Merge pull request #49 from MannLabs/FEAT-multi-fasta-gui

FEAT multi fasta gui

alphadia/cli.py

@@ -39,7 +39,7 @@ def gui():
     help="Extract DIA precursors from a list of raw files using a spectral library."
 )
 @click.argument(
-    "output-location",
+    "output-directory",
     type=click.Path(exists=True, file_okay=False, dir_okay=True),
     required=False,
 )
@@ -119,33 +119,34 @@ def extract(**kwargs):
         with open(kwargs['config'], 'r') as f:
             config_update = yaml.safe_load(f)
 
-    output_location = None
-    if kwargs['output_location'] is not None:
-        output_location = kwargs['output_location']
+    output_directory = None
+    if kwargs['output_directory'] is not None:
+        output_directory = kwargs['output_directory']
 
-    if "output" in config_update:
-        output_location = config_update['output']
+    if "output_directory" in config_update:
+        output_directory = config_update['output_directory']
 
-    if output_location is None:
-        logging.error("No output location specified.")
+    if output_directory is None:
+        logging.error("No output directory specified.")
         return
 
-    reporting.init_logging(kwargs['output_location'])
+    reporting.init_logging(kwargs['output_directory'])
     logger = logging.getLogger()
 
     # assert input files have been specified
-    files = None
+    files = []
     if kwargs['file'] is not None:
         files = list(kwargs['file'])
 
     if kwargs['directory'] is not None:
         files += [os.path.join(kwargs['directory'], f) for f in os.listdir(kwargs['directory'])]
 
-    if "files" in config_update:
-        files += config_update['files'] if type(config_update['files']) is list else [config_update['files']]
+    if "raw_file_list" in config_update:
+        files += config_update['raw_file_list'] if type(config_update['raw_file_list']) is list else [config_update['raw_file_list']]
 
+    print(config_update)
     if (files is None) or (len(files) == 0):
-        logging.error("No files specified.")
+        logging.error("No raw files specified.")
         return
 
     # assert library has been specified
@@ -164,7 +165,7 @@ def extract(**kwargs):
     for f in files:
         logger.progress(f"  {f}")
     logger.progress(f"Using library {library}.")
-    logger.progress(f"Saving output to {output_location}.")
+    logger.progress(f"Saving output to {output_directory}.")
 
     try:
 
@@ -178,7 +179,7 @@ def extract(**kwargs):
         #config_update = eval(kwargs['config_update']) if kwargs['config_update'] else None
 
         plan = Plan(
-            output_location,
+            output_directory,
             files,
             library,
             config_update = config_update

alphadia/libtransform.py

@@ -165,6 +165,7 @@ class AnnotateFasta(ProcessingStep):
     def __init__(self, 
                 fasta_path_list: typing.List[str],
                 drop_unannotated: bool = True,
+                drop_decoy: bool = True,
                 ) -> None:
         """Annotate the precursor dataframe with protein information from a FASTA file.
         Expects a `SpecLibBase` object as input and will return a `SpecLibBase` object.
@@ -183,6 +184,7 @@ def __init__(self,
         super().__init__()
         self.fasta_path_list = fasta_path_list
         self.drop_unannotated = drop_unannotated
+        self.drop_decoy = drop_decoy
 
     def validate(self, input: SpecLibBase) -> bool:
         """Validate the input object. It is expected that the input is a `SpecLibBase` object and that all FASTA files exist."""
@@ -201,6 +203,11 @@ def forward(self, input: SpecLibBase) -> SpecLibBase:
         protein_df = fasta.load_fasta_list_as_protein_df(
             self.fasta_path_list
         )
+
+        if self.drop_decoy and 'decoy' in input.precursor_df.columns:
+            logger.info(f'Dropping decoys from input library before annotation')
+            input._precursor_df = input._precursor_df[input._precursor_df['decoy'] == 0]
+
         input._precursor_df = fasta.annotate_precursor_df(input.precursor_df, protein_df)
 
         if self.drop_unannotated and 'cardinality' in input._precursor_df.columns:

alphadia/planning.py

@@ -141,8 +141,8 @@ def spectral_library(
 
     def load_library(self, spec_lib_path):
 
-        if 'fasta_files' in self.config:
-            fasta_files = self.config['fasta_files']
+        if 'fasta_list' in self.config:
+            fasta_files = self.config['fasta_list']
         else:
             fasta_files = []
 

gui/src/main/electron.js

@@ -79,7 +79,7 @@ async function handleGetUtilisation (event) {
 
 function handleStartWorkflow(workflow) {
 
-    const workflowFolder = workflow.output.path
+    const workflowFolder = workflow.output_directory.path
     const config = workflowToConfig(workflow)
 
     // check if workflow folder exists

gui/src/main/modules/cmd.js

@@ -74,7 +74,6 @@ const CondaEnvironment = class {
         }).then(() => {
             return this.checkCondaVersion().then((info) => {
 
-
                 // executing conda run -n envName in an alreadt activated conda environment causes an error
                 // this is a workaround
                 // check if info exist and active_prefix is not null
@@ -90,6 +89,9 @@ const CondaEnvironment = class {
                     this.checkPythonVersion(),
                     this.checkAlphadiaVersion(),
                 ])
+            }).catch((error) => {
+                console.log("Conda not found", "Conda could not be found on your system. Please make sure conda is installed and added to your PATH." + error)
+                dialog.showErrorBox("Conda not found", "Conda could not be found on your system. Please make sure conda is installed and added to your PATH." + error)
             })
         }).then(() => {
             this.ready = [this.exists.conda, this.exists.python, this.exists.alphadia].every(Boolean);
@@ -102,8 +104,11 @@ const CondaEnvironment = class {
 
     discoverCondaPATH(){
         return new Promise((resolve, reject) => {
-
-            const paths = [this.profile.config.conda.path, ...condaPATH(os.userInfo().username, os.platform())]
+
+            // 1st choice: conda is already in PATH
+            // 2nd choice: conda path from profile setting is used
+            // 3rd choice: default conda paths are tested
+            const paths = ["", this.profile.config.conda.path, ...condaPATH(os.userInfo().username, os.platform())]
             Promise.all(paths.map((path) => {
                 return testCommand("conda", path)
                 })).then((codes) => {

gui/src/main/modules/workflows.js

@@ -33,10 +33,10 @@ function validateWorkflow(workflow) {
     if (!workflow.hasOwnProperty('library')) {
         throw new Error('Workflow does not have a library field.')
     }
-    if (!workflow.hasOwnProperty('fasta')) {
+    if (!workflow.hasOwnProperty('fasta_list')) {
         throw new Error('Workflow does not have a fasta field.')
     }
-    if (!workflow.hasOwnProperty('files')) {
+    if (!workflow.hasOwnProperty('raw_file_list')) {
         throw new Error('Workflow does not have a files field.')
     }
     if (!workflow.hasOwnProperty('config')) {
@@ -52,18 +52,18 @@ function validateWorkflow(workflow) {
     }
 
     // make sure fasta has the following fields: [active, path]
-    if (!workflow.fasta.hasOwnProperty('active')) {
+    if (!workflow.fasta_list.hasOwnProperty('active')) {
         throw new Error('Workflow fasta does not have an active field.')
     }
-    if (!workflow.fasta.hasOwnProperty('path')) {
+    if (!workflow.fasta_list.hasOwnProperty('path')) {
         throw new Error('Workflow fasta does not have a path field.')
     }
 
     // make sure files has the following fields: [active, path]
-    if (!workflow.files.hasOwnProperty('active')) {
+    if (!workflow.raw_file_list.hasOwnProperty('active')) {
         throw new Error('Workflow files does not have an active field.')
     }
-    if (!workflow.files.hasOwnProperty('path')) {
+    if (!workflow.raw_file_list.hasOwnProperty('path')) {
         throw new Error('Workflow files does not have a path field.')
     }
 
@@ -82,16 +82,16 @@ function workflowToConfig(workflow) {
         output["library"] = workflow.library.path
     }
 
-    if (workflow.fasta.path != "") {
-        output["fasta"] = workflow.fasta.path
+    if (workflow.fasta_list.path != "") {
+        output["fasta_list"] = workflow.fasta_list.path
     }
 
-    if (workflow.files.path != "") {
-        output["files"] = workflow.files.path
+    if (workflow.raw_file_list.path != "") {
+        output["raw_file_list"] = workflow.raw_file_list.path
     }
 
-    if (workflow.output.path != "") {
-        output["output"] = workflow.output.path
+    if (workflow.output_directory.path != "") {
+        output["output_directory"] = workflow.output_directory.path
     }
 
     workflow.config.forEach((config) => {

gui/src/renderer/components/MultiSelect.js

@@ -0,0 +1,80 @@
+import { Grid, Stack, Typography, Tooltip, Button } from "@mui/material";
+import HelpOutlineIcon from "@mui/icons-material/HelpOutline";
+
+const MultiSelect = ({
+    label = "File",
+    active = true,
+    type = "file",
+    path = [],
+    tooltipText = "",
+    onChange = () => {},
+    ...props
+}) => {
+
+    // set color based on activity status
+    const color = active ? "primary" : "divider";
+    // get file name from path
+    // eslint-disable-next-line no-useless-escape
+    const fileNames = path.map((path) => path.replace(/^.*[\\\/]/, ''));
+
+    // handle select button click
+
+    let handleSelect = () => {}
+
+    if (type === "folder") {
+        handleSelect = () => {
+            window.electronAPI.getMultipleFolders().then((folder) => {
+                onChange(folder);
+            }).catch((err) => {
+                console.log(err);
+            })
+        }
+    } else {
+        handleSelect = () => {
+            window.electronAPI.getMultipleFiles().then((file) => {
+                onChange(file);
+            }).catch((err) => {
+                console.log(err);
+            })
+        }
+    }
+
+    return (
+    <Grid container spacing={2} sx={{color, minHeight:"100px"}} wrap="nowrap">
+        <Grid item xs={3}>
+            <Stack direction="row" alignItems="center" gap={1}>
+                <Typography component="span">{label}</Typography>
+                <Tooltip title = {active && tooltipText} sx= {{color}}>
+                    <HelpOutlineIcon fontSize="small" />
+                </Tooltip>
+            </Stack>
+        </Grid>
+        <Grid item xs={6} zeroMinWidth sx={{overflow: 'hidden', textOverflow: 'ellipsis'}}>
+            <Typography component="span" noWrap >
+                {
+                    // iterate fileNames and display with line break
+                    fileNames.map((fileName) => {
+                        return (
+                            <Typography component="span" noWrap key={fileName}>
+                                {fileName}
+                                <br/>
+                            </Typography>
+                        )
+                    })
+                }
+            </Typography>
+
+        </Grid>
+        <Grid item xs={3} position={'relative'}>
+            <Button 
+                variant="outlined" 
+                sx={{float: 'right', ml:1, minWidth: "115px"}} 
+                disabled={!active} 
+                onClick={handleSelect}>
+                Select Files
+            </Button>
+        </Grid>
+    </Grid>
+)}
+
+export default MultiSelect;

gui/src/renderer/components/RunButton.js

@@ -12,10 +12,10 @@ const validateMethod = (method) => {
     if (method.library.required && (method.library.path === "")) {
         return {valid: false, message: "Please select a spectral library."}
     }
-    if (method.fasta.required && (method.fasta.path === "")) {
+    if (method.fasta_list.required && (method.fasta_list.path === "")) {
         return {valid: false, message: "Please select a fasta file."}
     }
-    if (method.files.required && (method.files.path.length === 0)) {
+    if (method.raw_file_list.required && (method.raw_file_list.path.length === 0)) {
         return {valid: false, message: "Please select at least one Bruker .d folder."}
     }
     return {valid: true, message: ""}

gui/src/renderer/components/index.js

@@ -12,3 +12,4 @@ export {default as SingleSelect} from './SingleSelect'
 export {default as StyledLink} from './StyledLink'
 export {default as UtilMonitor} from './UtilMonitor'
 export {default as WorkflowMenu} from './WorkflowMenu'
+export {default as MultiSelect} from './MultiSelect'

gui/src/renderer/logic/context.js

@@ -7,16 +7,17 @@ const initialMethod = {
         active: false,
         path: ""
     },
-    fasta: {
+    fasta_list: {
         active: false,
-        path: ""
+        path: [
+        ]
     },
-    files: {
+    raw_file_list: {
         active: false,
         path: [
         ]
     },
-    output: {
+    output_directory: {
         active: true,
         path: ""
     },
@@ -31,11 +32,11 @@ export function methodReducer(method, action) {
             return {...method, library: {...method.library, path: action.path}}
 
         case 'updateFasta':
-            return {...method, fasta: {...method.fasta, path: action.path}}
+            return {...method, fasta_list: {...method.fasta_list, path: action.path}}
 
         case 'updateFiles':
             console.log(action)
-            return {...method, files: {...method.files, path: action.path}}
+            return {...method, raw_file_list: {...method.raw_file_list, path: action.path}}
 
         case 'updateParameter':
             console.log(action)
@@ -63,7 +64,7 @@ export function methodReducer(method, action) {
 
         case "updateOutput":
             console.log(action)
-            return {...method, output: {...method.output, path: action.path}}
+            return {...method, output_directory: {...method.output_directory, path: action.path}}
         default:
             throw new Error(`Unhandled action type: ${action.type}`);
     }

gui/src/renderer/pages/Files.js

@@ -3,7 +3,7 @@ import styled from '@emotion/styled'
 import { useMethod, useMethodDispatch } from '../logic/context'
 
 import { Box } from '@mui/material'
-import { SingleSelect, InputFileSelect, FileViewer } from '../components'
+import { SingleSelect, MultiSelect, InputFileSelect, FileViewer } from '../components'
 
 const FullWidthBox = styled(Box)(({ theme }) => ({
     width: '100%'
@@ -31,23 +31,23 @@ const Files = () => {
                     />
                 </FullWidthBox>
                 <FullWidthBox>
-                    <SingleSelect 
-                            label="Fasta File"
-                            active={method.fasta.active}
-                            path={method.fasta.path}
+                    <MultiSelect 
+                            label="Fasta File(s)"
+                            active={method.fasta_list.active}
+                            path={method.fasta_list.path}
                             tooltipText="Select the fasta file which you would like to use."
                             onChange={(path) => {dispatch({type: 'updateFasta', path: path})}}
                     />
                 </FullWidthBox>
                 <FullWidthBox>
                     <InputFileSelect
-                            active={method.files.active}
-                            path={method.files.path}
+                            active={method.raw_file_list.active}
+                            path={method.raw_file_list.path}
                             onChange={(path) => {dispatch({type: 'updateFiles', path: path})}}
                     />
                 </FullWidthBox>
                 <FullWidthBox sx={{flexGrow: 1}}>
-                    <FileViewer path={method.files.path}/>
+                    <FileViewer path={method.raw_file_list.path}/>
                 </FullWidthBox>
         </Box>  
     )