From 906436bafa5ee9949893ae04ab2c21ff29466bdd Mon Sep 17 00:00:00 2001
From: Antti Luomi <antti.luomi@id.ethz.ch>
Date: Mon, 25 Mar 2019 12:20:38 +0100
Subject: [PATCH] Paging of datasets and population of working directory in
download dialog
---
README.md | 20 +++
jupyter-openbis-extension/sample.py | 7 +-
.../static/downloadDialog.js | 142 ++++++++++++------
jupyter-openbis-extension/static/state.js | 8 +-
.../static/uploadDialog.js | 19 +--
vagrant/files/setup-vagrant.sh | 3 +
6 files changed, 139 insertions(+), 60 deletions(-)
diff --git a/README.md b/README.md
index 57e78cd..130717d 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,26 @@ The jupyter-openbis-extension needs at least **Python 3.3** in order to run. The
This extension has been successfully tested with Safari 12.0.3, Chrome 72.0 and Firefox 66.0. There is a known incompatibility before Firefox 61.0b13.
+## Development with Vagrant
+
+If you want to use a predefined development environment, follow these steps:
+
+1. Install latest version of VirtualBox (<https://www.virtualbox.org>)
+
+2. Install latest version of Vagrant (<https://www.vagrantup.com/downloads.html>)
+
+3. vagrant plugin install vagrant-vbguest vagrant-notify-forwarder vagrant-disksize
+
+4. cd vagrant
+
+5. vagrant up
+
+After the setup is complete, you'll have
+
+* Jupyter with openBIS extension running at <http://localhost:8888>.
+* openBIS running at <http://localhost:8122>, with credentials admin/password.
+* Experiment /DEFAULT/DEFAULT with a lot of datasets for testing.
+
## Install the extension
If you haven't done yet: download the latest jupyter-openbis-extension from pip. It will automatically install the various dependencies, e.g. Pandas and NumPy.
diff --git a/jupyter-openbis-extension/sample.py b/jupyter-openbis-extension/sample.py
index ace30bf..752dfe7 100644
--- a/jupyter-openbis-extension/sample.py
+++ b/jupyter-openbis-extension/sample.py
@@ -2,6 +2,8 @@ from notebook.base.handlers import IPythonHandler
import numpy as np
import os
from .connection import openbis_connections
+from urllib.parse import parse_qs
+
def get_entity_for_identifier(conn, identifier):
@@ -68,8 +70,9 @@ class SampleHandler(IPythonHandler):
})
return None
- start_with = params.get('start_with', None)
- count = params.get('count', None)
+ querystring = parse_qs(self.request.query)
+ start_with = querystring.get('start_with', ['0'])[0]
+ count = querystring.get('count', ['10'])[0]
datasets = get_datasets(entity, start_with=start_with, count=count)
if datasets is not None:
diff --git a/jupyter-openbis-extension/static/downloadDialog.js b/jupyter-openbis-extension/static/downloadDialog.js
index a78bb13..08f0f92 100644
--- a/jupyter-openbis-extension/static/downloadDialog.js
+++ b/jupyter-openbis-extension/static/downloadDialog.js
@@ -23,9 +23,15 @@ define([
}
}
- function show_datasets_table(data, datasets_table) {
+ function show_datasets_table(env, data, datasets_table, downloadPath, entityIdentifier) {
+ if (downloadPath.value === '') {
+ downloadPath.value = data.cwd
+ }
+
var table = document.createElement("TABLE")
table.className = "table-bordered table-striped table-condensed text-nowrap"
+ table.style.width = "100%"
+
var thead = table.createTHead()
var t_row = thead.insertRow()
var titles = ['', 'permId', 'Type', 'Experiment', 'Registration Date', 'Status', 'Size']
@@ -36,10 +42,12 @@ define([
for (dataSet of data.dataSets) {
- var permId = document.createElement("INPUT")
+ const permId = document.createElement("INPUT")
permId.type = "checkbox"
permId.name = "permId"
permId.value = dataSet.permId
+ permId.checked = state.selectedDatasets.has(permId.value)
+ permId.onclick = () => permId.checked ? state.selectedDatasets.add(permId.value) : state.selectedDatasets.delete(permId.value)
var row = tbody.insertRow()
row.insertCell().appendChild(permId)
@@ -55,6 +63,80 @@ define([
datasets_table.removeChild(datasets_table.firstChild);
}
datasets_table.appendChild(table)
+
+ const totalCount = parseInt(data.totalCount)
+ const count = parseInt(data.count)
+ const startWith = parseInt(data.start_with)
+ const hasNext = startWith + count < totalCount
+ const hasPrevious = startWith > 0
+ const nextCmd = () => getDatasets(env, startWith+5, 5, entityIdentifier, datasets_table, downloadPath)
+ const previousCmd = () => getDatasets(env, startWith-5, 5, entityIdentifier, datasets_table, downloadPath)
+
+ var previous = document.createElement("A")
+ var linkText = document.createTextNode("<<< Previous")
+ previous.appendChild(linkText)
+ previous.href = "#"
+ previous.onclick = previousCmd
+
+ var next = document.createElement("A")
+ var linkText = document.createTextNode("Next >>>")
+ next.appendChild(linkText)
+ next.href = "#"
+ next.onclick = nextCmd
+ next.style.float="right"
+
+ var paging = document.createElement("DIV")
+ paging.style.width = "100%"
+ if (hasPrevious) {
+ paging.appendChild(previous)
+ }
+ if (hasNext) {
+ paging.appendChild(next)
+ }
+
+ datasets_table.appendChild(paging)
+ }
+
+ function getDatasets(env, startWith, count, entityIdentifier, datasets_table, downloadPath) {
+ var connection_name = state.connection.name
+ if (!connection_name) {
+ alert('Please choose a connection')
+ return false
+ }
+
+ currentEntityIdentifier = entityIdentifier.value
+ if (!currentEntityIdentifier) {
+ alert('Please specify a Sample or Experiment identifier/permId')
+ return false
+ }
+ var url = env.notebook.base_url
+ + 'openbis/sample/'
+ + connection_name
+ + '/'
+ + encodeURIComponent(currentEntityIdentifier)
+ + "?start_with="
+ + startWith
+ + "&count="
+ + count
+
+ fetch(url)
+ .then(function (response) {
+ if (response.ok) {
+ response.json()
+ .then(function (data) {
+ show_datasets_table(env, data, datasets_table, downloadPath, entityIdentifier)
+ })
+ } else {
+ response.json()
+ .then(function (error) {
+ console.log(error.reason)
+ alert("Error: " + error.reason)
+ })
+ }
+ })
+ .catch(function (error) {
+ console.error('A serious network problem occured:', error)
+ })
}
@@ -63,6 +145,8 @@ define([
icon: 'fa-download',
help_index: '',
handler: function (env) {
+ state.selectedDatasets = new Set([])
+
conn_table = document.createElement("DIV")
conn_table.id = "openbis_connections"
@@ -80,62 +164,20 @@ define([
entityIdentifier.value = ''
var datasets_table = document.createElement("DIV")
- datasets_table.id = "dataset_table"
- datasets_table.className = "output output_scroll"
- datasets_table.style.maxHeight = "10em"
var show_datasets_btn = document.createElement("BUTTON")
show_datasets_btn.className = "btn-info btn-xs"
show_datasets_btn.textContent = "show datasets"
+ show_datasets_btn.style.margin="10px"
- show_datasets_btn.onclick = function () {
- var selected_conn = state.connection.name
- if (!selected_conn) {
- alert('Please choose a connection')
- return false
- }
- connection_name = state.connection.name
-
- currentConnection = connection_name
- currentEntityIdentifier = entityIdentifier.value
- if (!currentEntityIdentifier) {
- alert('Please specify a Sample or Experiment identifier/permId')
- return false
- }
- var url = env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentEntityIdentifier)
-
- fetch(url)
- .then(function (response) {
- if (response.ok) {
- response.json()
- .then(function (data) {
- show_datasets_table(data, datasets_table)
- })
- } else {
- response.json()
- .then(function (error) {
- console.log(error.reason)
- alert("Error: " + error.reason)
- })
- }
- })
- .catch(function (error) {
- console.error('A serious network problem occured:', error)
- })
-
- }
showDataSets.appendChild(entityIdentifier)
showDataSets.appendChild(show_datasets_btn)
showDataSets.appendChild(datasets_table)
- // dataSetPermId only
var dataset_direct = document.createElement("P")
dataset_direct.style.marginTop = '10px'
- dataset_direct.innerHTML = '<strong>enter DataSet permId directly: </strong>'
+ dataset_direct.innerHTML = '<strong>Enter DataSet permId directly: </strong>'
- //var dataset = $('<p>')
- // .css('margin-top', '10px')
- // .append($('<b>').text('... or enter DataSet permId directly: '))
var datasetPermId = document.createElement("INPUT")
datasetPermId.type = "text"
datasetPermId.name = "datasetPermId"
@@ -150,6 +192,9 @@ define([
downloadPath.size = "90"
downloadPath.value = ''
+ show_datasets_btn.onclick =
+ () => getDatasets(env, 0, 5, entityIdentifier, datasets_table, downloadPath)
+
var path = document.createElement("DIV")
path.innerHTML = "<strong>download data to path: </strong>"
path.appendChild(downloadPath)
@@ -202,8 +247,8 @@ define([
}
var selectedPermIds = []
- for (row of document.querySelectorAll('input[name=permId]:checked')) {
- selectedPermIds.push(row.value)
+ for (row of state.selectedDatasets) {
+ selectedPermIds.push(row)
}
if (datasetPermId.value) {
selectedPermIds.push(datasetPermId.value)
@@ -217,6 +262,7 @@ define([
alert('Please specify where you would like to download your files!')
return false
}
+
downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
}
diff --git a/jupyter-openbis-extension/static/state.js b/jupyter-openbis-extension/static/state.js
index e5008e9..6f05b5e 100644
--- a/jupyter-openbis-extension/static/state.js
+++ b/jupyter-openbis-extension/static/state.js
@@ -1,17 +1,23 @@
define([],
function () {
return {
+ // connection dialog
connection: {
name: null,
candidateName: null
},
+
+ // upload dialog
uploadDataSetType: null,
uploadDataSetTypes: {},
uploadEntityIdentifier: '',
datasetCheckboxes: [],
fileCheckboxes: [],
selectedFiles: [],
- unselectedDatasets: []
+ unselectedDatasets: [],
+
+ // download dialog
+ selectedDatasets: new Set([])
}
}
)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/uploadDialog.js b/jupyter-openbis-extension/static/uploadDialog.js
index fd84a46..0690d40 100644
--- a/jupyter-openbis-extension/static/uploadDialog.js
+++ b/jupyter-openbis-extension/static/uploadDialog.js
@@ -13,7 +13,7 @@ define([
element.textContent = ""
element.style.marginLeft = "8px"
element.style.color = "red"
- errorElements[name] = element
+ errorElements[name.toLowerCase()] = element
return element
}
function cleanErrors() {
@@ -50,7 +50,6 @@ define([
}
function get_dataset_list(env, container) {
- console.log(env.notebook.metadata.datasets)
var datasets = env.notebook.metadata.datasets
if (datasets != null) {
var values = Object.keys(datasets)
@@ -217,17 +216,19 @@ define([
entityIdentifier.style.width="100%"
var ds_title = document.createElement("STRONG")
- ds_title.textContent = "DataSets"
var dataSetListContainer = document.createElement("DIV")
- dataSetListContainer.style.height="150px"
- dataSetListContainer.style.overflow="scroll"
- get_dataset_list(env, dataSetListContainer)
+ if (env.notebook.metadata.datasets) {
+ ds_title.textContent = "DataSets"
+ dataSetListContainer.style.maxHeight="150px"
+ dataSetListContainer.style.overflow="auto"
+ get_dataset_list(env, dataSetListContainer)
+ }
var files_title = document.createElement("STRONG")
files_title.textContent = "Files"
var fileListContainer = document.createElement("DIV")
- fileListContainer.style.height="150px"
- fileListContainer.style.overflow="scroll"
+ fileListContainer.style.maxHeight="150px"
+ fileListContainer.style.overflow="auto"
get_file_list(env, fileListContainer)
var inputs = document.createElement("DIV")
@@ -321,7 +322,7 @@ define([
for (error of errors) {
let key, value
Object.keys(error).forEach(k => {
- key = k
+ key = k.toLowerCase()
value = error[k]
})
errorElements[key in errorElements ? key : "main"].textContent = value
diff --git a/vagrant/files/setup-vagrant.sh b/vagrant/files/setup-vagrant.sh
index 0d0ff35..37f4342 100755
--- a/vagrant/files/setup-vagrant.sh
+++ b/vagrant/files/setup-vagrant.sh
@@ -33,3 +33,6 @@ jupyter serverextension enable --py jupyter-openbis-extension
jupyter nbextension install --py jupyter-openbis-extension --user --symlink
jupyter nbextension enable jupyter-openbis-extension --user --py
cd
+
+mkdir -p /home/vagrant/dss_root/incoming-default
+for i in $(seq 1 100); do touch /home/vagrant/dss_root/incoming-default/dataset${i}.txt; done
--
GitLab