From 0993e0d24f6cdb08f644db4efe766bb3facabeb8 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 12 Jul 2019 12:22:55 +0200
Subject: [PATCH] all recent changes
---
CHANGELOG.md | 5 +--
jupyter-openbis-extension/connection.py | 16 ++++-----
jupyter-openbis-extension/dataset.py | 2 +-
jupyter-openbis-extension/server.py | 11 ++----
jupyter-openbis-extension/static/common.js | 11 +++++-
.../static/connectionDialog.js | 35 ++++++++++++++++++-
.../static/downloadDialog.js | 31 ++++++++++------
jupyter-openbis-extension/static/state.js | 4 ++-
.../static/uploadDialog.js | 25 ++++++-------
9 files changed, 96 insertions(+), 44 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf65abb..550e809 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,9 @@
-## new in jupyter-openbis-extension 0.2.8
+## new in jupyter-openbis-extension 0.3.0
- removed search-as-you-type feature, as it is not mature yet
+- fixed notebook path problem in special environments
- connection dialog: show when connection is being established
-- upload dialog: better and faster file chooser
+- upload dialog: better (and faster) file chooser
- upload dialog: save notebook automatically before upload
## new in jupyter-openbis-extension 0.2.4
diff --git a/jupyter-openbis-extension/connection.py b/jupyter-openbis-extension/connection.py
index f6974e0..d256581 100644
--- a/jupyter-openbis-extension/connection.py
+++ b/jupyter-openbis-extension/connection.py
@@ -96,9 +96,9 @@ class OpenBISConnections(IPythonHandler):
connections.append(conn.get_info())
self.write({
- 'status' : 200,
- 'connections': connections,
- 'cwd' : os.getcwd()
+ 'status' : 200,
+ 'connections' : connections,
+ 'notebook_dir' : self.config.NotebookApp.notebook_dir
})
return
@@ -145,8 +145,8 @@ class OpenBISConnectionHandler(IPythonHandler):
self.write({
'status' : 200,
- 'connection': conn.get_info(),
- 'cwd' : os.getcwd()
+ 'connection' : conn.get_info(),
+ '' : self.config.NotebookApp.notebook_dir
})
def get(self, connection_name):
@@ -165,9 +165,9 @@ class OpenBISConnectionHandler(IPythonHandler):
conn.check_status()
self.write({
- 'status' : 200,
- 'connection': conn.get_info(),
- 'cwd' : os.getcwd()
+ 'status' : 200,
+ 'connection' : conn.get_info(),
+ 'noteboook_dir' : self.config.NotebookApp.notebook_dir
})
return
diff --git a/jupyter-openbis-extension/dataset.py b/jupyter-openbis-extension/dataset.py
index 8b7713d..97bb085 100644
--- a/jupyter-openbis-extension/dataset.py
+++ b/jupyter-openbis-extension/dataset.py
@@ -6,7 +6,6 @@ from .connection import openbis_connections
class DataSetDownloadHandler(IPythonHandler):
"""Handle the requests for /openbis/dataset/connection/permId"""
-
def download_data(self, conn, permId, downloadPath=None):
if not conn.is_session_active():
try:
@@ -46,6 +45,7 @@ class DataSetDownloadHandler(IPythonHandler):
'dataStore' : dataset.dataStore,
'location' : dataset.physicalData.location,
'size' : dataset.physicalData.size,
+ 'files' : dataset.file_list,
'statusText': 'Data for DataSet {} was successfully downloaded to: {}.'.format(dataset.permId, path)
})
diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index 310a1ce..6d95bd5 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -3,7 +3,7 @@ import os
import yaml
from .connection import OpenBISConnections, OpenBISConnectionHandler, register_connection
-from .dataset import DataSetTypesHandler, DataSetDownloadHandler, DataSetUploadHandler, FileListHandler
+from .dataset import DataSetTypesHandler, DataSetDownloadHandler, DataSetUploadHandler
from .sample import SampleHandler
@@ -48,6 +48,7 @@ def load_jupyter_server_extension(nb_server_app):
filename = 'openbis-connections.yaml'
)
+
for connection_info in connections:
conn = register_connection(connection_info)
print("Registered: {}".format(conn.url))
@@ -66,13 +67,6 @@ def load_jupyter_server_extension(nb_server_app):
host_pattern = '.*$'
base_url = web_app.settings['base_url']
- # get the file list
- web_app.add_handlers(
- host_pattern,
- [(url_path_join( base_url, '/general/filelist/?(?P<path>.*)'),
- FileListHandler
- )]
- )
# DataSet download
web_app.add_handlers(
@@ -138,3 +132,4 @@ def load_jupyter_server_extension(nb_server_app):
)
+
diff --git a/jupyter-openbis-extension/static/common.js b/jupyter-openbis-extension/static/common.js
index 15280a1..edcb4af 100644
--- a/jupyter-openbis-extension/static/common.js
+++ b/jupyter-openbis-extension/static/common.js
@@ -39,9 +39,18 @@ define([
return "";
}
+ function createErrorElement() {
+ var element = document.createElement("STRONG")
+ element.textContent = ""
+ element.style.marginLeft = "8px"
+ element.style.color = "red"
+ return element
+ }
+
return {
createFeedback: createFeedback,
- getCookie: getCookie
+ getCookie: getCookie,
+ createErrorElement: createErrorElement
}
}
)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/connectionDialog.js b/jupyter-openbis-extension/static/connectionDialog.js
index cbdd45c..81eed5f 100644
--- a/jupyter-openbis-extension/static/connectionDialog.js
+++ b/jupyter-openbis-extension/static/connectionDialog.js
@@ -10,6 +10,7 @@ define(
let currentDownloadPath = null;
function show_available_connections(env, data, conn_table) {
+
if (!currentDownloadPath) {
currentDownloadPath = data.cwd
}
@@ -214,10 +215,41 @@ define(
uname_pw_cell.appendChild(create_btn)
conn_table.innerHTML = ""
- table_title = document.createElement("STRONG")
+ let table_title = document.createElement("STRONG")
table_title.textContent = "Please choose a connection"
+
+ let working_dir_title = document.createElement("STRONG")
+ working_dir_title.textContent = "Your working directory "
+ let working_dir_in = document.createElement("INPUT")
+ working_dir_in.type = "text"
+ working_dir_in.name = "working_dir"
+ working_dir_in.autocomplete = "on"
+ working_dir_in.style.width = "100%"
+
+
+ // calculate the default working directory
+ // by combining the notebook_dir (from the jupyter configuration) and the relative notebook_path
+ let re = new RegExp(env.notebook.notebook_name+"$")
+ rel_path = env.notebook.notebook_path.replace(re, "")
+ let default_working_dir = data.notebook_dir + "/" + rel_path
+
+ working_dir_in.value = state.working_dir ? state.working_dir : default_working_dir
+ state.working_dir_element = working_dir_in
+
+ let working_dir_reset = document.createElement("A")
+ working_dir_reset.innerText = "reset to default"
+ working_dir_reset.onclick = function() {
+ working_dir_in.value = default_working_dir
+ }
+
conn_table.appendChild(table_title)
conn_table.appendChild(table)
+
+ conn_table.appendChild(working_dir_title)
+ conn_table.appendChild(working_dir_reset)
+ conn_table.appendChild(document.createElement("BR"))
+ conn_table.append(working_dir_in)
+
}
return {
@@ -247,6 +279,7 @@ define(
function onOk() {
state.connection.name = state.connection.candidateName
state.connection.dto = state.connection.candidateDTO
+ state.working_dir = state.working_dir_element.value
}
function onCancel() {
diff --git a/jupyter-openbis-extension/static/downloadDialog.js b/jupyter-openbis-extension/static/downloadDialog.js
index 7a9c399..bd251b8 100644
--- a/jupyter-openbis-extension/static/downloadDialog.js
+++ b/jupyter-openbis-extension/static/downloadDialog.js
@@ -31,16 +31,13 @@ define([
"dataStore": data.dataStore,
"location": data.location,
"size": data.size,
+ "files": data.files,
"status": data.statusText
}
}
}
function show_datasets_table(env, data, datasets_table, pagingContainer, 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%"
@@ -183,6 +180,7 @@ define([
icon: 'fa-download',
help_index: '',
handler: function (env) {
+ console.log(env);
state.selectedDatasets = new Set([])
conn_table = document.createElement("DIV")
@@ -232,7 +230,7 @@ define([
downloadPath.type = "text"
downloadPath.name = "downloadPath"
downloadPath.size = "90"
- downloadPath.value = state.workingDirectory
+ downloadPath.value = state.download_dir ? state.download_dir : state.working_dir
show_datasets_btn.onclick =
() => getDatasets(env, 0, 5, entityIdentifier, datasets_table, pagingContainer, downloadPath)
@@ -243,16 +241,28 @@ define([
path.appendChild(downloadPath)
var download_dialog_box = document.createElement("DIV")
+
+ let mainError = common.createErrorElement()
+ if (!state.connection.name) {
+ mainError.textContent = "Please choose a connection first."
+ //mainError.textContent = "Network problem: please check your connection first."
+ }
+ download_dialog_box.appendChild(mainError)
download_dialog_box.appendChild(spinner)
download_dialog_box.appendChild(conn_table)
download_dialog_box.appendChild(showDataSets)
download_dialog_box.appendChild(dataset_direct)
download_dialog_box.appendChild(path)
- function saveState() {
+ function onOk() {
+ state.entityIdentifier = entityIdentifier.value
+ state.directPermId = datasetPermId.value
+ state.download_dir = downloadPath.value
+ }
+
+ function onCancel() {
state.entityIdentifier = entityIdentifier.value
state.directPermId = datasetPermId.value
- state.workingDirectory = downloadPath.value
}
function downloadDataset(connection_name, selectedPermIds, downloadPath) {
@@ -282,7 +292,8 @@ define([
// keep current download path for later use
currentDownloadPath = downloadPath
})
- } else {
+ }
+ else {
response.json()
.then(function (error) {
console.log(error.reason)
@@ -322,7 +333,7 @@ define([
downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
showSpinner()
- saveState()
+ onOk()
return false
}
@@ -331,7 +342,7 @@ define([
title: 'Download openBIS DataSets',
buttons: {
'Cancel': {
- click: () => saveState()
+ click: () => onCancel()
},
'Download': {
class: 'btn-primary btn-large',
diff --git a/jupyter-openbis-extension/static/state.js b/jupyter-openbis-extension/static/state.js
index 71ea8e2..bcbe83f 100644
--- a/jupyter-openbis-extension/static/state.js
+++ b/jupyter-openbis-extension/static/state.js
@@ -8,6 +8,9 @@ define([],
candidateName: null,
candidateDTO: null
},
+ working_dir: null,
+ working_dir_element: null,
+ download_dir: null,
// upload dialog
uploadDataSetType: null,
@@ -21,7 +24,6 @@ define([],
// download dialog
selectedDatasets: new Set([]),
entity: null,
- workingDirectory: '',
// openBIS v3 connection
openbisService : null
diff --git a/jupyter-openbis-extension/static/uploadDialog.js b/jupyter-openbis-extension/static/uploadDialog.js
index a8bdb9a..5cbfae4 100644
--- a/jupyter-openbis-extension/static/uploadDialog.js
+++ b/jupyter-openbis-extension/static/uploadDialog.js
@@ -355,7 +355,10 @@ define([
var fileListContainer = document.createElement("DIV")
fileListContainer.style.height="200px"
fileListContainer.style.overflow="auto"
- get_file_list(env, fileListContainer, "")
+ // get the relative path
+ let re = new RegExp(env.notebook.notebook_name+"$")
+ rel_path = env.notebook.notebook_path.replace(re, "")
+ get_file_list(env, fileListContainer, rel_path)
var inputs = document.createElement("DIV")
inputs.style.marginTop = '10px'
@@ -398,13 +401,11 @@ define([
}
var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
- var notebook = IPython.notebook
- //var files = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
+
+ // add this notebook to the list of files
var files = state.selectedFiles
- var re = /\/notebooks\/(.*?)$/
- var filepath = window.location.pathname.match(re)[1]
- if (! files.includes(filepath)) {
- files.push(filepath)
+ if (! files.includes(env.notebook.notebook_path)) {
+ files.push(env.notebook.notebook_path)
}
console.log(files)
@@ -436,14 +437,14 @@ define([
common.createFeedback('success', data.statusText)
// write statusText from returned data to notebooks metadata
- if (typeof notebook.metadata.openbis === 'undefined') {
- notebook.metadata.openbis = {}
+ if (typeof env.notebook.metadata.openbis === 'undefined') {
+ env.notebook.metadata.openbis = {}
}
- if (typeof notebook.metadata.openbis.permIds === 'undefined') {
- notebook.metadata.openbis.permIds = {}
+ if (typeof env.notebook.metadata.openbis.permIds === 'undefined') {
+ env.notebook.metadata.openbis.permIds = {}
}
if (data.permId) {
- notebook.metadata.openbis.permIds[data.permId] = data.statusText
+ env.notebook.metadata.openbis.permIds[data.permId] = data.statusText
}
},
error: function (data) {
--
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