mass tolerance", "min_value": 0.0, "max_value": 100.0, "format": "%.4f"}, "fragment_mass_tolerance_unit": {"type": "selectbox", "label": "Fragment mass tolerance unit", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "PPM", "Da"]}, "search_enzyme_name": {"type": "selectbox", "label": "Enzyme", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "Trypsin", "Chemotrypsin"]}, "allowed_missed_cleavage": {"type": "number_input", "label": "Maximum allowed number of missed cleavage",  "min_value": 0, "max_value": 10,"format": "%d"}, "fixed_mods": {"type": "text_input", "label": "Specify the fixed mods that were set", "placeholder": "CAM"}, "variable_mods": {"type": "text_input", "label": "Specify the variable mods that were set (separated by a comma)", "placeholder": "MOxid, N-term Acetyl"}, "precursor_charge": {"type": "text_input", "label": "Possible charge states (separated by a comma)", "placeholder": "2,3,4,5,6"}, "max_num_mods_on_peptide": {"type": "number_input", "label": "Maximum number of modifications on peptides",  "min_value": 0, "max_value": 10,"format": "%d"}, "min_peptide_length": {"type": "number_input", "label": "Minimum peptide length",  "min_value": 0, "max_value": 100,"format": "%d"}, "max_peptide_length": {"type": "number_input", "label": "Maximum peptide length",  "min_value": 0, "max_value": 1000,"format": "%d"}, "mbr": {"type": "checkbox", "label": "Quantified with MBR", "value": {"MaxQuant": false, "AlphaPept": false, "MSFragger": false, "Proline": false, "WOMBAT": false}}, "workflow_description": {"type": "text_area", "label": "Fill in details not specified above", "placeholder": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...'", "height": 275}}

webinterface/pages/DDA_Quant.py

@@ -27,6 +27,7 @@
 FIG1 = "fig1"
 FIG2 = "fig2"
 RESULT_PERF = "result_perf"
+META_DATA = "meta_data"
 
 if "submission_ready" not in st.session_state:
     st.session_state["submission_ready"] = False
@@ -53,12 +54,17 @@ def __init__(self):
 
     def generate_input_field(self, input_format: str, content: dict):
         if content["type"] == "text_input":
-            return st.text_input(content["label"], content["value"][input_format])
+            if "placeholder" in content:
+                return st.text_input(content["label"], placeholder=content["placeholder"])
+            elif "value" in content:
+                return st.text_input(content["label"], content["value"][input_format])
         if content["type"] == "number_input":
             return st.number_input(
                 content["label"],
-                value=content["value"][input_format],
+                value=None,
                 format=content["format"],
+                min_value=content["min_value"],
+                max_value=content["max_value"]
             )
         if content["type"] == "selectbox":
             return st.selectbox(
@@ -148,6 +154,7 @@ def _main_page(self):
                     self.user_input[key] = self.generate_input_field(
                         self.user_input["input_format"], value
                     )
+
             submit_button = st.form_submit_button(
                 "Parse and bench", help=self.texts.Help.additional_parameters
             )
@@ -157,7 +164,11 @@ def _main_page(self):
             self._populate_results()
 
         if submit_button:
-            self._run_proteobench()
+            if self.user_input["input_csv"]:
+                self._run_proteobench()
+            else:
+                 error_message = st.error(":x: Please provide a result file")
+                 print(":x: Proteobench ran into a problem")
 
     def _populate_results(self):
         self.generate_results("", None, None, False)
@@ -253,11 +264,18 @@ def generate_results(
         st.session_state[RESULT_PERF] = result_performance
         st.session_state[ALL_DATAPOINTS] = all_datapoints
 
+        self.user_input[META_DATA] = st.file_uploader(
+                "Meta data for searches", help=self.texts.Help.meta_data_file
+            )
+        self.user_input["comments_for_submission"] = st.text_area("Comments for submission", 
+            placeholder="Anything else you want to let us know? Please specifically add changes in your search parameters here, that are not obvious from the parameter file.",
+            height=200)
         checkbox = st.checkbox("I confirm that the metadata is correct")
-        if checkbox:
+
+        if checkbox and self.user_input[META_DATA]:
             st.session_state["submission_ready"] = True
             submit_pr = st.button("I really want to upload it")
-            # TODO: check if parameters are filled
+            # TODO: update parameters of point to submit with parsed metadata parameters
             # submit_pr = False
             if submit_pr:
                 st.session_state[SUBMIT] = True
@@ -315,6 +333,10 @@ class Help:
             Please provide all details about the used parameter for the database search. They will facilitate the comparison.
         """
 
+        meta_data_file = """
+            Please add a file with meta data that contains all relevant information about your search parameters
+        """
+
     class Errors:
         missing_peptide_csv = """
             Upload a peptide CSV file or select the _Use example data_ checkbox.