Merge branch 'master' of https://github.com/interactivereport/cellxgene_VIP

Conflicts:
	VIPInterface.py
	config.sh
	update.index_template.sh

Author: Baohong Zhang

README.md

@@ -38,9 +38,9 @@ whole or sliced single cell dataset.
 
 # Installation instruction
 
-## 0. Install anaconda python 3.7 and nodejs if not available on server
+## 0. Install anaconda python 3.7 if not available on server
     - Anaconda3-2020.02-Linux-x86_64.sh
-    - node-v12.16.2-linux-x64
+    - jq is needed for cellxgene ver > 0.16 ("yum install jq" or "apt-get install jq" or "brew install jq")
 
 ## 1. create and enable conda environment
 ``` bash

VIPInterface.py

@@ -38,6 +38,7 @@
 api_version = "/api/v0.2"
 
 def route(data,appConfig=None,CLItmp="/tmp"):
+  ppr.pprint("current working dir:%s"%os.getcwd())
   if appConfig is None:
     data["url"] = f'http://127.0.0.1:8888/{api_version}'
   else:
@@ -1146,7 +1147,12 @@ def CLI(data):
     f.write(script)
 
   res = subprocess.run('jupytext --to notebook --output - %s | jupyter nbconvert --ExecutePreprocessor.timeout=1800 --to html --execute --stdin --stdout'%strScript,capture_output=True,shell=True)
+<<<<<<< HEAD
 # ppr.pprint(res)
+=======
+  if 'Error' in res.stderr.decode('utf-8'):
+    raise ValueError(res.stderr.decode('utf-8'))
+>>>>>>> 062b82c9e32d649226ea12dd019b458f6aa5782d
   html = res.stdout.decode('utf-8')
   h,s,e = html.partition('<div class="cell border-box-sizing code_cell rendered">')
   h1,s,e = e.partition('<div class="cell border-box-sizing code_cell rendered">') ## remove the first cell

config.sh

@@ -15,7 +15,11 @@ conda install -c conda-forge -y nodejs=13 fsspec=0.8.2
 rm -rf cellxgene
 git clone https://github.com/chanzuckerberg/cellxgene.git
 cd cellxgene
+<<<<<<< HEAD
 git checkout d99aac49564b98a51ebfab114fd59846c693fd62 # 735eb11eb78b5e6c35ba84438970d0ce369604e1 (v0.15.0)
+=======
+git checkout 735eb11eb78b5e6c35ba84438970d0ce369604e1
+>>>>>>> 062b82c9e32d649226ea12dd019b458f6aa5782d
 cd ..
 
 ## update the client-side source code of cellxgene for VIP

update.index_template.sh

@@ -1,6 +1,12 @@
 #!/usr/bin/env bash
 ## obtain original index_template.html etc.
+<<<<<<< HEAD
 cd cellxgene; git checkout d99aac49564b98a51ebfab114fd59846c693fd62 client/index_template.html client/src/components/leftSidebar/topLeftLogoAndTitle.js client/src/components/leftSidebar/index.js; cd ..
+=======
+cd cellxgene
+git checkout 735eb11eb78b5e6c35ba84438970d0ce369604e1 client/index_template.html client/src/components/leftSidebar/topLeftLogoAndTitle.js client/src/components/leftSidebar/index.js
+cd ..
+>>>>>>> 062b82c9e32d649226ea12dd019b458f6aa5782d
 
 read -d '' insertL << EOF
 <script src="https://interactivereport.github.io/cellxgene_VIP/static/jquery.min.js"></script>
@@ -39,7 +45,11 @@ read -d '' insertL << EOF
         },
         headerTitle: function () {return '<strong>Visualization in Plugin</strong>'},
         contentAjax: {
+<<<<<<< HEAD
             url: 'static/interface.html',
+=======
+            url: window.location.href.replace(/\\\/+$/,'')+'/static/interface.html',
+>>>>>>> 062b82c9e32d649226ea12dd019b458f6aa5782d
             done: function (panel) {
                    setInnerHTML(panel.content, this.responseText);
             }
@@ -71,9 +81,13 @@ sed -i "s|<div id=\"root\"></div>|$insertL\n&|" "cellxgene/client/index_template
 sed -i "s|logoRelatedPadding = 50|logoRelatedPadding = 60|" "cellxgene/client/src/components/leftSidebar/index.js"
 
 strPath=$(python -c "import server as _; print(_.__file__.replace('/server/__init__.py',''))")
+<<<<<<< HEAD
 cd cellxgene/client; make build
 cp build/index.html $strPath/server/common/web/templates/
 rm $strPath/server/common/web/static/main-*.*
 rm $strPath/server/common/web/static/obsolete-*.*
 cp build/static/*   $strPath/server/common/web/static/
 cd ../..
+=======
+cd cellxgene/client; make build; cp build/index.html $strPath/server/common/web/templates/; cd ../..
+>>>>>>> 062b82c9e32d649226ea12dd019b458f6aa5782d