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Henry committed Oct 12, 2023
1 parent 7e08524 commit c5b3bd6
Showing 1 changed file with 19 additions and 17 deletions.
36 changes: 19 additions & 17 deletions webinterface/pages/DDA_Quant.py
Original file line number Diff line number Diff line change
Expand Up @@ -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__)

Expand Down Expand Up @@ -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!**
"""
Expand Down Expand Up @@ -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
)
Expand All @@ -168,22 +168,22 @@ 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)

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,
Expand All @@ -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
Expand Down Expand Up @@ -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")
Expand Down

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