diff --git a/webinterface/pages/DDA_Quant.py b/webinterface/pages/DDA_Quant.py index 84797eff..2773a05d 100644 --- a/webinterface/pages/DDA_Quant.py +++ b/webinterface/pages/DDA_Quant.py @@ -19,7 +19,7 @@ from streamlit_extras.let_it_rain import rain import uuid -#from proteobench.github.gh import clone_pr, write_json_local_development +# from proteobench.github.gh import clone_pr, write_json_local_development logger = logging.getLogger(__name__) @@ -111,12 +111,12 @@ def _main_page(self): The raw files used for this module were acquired on an Orbitrap Q-Exactive H-FX (ThermoScientific). They can be downloaded from the proteomeXchange repository PXD028735. You can download them here: - [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw) - [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw) - [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw) - [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw) - [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw) - [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw) + [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw) + [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw) + [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw) + [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw) + [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw) + [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw) **It is imperative not to rename the files once downloaded!** """ @@ -155,7 +155,7 @@ 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 ) @@ -168,7 +168,7 @@ def _main_page(self): if self.user_input["input_csv"]: self._run_proteobench() else: - error_message = st.error(":x: Please provide a result file") + error_message = st.error(":x: Please provide a result file") def _populate_results(self): self.generate_results("", None, None, False) @@ -176,14 +176,14 @@ def _populate_results(self): def _sidebar(self): """Format sidebar.""" st.sidebar.image("https://github.com/Proteobench/ProteoBench/raw/Add-logos/webinterface/logos/logo_proteobench/proteobench-logo-horizontal.svg", - width=300) + width=300) st.sidebar.image("https://raw.githubusercontent.com/Proteobench/ProteoBench/b6d40e853df10e486e0000aed9fe7b5ddc3f9286/webinterface/logos/logo_funding/DDSA_PrimaryLogo_Screen_Black.svg", - width=300) + width=300) mainlogo_list = [ "https://github.com/Proteobench/ProteoBench/blob/Add-logos/webinterface/logos/logo_funding/eubic_logo_transparent.png?raw=true", "https://github.com/Proteobench/ProteoBench/blob/Add-logos/webinterface/logos/logo_funding/eupa-logo-transparent.png?raw=true" ] - for i in range(0,len(mainlogo_list),3): + for i in range(0, len(mainlogo_list), 3): st.sidebar.image( mainlogo_list[i:i+3], width=140, @@ -196,7 +196,8 @@ def _run_proteobench(self): # Run Proteobench st.header("Running Proteobench") status_placeholder = st.empty() - status_placeholder.info(":hourglass_flowing_sand: Running Proteobench...") + status_placeholder.info( + ":hourglass_flowing_sand: Running Proteobench...") if ALL_DATAPOINTS not in st.session_state: st.session_state[ALL_DATAPOINTS] = None @@ -276,13 +277,14 @@ def generate_results( 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", + "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 and self.user_input[META_DATA]: st.session_state["submission_ready"] = True submit_pr = st.button("I really want to upload it")