diff --git a/resources/biseps b/resources/biseps
index 22d06ad27c3e77ce71ed3c7cd02117ef6a7a64c2..ee3bcb244d424a7ae1fad451a41885f3bdceb884 160000
--- a/resources/biseps
+++ b/resources/biseps
@@ -1 +1 @@
-Subproject commit 22d06ad27c3e77ce71ed3c7cd02117ef6a7a64c2
+Subproject commit ee3bcb244d424a7ae1fad451a41885f3bdceb884
diff --git a/resources/snakeReport.yaml b/resources/snakeReport.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..960a435bf90c716b9e29347a22b96b6ff88717cd
--- /dev/null
+++ b/resources/snakeReport.yaml
@@ -0,0 +1,126 @@
+name: /home/shatira/mnt/local_workflows/bisspropgui/resources/snakemake
+channels:
+ - anaconda
+ - bioconda
+ - defaults
+ - conda-forge
+dependencies:
+ - _libgcc_mutex=0.1=conda_forge
+ - _openmp_mutex=4.5=1_gnu
+ - amply=0.1.4=py_0
+ - appdirs=1.4.4=pyh9f0ad1d_0
+ - atk-1.0=2.36.0=h3371d22_4
+ - attrs=20.3.0=pyhd3deb0d_0
+ - brotlipy=0.7.0=py39h3811e60_1001
+ - ca-certificates=2020.10.14=0
+ - cairo=1.16.0=hf32fb01_1
+ - certifi=2021.5.30=py39h06a4308_0
+ - cffi=1.14.5=py39he32792d_0
+ - chardet=4.0.0=py39hf3d152e_1
+ - coincbc=2.10.5=hcee13e7_1
+ - configargparse=1.3=pyhd8ed1ab_0
+ - cryptography=3.4.4=py39h95dcef6_0
+ - datrie=0.8.2=py39h07f9747_1
+ - decorator=4.4.2=py_0
+ - docutils=0.16=py39hf3d152e_3
+ - expat=2.4.1=h2531618_2
+ - font-ttf-dejavu-sans-mono=2.37=h6964260_0
+ - font-ttf-inconsolata=2.001=hcb22688_0
+ - font-ttf-source-code-pro=2.030=h7457263_0
+ - font-ttf-ubuntu=0.83=h8b1ccd4_0
+ - fontconfig=2.13.1=h6c09931_0
+ - fonts-conda-ecosystem=1=0
+ - fonts-conda-forge=1=0
+ - freetype=2.10.4=h5ab3b9f_0
+ - fribidi=1.0.10=h7b6447c_0
+ - gdk-pixbuf=2.42.6=h04a7f16_0
+ - gettext=0.19.8.1=h9b4dc7a_1
+ - giflib=5.1.4=h14c3975_1
+ - gitdb=4.0.5=pyhd8ed1ab_1
+ - gitpython=3.1.13=pyhd8ed1ab_0
+ - glib=2.68.3=h9c3ff4c_0
+ - glib-tools=2.68.3=h9c3ff4c_0
+ - graphite2=1.3.14=h23475e2_0
+ - graphviz=2.48.0=h85b4f2f_0
+ - gtk2=2.24.33=h539f30e_1
+ - gts=0.7.6=h64030ff_2
+ - harfbuzz=2.8.2=h83ec7ef_0
+ - icu=68.1=h2531618_0
+ - idna=2.10=pyh9f0ad1d_0
+ - importlib-metadata=3.4.0=py39hf3d152e_0
+ - importlib_metadata=3.4.0=hd8ed1ab_0
+ - ipython_genutils=0.2.0=py_1
+ - jinja2=2.11.2=py_0
+ - jpeg=9d=h36c2ea0_0
+ - jsonschema=3.2.0=py_2
+ - jupyter_core=4.7.1=py39hf3d152e_0
+ - ld_impl_linux-64=2.35.1=hea4e1c9_2
+ - libblas=3.9.0=8_openblas
+ - libcblas=3.9.0=8_openblas
+ - libffi=3.3=h58526e2_2
+ - libgcc-ng=11.1.0=hc902ee8_8
+ - libgd=2.3.2=h78a0170_0
+ - libgfortran-ng=9.3.0=hff62375_18
+ - libgfortran5=9.3.0=hff62375_18
+ - libglib=2.68.3=h3e27bee_0
+ - libgomp=11.1.0=hc902ee8_8
+ - libiconv=1.16=h516909a_0
+ - liblapack=3.9.0=8_openblas
+ - libopenblas=0.3.12=pthreads_h4812303_1
+ - libpng=1.6.37=hbc83047_0
+ - librsvg=2.50.7=hc3c00ef_0
+ - libstdcxx-ng=9.3.0=h6de172a_18
+ - libtiff=4.2.0=h85742a9_0
+ - libtool=2.4.6=h7b6447c_1005
+ - libuuid=1.0.3=h1bed415_2
+ - libwebp=1.1.0=hd31223b_0
+ - libwebp-base=1.1.0=h7b6447c_3
+ - libxcb=1.14=h7b6447c_0
+ - libxml2=2.9.12=h72842e0_0
+ - lz4-c=1.9.2=heb0550a_3
+ - markupsafe=2.0.1=py39h27cfd23_0
+ - nbformat=5.1.2=pyhd8ed1ab_1
+ - ncurses=6.2=h58526e2_4
+ - networkx=2.5=py_0
+ - numpy=1.20.1=py39hdbf815f_0
+ - openssl=1.1.1k=h27cfd23_0
+ - pandas=1.2.2=py39ha9443f7_0
+ - pango=1.48.8=hb8ff022_0
+ - pcre=8.44=he6710b0_0
+ - pip=21.0.1=pyhd8ed1ab_0
+ - pixman=0.40.0=h7b6447c_0
+ - psutil=5.8.0=py39h3811e60_1
+ - pulp=2.3.1=py39hde42818_0
+ - pycparser=2.20=pyh9f0ad1d_2
+ - pygments=2.7.1=py_0
+ - pygraphviz=1.7=py39h78163bd_0
+ - pyopenssl=20.0.1=pyhd8ed1ab_0
+ - pyparsing=2.4.7=pyh9f0ad1d_0
+ - pyrsistent=0.17.3=py39h3811e60_2
+ - pysocks=1.7.1=py39hf3d152e_3
+ - python=3.9.2=hffdb5ce_0_cpython
+ - python-dateutil=2.8.1=py_0
+ - python_abi=3.9=1_cp39
+ - pytz=2021.1=pyhd3eb1b0_0
+ - pyyaml=5.4.1=py39h3811e60_0
+ - ratelimiter=1.2.0=py_1002
+ - readline=8.1=h27cfd23_0
+ - requests=2.25.1=pyhd3deb0d_0
+ - setuptools=52.0.0=py39h06a4308_0
+ - six=1.15.0=pyh9f0ad1d_0
+ - smmap=3.0.5=pyh44b312d_0
+ - snakemake-minimal=5.32.2=py_0
+ - sqlite=3.34.0=h74cdb3f_0
+ - tk=8.6.10=hed695b0_1
+ - toposort=1.6=pyhd8ed1ab_0
+ - traitlets=5.0.5=py_0
+ - tzdata=2021a=he74cb21_0
+ - urllib3=1.26.3=pyhd8ed1ab_0
+ - wheel=0.36.2=pyhd3deb0d_0
+ - wrapt=1.12.1=py39h3811e60_3
+ - xz=5.2.5=h516909a_1
+ - yaml=0.2.5=h516909a_0
+ - zipp=3.4.0=py_0
+ - zlib=1.2.11=h516909a_1010
+ - zstd=1.4.5=h9ceee32_0
+prefix: /home/shatira/mnt/local_workflows/bisspropgui/resources/snakemake
diff --git a/resources/snakemake.sh b/resources/snakemake.sh
index 239fa79cb674c6667c9695832c945905f05a1f08..1331d8dc1eac19b475996aa178f274905475fb2f 100755
--- a/resources/snakemake.sh
+++ b/resources/snakemake.sh
@@ -7,5 +7,7 @@ which python
source $sourceEnv/activate
cd $workflow
pwd
-$sourceEnv/snakemake --profile $profile --unlock > $profile/../../../biseps.txt
-$sourceEnv/snakemake --profile $profile --rerun-incomplete >> $profile/../../../biseps.txt
\ No newline at end of file
+$sourceEnv/snakemake --profile $profile --unlock &> $profile/../../../biseps.txt
+$sourceEnv/snakemake --profile $profile --rerun-incomplete &>> $profile/../../../biseps.txt
+$sourceEnv/snakemake --profile $profile --report $profile/../../../report.html
+
diff --git a/src/backend/helpers/spawnJbrowse.js b/src/backend/helpers/spawnJbrowse.js
index d76a540ca49b0c886ef92b3c63d20dfd7fae8954..b3db2528c34ffa7e5bf4eb0a414d7370f4667122 100644
--- a/src/backend/helpers/spawnJbrowse.js
+++ b/src/backend/helpers/spawnJbrowse.js
@@ -76,7 +76,7 @@ const spawnChild = (body) => {
});
if (exitCode) {
- throw new Error(`subprocess error exit ${exitCode}, ${error}`);
+ // throw new Error(`subprocess error exit ${exitCode}, ${error}`);
}
return data;
});
diff --git a/src/backend/models/Comparison.js b/src/backend/models/Comparison.js
index fdaae34e42a6c9675d418b0bdd76abcc4d8c2d77..232b91597f9bd72c9d25c8ccbd674ea74b117b97 100644
--- a/src/backend/models/Comparison.js
+++ b/src/backend/models/Comparison.js
@@ -7,7 +7,12 @@ const comparisonSchema = new Schema({
outdir: { type: String, required: true },
remoteDir: { type: String, required: false },
method: { type: String, required: false },
+ date: {
+ type: Date,
+ default: Date.now,
+ },
stat: { type: String, required: false },
+ contexts: [{ type: String, required: false }],
binSize: { type: Number, required: false },
pseudocountN: { type: Number, required: false },
pseudocountM: { type: Number, required: false },
diff --git a/src/backend/routes/api/comparisonController.js b/src/backend/routes/api/comparisonController.js
index b7b351f1ee6e7571f2f1bf215ac4d7f4b6d84d1e..76729e519b6947afe43482d942a9e411bd49a05e 100644
--- a/src/backend/routes/api/comparisonController.js
+++ b/src/backend/routes/api/comparisonController.js
@@ -13,7 +13,7 @@ const validateConfigurationInput = require("../../validation/comparisonConfigura
const Comparison = require("../../models/Comparison");
const User = require("../../models/User");
-// @route POST api/runs/Run
+// @route POST api/comparisons/Run
// @desc Run
// @access Public
@@ -51,6 +51,7 @@ router.post("/comparison", (req, res) => {
comparisons: req.body.comparisons,
method: req.body.method,
stat: req.body.stat,
+ contexts: req.body.contexts,
binSize: req.body.binSize,
pseudocountN: req.body.pseudocountN,
pseudocountM: req.body.pseudocountM,
@@ -105,6 +106,7 @@ router.post("/comparison", (req, res) => {
comparisons: req.body.comparisons,
method: req.body.method,
stat: req.body.stat,
+ contexts: req.body.contexts,
binSize: req.body.binSize,
pseudocountN: req.body.pseudocountN,
pseudocountM: req.body.pseudocountM,
@@ -154,4 +156,39 @@ router.get("/", function (req, res) {
}).populate("createdBy");
console.log("GET method");
});
+router.delete("/:id", function (req, res) {
+ const id = req.params.id;
+ const userId = req.user._id;
+ console.log(req.outdir);
+ console.log(req.user);
+ Comparison.deleteOne({ _id: id })
+ .then((result) => {
+ res.json(`Deleted ${id}`);
+ })
+ .catch((error) => console.error(error));
+ User.findByIdAndUpdate(
+ userId,
+ { $pull: { comparisons: id } },
+ { safe: true, upsert: true, new: true },
+ function (err, model) {
+ console.log(err);
+ }
+ );
+});
+
+router.post("/rerun", function (req, res) {
+ console.log(req.body);
+
+ if (!req.body.remote) {
+ const profile = path.join(req.body.outdir, "config/profiles/local");
+ spawnChild(req.body, profile);
+ console.log("Rerun Snakemake", profile);
+ } else {
+ const profile = path.join(req.body.remoteDir, "config/profiles/local");
+ const uniqueDir = req.body.outdir;
+ const uniqueDirRemote = req.body.remoteDir;
+ const homeDir = path.join(req.body.remoteDir, uniqueDirRemote);
+ spawnChild(req.body, profile, uniqueDir, uniqueDirRemote, homeDir);
+ }
+});
module.exports = router;
diff --git a/src/backend/routes/api/runController.js b/src/backend/routes/api/runController.js
index f60ea7b7ead126cb22e4c9a8c5531fb7e14b9f74..fc6de7d8fa07c35f290d63078fb0c5fdcd9fd6a4 100644
--- a/src/backend/routes/api/runController.js
+++ b/src/backend/routes/api/runController.js
@@ -161,13 +161,13 @@ router.get("/:id", function (req, res) {
});
router.post("/rerun", function (req, res) {
console.log(req.body);
+ const uniqueDir = req.body.outdir;
if (!req.body.remote) {
const profile = path.join(req.body.outdir, "config/profiles/local");
- spawnChild(req.body, profile);
+ spawnChild(req.body, profile, uniqueDir);
console.log("Rerun Snakemake", profile);
} else {
- const uniqueDir = req.body.outdir;
const uniqueDirRemote = req.body.remoteDir;
const homeDir = path.join(req.body.remoteDir, uniqueDirRemote);
spawnChild(req.body, profile, uniqueDir, uniqueDirRemote, homeDir);
diff --git a/src/backend/snakemake.js b/src/backend/snakemake.js
index 1de0fd507d324fb04e5694dbe28198794b057882..cc10116f9a3c98bca5178326864cea7a13e0afa3 100644
--- a/src/backend/snakemake.js
+++ b/src/backend/snakemake.js
@@ -5,7 +5,7 @@ const spawnChild = async (
uniqueDirRemote,
homeDir
) => {
- const { execFile, exec } = require("child_process");
+ const { execFile, exec, spawn } = require("child_process");
let Client = require("ssh2-sftp-client");
const path = require("path");
const env = path.join(__dirname, "../resources/snakemake/bin");
@@ -50,7 +50,7 @@ const spawnChild = async (
});
if (exitCode) {
- throw new Error(`subprocess error exit ${exitCode}, ${error}`);
+ // throw new Error(`subprocess error exit ${exitCode}, ${error}`);
}
const connect = require("ssh2-connect");
@@ -153,8 +153,19 @@ const spawnChild = async (
} else {
console.log("this is env", env);
console.log("this is profile", profile);
-
+ console.log(options);
console.log("this is workflow", workflow);
+ const logfile = `${uniqueDir}/biseps.txt`;
+ // const child = spawn(
+ // process.platform === "darwin" ? "bash" : "bash",
+
+ // [localScript, env, profile, workflow],
+ // options
+ // );
+ // const child = exec(
+ // `bash ${localScript} ${env} ${profile} ${workflow} > ${logfile}`,
+ // options
+ // );
const child = execFile(localScript, [env, profile, workflow], options);
let data = "";
@@ -172,7 +183,7 @@ const spawnChild = async (
});
if (exitCode) {
- throw new Error(`subprocess error exit ${exitCode}, ${error}`);
+ // throw new Error(`subprocess error exit ${exitCode}, ${error}`);
}
return data;
}
diff --git a/src/components/Comparisons/ComparisonForm.js b/src/components/Comparisons/ComparisonForm.js
index 410c5209f713ce54e76486c223b282f090f0c47e..84abfef715cf9adcd6af76fd843da38dc940a65a 100644
--- a/src/components/Comparisons/ComparisonForm.js
+++ b/src/components/Comparisons/ComparisonForm.js
@@ -41,6 +41,8 @@ import classnames from "classnames";
const path = require("path");
const fs = require("fs");
const http = require("http");
+const homedir = require("os").homedir();
+const bisepsTemp = path.join(homedir, ".bisepsTemp/");
function descendingComparator(a, b, orderBy) {
if (b[orderBy] < a[orderBy]) {
@@ -336,11 +338,18 @@ export default function ComparisonForm() {
let result = [];
data.map((row) => {
row.samples.map((sample) => {
- result.push(
- `${row.outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt`
- );
+ if (row.remote) {
+ result.push(
+ `${bisepsTemp}${sample.samplePath}.deduplicated.CX_report.txt`
+ );
+ } else {
+ result.push(
+ `${row.outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt`
+ );
+ }
});
});
+ console.log(result);
// const blankSample = {};
// const helper = {};
// const result = data.reduce(function (r, o) {
diff --git a/src/components/Comparisons/ComparisonTable.js b/src/components/Comparisons/ComparisonTable.js
index 502e382404d2aded2764cd105fc178c9eed43a9e..e86f6238bcf343ac645f3418244336cb968cdf78 100644
--- a/src/components/Comparisons/ComparisonTable.js
+++ b/src/components/Comparisons/ComparisonTable.js
@@ -21,12 +21,26 @@ import FolderIcon from "@material-ui/icons/Folder";
import DeleteIcon from "@material-ui/icons/Delete";
import { Link } from "react-router-dom";
import Iframe from "react-iframe";
-
+import Icon from "@material-ui/core/Icon";
+import RefreshIcon from "@material-ui/icons/Refresh";
+import Dialog from "@material-ui/core/Dialog";
+import DialogActions from "@material-ui/core/DialogActions";
+import DialogContent from "@material-ui/core/DialogContent";
+import DialogContentText from "@material-ui/core/DialogContentText";
+import DialogTitle from "@material-ui/core/DialogTitle";
+import TextField from "@material-ui/core/TextField";
+import { useAuth } from "../../hooks/useAuth";
+import Snackbar from "@material-ui/core/Snackbar";
+import MuiAlert from "@material-ui/lab/Alert";
+const path = require("path");
+function Alert(props) {
+ return <MuiAlert elevation={6} variant="filled" {...props} />;
+}
const fs = require("fs");
const portastic = require("portastic");
const electron = window.require("electron");
const remote = electron.remote;
-const { BrowserWindow } = remote;
+const { BrowserWindow, shell } = remote;
const http = require("http");
const useStyles = makeStyles((theme) => ({
@@ -38,6 +52,9 @@ const useStyles = makeStyles((theme) => ({
title: {
margin: theme.spacing(4, 0, 2),
},
+ button: {
+ margin: theme.spacing(1),
+ },
}));
export default function InteractiveList() {
@@ -45,6 +62,114 @@ export default function InteractiveList() {
const [dense, setDense] = useState(false);
const [secondary, setSecondary] = useState(false);
const [data, setData] = useState([]);
+ const [open, setOpen] = useState(false);
+ const [deleted, setDeleted] = useState("");
+ const [openAlert, setOpenAlert] = useState(false);
+ const { user } = useAuth();
+ const [errors, setErrors] = useState("");
+
+ const [selectedRow, setSelectedRow] = useState({});
+ const handleChange = (e) => {
+ setDeleted(e.target.value);
+ };
+ const handleDelete = (id, user, outdir, deleted) => {
+ console.log(id);
+
+ if (deleted === "DELETE") {
+ const request = {
+ user: user.user,
+ };
+ const token = sessionStorage.jwtToken;
+ const options = {
+ method: "DELETE",
+ path: `http://localhost/api/comparisons/${id}`,
+ socketPath: sessionStorage.Sock,
+ hostname: "unix",
+ port: null,
+ data: request,
+ headers: {
+ "Content-Type": "application/json",
+ Authorization: token,
+ },
+ };
+ const req = http.request(options, function (res) {
+ const chunks = [];
+ console.log("STATUS: " + res.statusCode);
+ console.log("HEADERS: " + JSON.stringify(res.headers));
+ res.on("data", function (chunk) {
+ chunks.push(chunk);
+ });
+ res.on("error", (err) => console.log(err));
+ res.on("end", function () {
+ const body = Buffer.concat(chunks).toString();
+
+ const jsbody = JSON.parse(body);
+ if (res.statusCode !== 200) {
+ console.log("failed post request");
+ } else {
+ console.log("successful post request");
+ }
+ });
+ });
+ req.on("error", (err) => console.log(err));
+ console.log(request);
+ req.end();
+ fs.rmdirSync(outdir, { recursive: true });
+
+ handleClose();
+ window.location.reload(false);
+ } else {
+ console.log("write DELETE to confirm");
+ setErrors("write DELETE to confirm or Cancel");
+ handleOpenAlert();
+ }
+ };
+ const handleCloseAlert = () => {
+ setOpenAlert(false);
+ };
+ const handleOpenAlert = () => {
+ setOpenAlert(true);
+ };
+ const handleRerun = (row) => {
+ const request = {
+ ...row,
+ };
+ const token = sessionStorage.jwtToken;
+ const options = {
+ method: "POST",
+ path: "http://localhost/api/comparisons/rerun",
+ socketPath: sessionStorage.Sock,
+ hostname: "unix",
+ port: null,
+ headers: {
+ "Content-Type": "application/json",
+ Authorization: token,
+ },
+ };
+ const req = http.request(options, function (res) {
+ const chunks = [];
+ console.log("STATUS: " + res.statusCode);
+ console.log("HEADERS: " + JSON.stringify(res.headers));
+ res.on("data", function (chunk) {
+ chunks.push(chunk);
+ });
+ res.on("error", (err) => console.log(err));
+ res.on("end", function () {
+ const body = Buffer.concat(chunks).toString();
+
+ const jsbody = JSON.parse(body);
+ if (res.statusCode !== 200) {
+ console.log("failed post request");
+ } else {
+ console.log("successful post request");
+ }
+ });
+ });
+ req.on("error", (err) => console.log(err));
+ req.write(JSON.stringify(request));
+ req.end();
+ window.location.reload(false);
+ };
useEffect(() => {
const fetchData = async () => {
const token = sessionStorage.jwtToken;
@@ -114,9 +239,69 @@ export default function InteractiveList() {
console.log(port);
});
};
+ const openInFolder = (path) => {
+ shell.showItemInFolder(path);
+ };
+ console.log(data);
+ const handleLog = (row) => {
+ console.log(row);
+ let remotePath = `${row.remoteDir}/biseps.txt`;
+ let localPath = row.date + "biseps.txt";
+ console.log(path.join(bisepsTemp, localPath));
+ sftp
+ .connect({
+ host: row.machine.hostname,
+ port: row.machine.port,
+ username: row.machine.username,
+ ...(!(row.machine.privateKey === "") && {
+ privateKey: require("fs").readFileSync(row.machine.privateKey),
+ }),
+ password: row.machine.password,
+ })
+ .then(() => {
+ console.log(remotePath);
+ console.log(localPath);
+ console.log("made it all the way here?");
+ if (!fs.existsSync(path.join(bisepsTemp, localPath))) {
+ return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
+ }
+ })
+ .then((data) => {
+ console.log("done done done");
+ createBrowserWindow(path.join(bisepsTemp, localPath));
+ sftp.end();
+ })
+ .catch((err) => {
+ console.log(err, "catch error");
+ setErrors("File isn't ready yet");
+ handleOpenAlert();
+ sftp.end();
+ });
+ };
+ const handleClickOpen = (row) => {
+ setSelectedRow(row);
+ setOpen(true);
+ };
+ const handleClose = () => {
+ setOpen(false);
+ };
return (
- <Container maxWidth="lg" className={classes.container} gutterBottom>
- <Grid container direction="column" alignItems="center" gutterBottom>
+ <Container maxWidth="lg" className={classes.container}>
+ <Snackbar
+ open={openAlert}
+ autoHideDuration={10000}
+ onClose={handleCloseAlert}
+ >
+ <Alert
+ onClose={handleCloseAlert}
+ severity={errors && errors.length > 0 ? "error" : "success"}
+ >
+ {errors && errors.length > 0
+ ? `Error : ${errors}`
+ : "Remote file copied locally successfully"}
+ </Alert>
+ </Snackbar>
+ <Grid container direction="column" alignItems="center">
<Box m={3}>
<Button
alignItems="center"
@@ -132,39 +317,134 @@ export default function InteractiveList() {
</Grid>
<Grid container spacing={2}>
+ <Dialog
+ key={selectedRow._id}
+ open={open}
+ onClose={handleClose}
+ aria-labelledby="form-dialog-title"
+ >
+ <DialogTitle id="form-dialog-title">Confirm Delete for</DialogTitle>
+ <DialogContent>
+ <DialogContentText>
+ This action will definitively delete all Run information as well
+ as corresponding files, please Confirm by writing DELETE in all
+ caps.
+ </DialogContentText>
+ <TextField
+ autoFocus
+ margin="dense"
+ id="confirmation"
+ value={deleted}
+ onChange={handleChange}
+ label="write DELETE"
+ type="text"
+ fullWidth
+ />
+ </DialogContent>
+ <DialogActions>
+ <Button onClick={handleClose} color="primary">
+ Cancel
+ </Button>
+ <Button
+ onClick={() => {
+ handleDelete(
+ selectedRow._id,
+ user,
+ selectedRow.outdir,
+ deleted
+ );
+ }}
+ color="primary"
+ >
+ Delete
+ </Button>
+ </DialogActions>
+ </Dialog>
{data.length > 0 ? (
data.map((row) => (
<Grid key={row._id} item xs={12} md={6}>
<Typography variant="h6" className={classes.title}>
- Comparison created by {row.createdBy.name}
+ Comparison created by {row.createdBy.name} on{" "}
+ {/* {row.date.split("T")[0]} */}
</Typography>
+ <div>
+ <Button
+ variant="contained"
+ color="secondary"
+ onClick={() => handleClickOpen(row)}
+ className={classes.button}
+ startIcon={<DeleteIcon />}
+ >
+ Delete
+ </Button>
+ {/* This Button uses a Font Icon, see the installation instructions in the Icon component docs. */}
+
+ <Button
+ variant="contained"
+ color="primary"
+ disabled={row.remote ? true : false}
+ onClick={() => openInFolder(`${row.outdir}/results`)}
+ className={classes.button}
+ endIcon={row.remote ? <Icon>cloud</Icon> : <Icon>send</Icon>}
+ >
+ {row.remote ? "Remote" : "Open Folder"}
+ </Button>
+ <Button
+ variant="contained"
+ color="default"
+ onClick={() => handleRerun(row)}
+ className={classes.button}
+ startIcon={<RefreshIcon />}
+ >
+ Rerun
+ </Button>
+
+ <Button
+ variant="contained"
+ color="default"
+ onClick={
+ row.remote
+ ? () => handleLog(row)
+ : () =>
+ createBrowserWindow(
+ path.join(row.outdir, "biseps.txt")
+ )
+ }
+ className={classes.button}
+ startIcon={<RefreshIcon />}
+ >
+ Show Log
+ </Button>
+ </div>
<div className={classes.demo}>
<List dense={dense}>
- {row.comparisons.map((comparison) => (
- <ListItem
- button
- // disabled={
- // fileExist(
- // `${row.outdir}/results/${sample.samplePath}/multiqc_report.html`
- // )
- // ? false
- // : true
- // }
- key={comparison._id}
- // onClick={() => {
- // const path = `${row.outdir}/results/${sample.samplePath}/multiqc_report.html`;
- // console.log(path);
- // createBrowserWindow(path);
- // }}
- >
- <ListItemAvatar>
- <Avatar>
- <FolderIcon />
- </Avatar>
- </ListItemAvatar>
- <ListItemText primary={comparison.name} />
- </ListItem>
- ))}
+ {row.comparisons.map((comparison) =>
+ row.contexts.map((context) => (
+ <ListItem
+ key={context}
+ button
+ disabled={
+ fileExist(
+ `${row.outdir}/${comparison.id}/${comparison.id}-CG.bed`
+ )
+ ? false
+ : true
+ }
+ onClick={() => {
+ const path = `${row.outdir}/${comparison.id}/${comparison.id}-${context}.bed`;
+ console.log(path);
+ createBrowserWindow(path);
+ }}
+ >
+ <ListItemAvatar>
+ <Avatar>
+ <FolderIcon />
+ </Avatar>
+ </ListItemAvatar>
+ <ListItemText primary={`${comparison.id}-${context}`} />
+ </ListItem>
+ ))
+ )}
{/* {generate(
<ListItem>
<ListItemAvatar>
diff --git a/src/components/Table/Table.js b/src/components/Table/Table.js
index 383c49af969b37619dd857828890f49939adbd89..49e2591499666c611c4e3a04d6b68ec6a342560f 100644
--- a/src/components/Table/Table.js
+++ b/src/components/Table/Table.js
@@ -100,6 +100,7 @@ import ActionRowing from "material-ui/svg-icons/action/rowing";
import uuid from "react-uuid";
import Snackbar from "@material-ui/core/Snackbar";
import MuiAlert from "@material-ui/lab/Alert";
+const { clipboard } = require("electron");
function Alert(props) {
return <MuiAlert elevation={6} variant="filled" {...props} />;
@@ -108,7 +109,6 @@ const fs = require("fs");
const path = require("path");
const portastic = require("portastic");
let Client = require("ssh2-sftp-client");
-let sftp = new Client();
const electron = window.require("electron");
const remote = electron.remote;
const { BrowserWindow, shell } = remote;
@@ -130,7 +130,7 @@ const useStyles = makeStyles((theme) => ({
margin: theme.spacing(1),
},
}));
-
+// let clipboardStr = clipboard.readText();
function generate(element) {
return [0, 1, 2].map((value) =>
React.cloneElement(element, {
@@ -160,6 +160,8 @@ export default function InteractiveList() {
setOpen(true);
};
const handleLog = (row) => {
+ let sftp = new Client();
+
console.log(row);
let remotePath = `${row.remoteDir}/biseps.txt`;
let localPath = row.date + "biseps.txt";
@@ -178,9 +180,8 @@ export default function InteractiveList() {
console.log(remotePath);
console.log(localPath);
console.log("made it all the way here?");
- if (!fs.existsSync(path.join(bisepsTemp, localPath))) {
- return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
- }
+
+ return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
})
.then((data) => {
console.log("done done done");
@@ -194,12 +195,125 @@ export default function InteractiveList() {
sftp.end();
});
};
+ const getFile = () => {
+ console.log("getfile");
+ };
+ // const downloadFiles = (row, reports) => {
+ // if (!fs.existsSync(bisepsTemp)) {
+ // fs.mkdirSync(bisepsTemp);
+ // }
+
+ // sftp
+ // .connect({
+ // host: row.machine.hostname,
+ // port: row.machine.port,
+ // username: row.machine.username,
+ // ...(!(row.machine.privateKey === "") && {
+ // privateKey: require("fs").readFileSync(row.machine.privateKey),
+ // }),
+ // password: row.machine.password,
+ // })
+ // .then(async () => {
+ // for (const report in reports) {
+ // if (
+ // !fs.existsSync(
+ // path.join(bisepsTemp, path.basename(reports[report]))
+ // )
+ // ) {
+ // console.log(report);
+ // console.log(path.join(bisepsTemp, path.basename(reports[report])));
+ // try {
+ // await sftp.fastGet(
+ // reports[report],
+ // path.join(bisepsTemp, path.basename(reports[report]))
+ // );
+ // } catch (err) {
+ // console.log(err);
+ // }
+ // }
+ // }
+ // // });
+ // })
+ // .finally((data) => {
+ // console.log("done done done");
+ // sftp.end();
+ // })
+ // .catch((err) => {
+ // console.log(err, "catch error");
+ // sftp.end();
+ // });
+ // };
+ const downloadFiles = (row, sample, tracks) => {
+ let sftp = new Client();
+
+ console.log(tracks);
+ console.log(row, sample);
+ console.log("download files");
+
+ console.log(homedir);
+ console.log(row.machine);
+ console.log(sample);
+
+ if (!fs.existsSync(bisepsTemp)) {
+ fs.mkdirSync(bisepsTemp);
+ }
+
+ sftp
+ .connect({
+ host: row.machine.hostname,
+ port: row.machine.port,
+ username: row.machine.username,
+ ...(!(row.machine.privateKey === "") && {
+ privateKey: require("fs").readFileSync(row.machine.privateKey),
+ }),
+ password: row.machine.password,
+ })
+ .then(async () => {
+ console.log("made it all the way here?");
+ // return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
+ // tracks.map((track) => {
+ // console.log(track);
+ for (const track in tracks) {
+ if (
+ !fs.existsSync(path.join(bisepsTemp, path.basename(tracks[track])))
+ ) {
+ console.log(path.join(bisepsTemp, path.basename(tracks[track])));
+ try {
+ await sftp.fastGet(
+ tracks[track],
+ path.join(bisepsTemp, path.basename(tracks[track]))
+ );
+ } catch (err) {
+ console.log(err);
+ }
+ }
+ }
+ // });
+ })
+ .finally((data) => {
+ createBrowserWindow(
+ path.join(
+ bisepsTemp,
+ path.join(`${sample.samplePath}-multiqc_report.html`)
+ )
+ );
+ console.log("done done done");
+ sftp.end();
+ })
+ .catch((err) => {
+ console.log(err, "catch error");
+ setErrors("File isn't ready yet");
+ handleOpenAlert();
+ sftp.end();
+ });
+ };
+
const handleRemoteFiles = (row, sample) => {
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
}
let remoteDir = row.remoteDir;
- let remotePath = `${remoteDir}/results/${sample.samplePath}/multiqc_report.html`;
+ let remotePath = `${remoteDir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
let localPath = sample.samplePath + "-multiqc_report.html";
sftp
.connect({
@@ -209,9 +323,7 @@ export default function InteractiveList() {
...(!(row.machine.privateKey === "") && {
privateKey: require("fs").readFileSync(row.machine.privateKey),
}),
- ...(row.machine.privateKey === "" && {
- password: row.machine.password,
- }),
+ password: row.machine.password,
})
.then(() => {
console.log(remotePath);
@@ -536,100 +648,122 @@ export default function InteractiveList() {
</DialogActions>
</Dialog>
{data.length > 0 ? (
- data.map((row) => (
- <Grid key={row._id} item xs={12} md={6}>
- <Typography variant="h6" className={classes.title}>
- Analysis created by {row.createdBy.name} on{" "}
- {row.date.split("T")[0]}
- </Typography>
+ data.map((row) => {
+ const reports = [];
+ row.samples.map((sample) => {
+ reports.push(
+ `${row.remoteDir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt`
+ );
+ });
+ return (
+ <Grid key={row._id} item xs={12} md={6}>
+ <Typography variant="h6" className={classes.title}>
+ {row.remote ? "Remote " : "Local "}Analysis created by{" "}
+ {row.createdBy.name} on {row.date.split("T")[0]}
+ </Typography>
- <div>
- <Button
- variant="contained"
- color="secondary"
- onClick={() => handleClickOpen(row)}
- className={classes.button}
- startIcon={<DeleteIcon />}
- >
- Delete
- </Button>
- {/* This Button uses a Font Icon, see the installation instructions in the Icon component docs. */}
+ <div>
+ <Button
+ variant="contained"
+ color="secondary"
+ onClick={() => handleClickOpen(row)}
+ className={classes.button}
+ startIcon={<DeleteIcon />}
+ >
+ Delete
+ </Button>
+ {/* This Button uses a Font Icon, see the installation instructions in the Icon component docs. */}
- <Button
- variant="contained"
- color="primary"
- disabled={row.remote ? true : false}
- onClick={() => openInFolder(`${row.outdir}/results`)}
- className={classes.button}
- endIcon={row.remote ? <Icon>cloud</Icon> : <Icon>send</Icon>}
- >
- {row.remote ? "Remote" : "Open Folder"}
- </Button>
- <Button
- variant="contained"
- color="default"
- onClick={() => handleRerun(row)}
- className={classes.button}
- startIcon={<RefreshIcon />}
- >
- Rerun
- </Button>
+ <Button
+ variant="contained"
+ color="primary"
+ onClick={
+ row.remote
+ ? () => clipboard.writeText(`${row.remoteDir}/results/`)
+ : () => openInFolder(`${row.outdir}/results`)
+ }
+ className={classes.button}
+ endIcon={
+ row.remote ? <Icon>cloud</Icon> : <Icon>send</Icon>
+ }
+ >
+ {row.remote ? "Copy Remote Path" : "Open Folder"}
+ </Button>
+ <Button
+ variant="contained"
+ color="default"
+ onClick={() => handleRerun(row)}
+ className={classes.button}
+ startIcon={<RefreshIcon />}
+ >
+ Rerun
+ </Button>
- <Button
- variant="contained"
- color="default"
- onClick={
- row.remote
- ? () => handleLog(row)
- : () =>
- createBrowserWindow(
- path.join(row.outdir, "biseps.txt")
- )
- }
- className={classes.button}
- startIcon={<RefreshIcon />}
- >
- Show Log
- </Button>
- </div>
- <div className={classes.demo}>
- <List dense={dense}>
- {row.samples.map((sample) => (
- <ListItem
- button
- disabled={
- row.remote
- ? false
- : fileExist(
- `${row.outdir}/results/${sample.samplePath}/multiqc_report.html`
+ <Button
+ variant="contained"
+ color="default"
+ onClick={
+ row.remote
+ ? () => handleLog(row)
+ : () =>
+ createBrowserWindow(
+ path.join(row.outdir, "biseps.txt")
)
- ? false
- : true
- }
- key={sample._id}
- onClick={() => {
- if (row.remote) {
- handleRemoteFiles(row, sample);
- } else {
- console.log(sample);
- const path = `${row.outdir}/results/${sample.samplePath}/multiqc_report.html`;
- console.log(path);
- createBrowserWindow(path);
- }
- }}
- >
- <ListItemAvatar>
- <Avatar>
- <FolderIcon />
- </Avatar>
- </ListItemAvatar>
- <ListItemText
- primary={`${sample.sample} MultiQC Report`}
- secondary={secondary ? "Secondary text" : null}
- />
- </ListItem>
- ))}
- {/* {generate(
+ }
+ className={classes.button}
+ startIcon={<RefreshIcon />}
+ >
+ Show Log
+ </Button>
+ </div>
+ <div className={classes.demo}>
+ <List dense={dense}>
+ {row.samples.map((sample) => {
+ const outdir = row.remote
+ ? `${row.remoteDir}`
+ : row.outdir;
+
+ const Multiqc = `${outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
+ const CX = `${outdir}/results/${sample.samplePath}/methylation_extraction_bismark/${sample.samplePath}.deduplicated.CX_report.txt`;
+ const tracks = [Multiqc, CX];
+ return (
+ <ListItem
+ button
+ disabled={
+ row.remote
+ ? false
+ : fileExist(
+ `${row.outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`
+ )
+ ? false
+ : true
+ }
+ key={sample._id}
+ onClick={() => {
+ if (row.remote) {
+ // handleRemoteFiles(row, sample);
+ downloadFiles(row, sample, tracks);
+ } else {
+ console.log(sample);
+ const path = `${row.outdir}/results/${sample.samplePath}/${sample.samplePath}-multiqc_report.html`;
+ console.log(path);
+ createBrowserWindow(path);
+ }
+ }}
+ >
+ <ListItemAvatar>
+ <Avatar>
+ <FolderIcon />
+ </Avatar>
+ </ListItemAvatar>
+ <ListItemText
+ primary={`${sample.sample} MultiQC Report`}
+ secondary={secondary ? "Secondary text" : null}
+ />
+ </ListItem>
+ );
+ })}
+ {/* {generate(
<ListItem>
<ListItemAvatar>
<Avatar>
@@ -647,10 +781,11 @@ export default function InteractiveList() {
</ListItemSecondaryAction>
</ListItem>
)} */}
- </List>
- </div>
- </Grid>
- ))
+ </List>
+ </div>
+ </Grid>
+ );
+ })
) : (
<Grid
key={0}
diff --git a/src/components/Visualization/VisualizationFill.js b/src/components/Visualization/VisualizationFill.js
index 570dd17ef21b6443609746ab01245b7ff5f768b9..d86ca52ca080f1e0178dadfc90a6082be199958a 100644
--- a/src/components/Visualization/VisualizationFill.js
+++ b/src/components/Visualization/VisualizationFill.js
@@ -48,6 +48,9 @@ const useStyles = makeStyles((theme) => ({
maxWidth: 360,
backgroundColor: theme.palette.background.paper,
},
+ button: {
+ margin: theme.spacing(1),
+ },
}));
export default function VisualizationFill() {
@@ -156,9 +159,7 @@ export default function VisualizationFill() {
if (!fs.existsSync(bisepsTemp)) {
fs.mkdirSync(bisepsTemp);
}
- let remoteDir = row.remoteDir;
- let remotePath = `${remoteDir}/results/${sample.samplePath}/multiqc_report.html`;
- let localPath = sample.samplePath + "-multiqc_report.html";
+
sftp
.connect({
host: row.machine.hostname,
@@ -170,8 +171,6 @@ export default function VisualizationFill() {
password: row.machine.password,
})
.then(async () => {
- console.log(remotePath);
- console.log(localPath);
console.log("made it all the way here?");
// return sftp.fastGet(remotePath, path.join(bisepsTemp, localPath));
// tracks.map((track) => {
@@ -339,6 +338,7 @@ export default function VisualizationFill() {
aria-label="outlined primary button group"
>
<Button
+ className={classes.button}
alignItems="center"
variant="contained"
color="default"
@@ -347,6 +347,7 @@ export default function VisualizationFill() {
Start Jbrowse{" "}
</Button>
<Button
+ className={classes.button}
onClick={handleReset}
alignItems="center"
variant="contained"
@@ -355,6 +356,7 @@ export default function VisualizationFill() {
Reset Jbrowse{" "}
</Button>
<Button
+ className={classes.button}
onClick={handlePopulate}
alignItems="center"
variant="contained"
@@ -408,7 +410,7 @@ export default function VisualizationFill() {
);
})}
</List>
- <List subheader={result.length > 0 ? "Bam Files" : ""}>
+ <List subheader={result.length > 0 ? "Alignments" : ""}>
{data.map((row) => {
const labelId = `checkbox-list-label-${row}`;
return (
diff --git a/src/hooks/useConfig.js b/src/hooks/useConfig.js
index a4206409ce1250fd42a6d34fac2a2ba30c069f47..5eaabc392f35d95a14c99f49939b529d85832aae 100644
--- a/src/hooks/useConfig.js
+++ b/src/hooks/useConfig.js
@@ -20,7 +20,6 @@ const useProvideConfig = () => {
genome: "",
outdir: "",
remoteDir: "",
-
machine: {},
minlen: 80,
minscore: -0.6,