diff --git a/README.md b/README.md index 97dbda4cf..85ce5fa6b 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,9 @@ 2018 ESIP Lab Incubator Project -Geoweaver is a web system allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It is a perfect alternative to SSH client (e.g., Putty), FTP client, and scientific workflow software. +Geoweaver is a browser-based software allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It provides all-in-one capacity including SSH client (e.g., Putty), FTP client, and scientific workflow software. + +It can be run from local machines. GeoWeaver is a community effort. Any contribution is welcome and greatly appreciated! @@ -12,7 +14,7 @@ GeoWeaver is a community effort. Any contribution is welcome and greatly appreci ##### Table of Contents -- [Project Goals](#project-goals) +- [Software Goals](#software-goals) - [Installation](#installation) * [Dependencies](#dependencies) * [Quick Install (Recommended)](#quick-install) @@ -31,7 +33,7 @@ GeoWeaver is a community effort. Any contribution is welcome and greatly appreci - [License](#license) -# Project Goals +# Software Goals 1) turning large-scale distributed deep network into manageable modernized workflows; @@ -68,7 +70,7 @@ Java 1.8+ (OpenJDK 8 or higher) java -jar geoweaver.jar ``` -* Step 3: Open browser and entry: http://localhost:8070/Geoweaver/ .That's it! +* Step 3: Open browser and enter: http://localhost:8070/Geoweaver/ .That's it! ## Developer Install @@ -93,7 +95,7 @@ chmod 755 install-linux.sh ./install-linux.sh ``` -* Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.sh`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.sh` @@ -113,7 +115,7 @@ chmod 755 install-mac.sh ./install-mac.sh ``` -* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.sh`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.sh` @@ -132,7 +134,7 @@ cd Geoweaver ./install-windows.bat ``` -* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.bat`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.bat` @@ -164,9 +166,9 @@ The address is: http://your-ip:your-port/Geoweaver/web/geoweaver ``` -Replace the `your-ip`, `your-port` with the real domain of your tomcat. For example, `localhost:8080`. +Replace the `your-ip`, `your-port` with the real domain of your tomcat. For example, `localhost:8070`. -Notice: Make sure the local services like mysql and tomcat are shut down before starting `docker-compose`. Otherwise there might be port conflict error on `3306` and `8080`. Or you can change the port to some other free ports in the docker-compose.yml. +Notice: Make sure the local services like mysql and tomcat are shut down before starting `docker-compose`. Otherwise there might be port conflict error on `3306` and `8070`. Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. [docker](https://docs.docker.com/install) [docker-compose](https://docs.docker.com/compose/install/) diff --git a/docs/index.md b/docs/index.md index 170dd64d8..85ce5fa6b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,38 +4,36 @@ 2018 ESIP Lab Incubator Project -Geoweaver is a web system allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It is a perfect alternative to SSH client (e.g., Putty), FTP client, and scientific workflow software. +Geoweaver is a browser-based software allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It provides all-in-one capacity including SSH client (e.g., Putty), FTP client, and scientific workflow software. + +It can be run from local machines. + +GeoWeaver is a community effort. Any contribution is welcome and greatly appreciated! + +[Geoweaver Online API](https://zihengsun.github.io/Geoweaver/) ##### Table of Contents -- [1. Project Goals](#project-goals) -- [2. Installation](#installation) - * [2.1 Dependencies](#dependencies) - * [2.2 Quick Install](#quick-install) +- [Software Goals](#software-goals) +- [Installation](#installation) + * [Dependencies](#dependencies) + * [Quick Install (Recommended)](#quick-install) + * [Developer Install](#developer-install) + [Linux](#linux) + [Mac](#mac) + [Windows](#windows) - * [2.3 Developer Install](#developer-install) + [Docker](#docker) + [Tomcat War](#tomcat-war) + [Cloud VM Template](#cloud-vm-template) - * [2.4 Build from source](#build-from-source) -- [3. Demo](#demo) -- [4. Usage](#usage) - * [4.1 Add A Server](#add-a-server) - * [4.2 Create A Process](#create-a-process) - * [4.3 Create A Workflow](#create-a-workflow) - * [4.4 Run Workflow](#run-workflow) - * [4.5 Browse Provenance](#browse-provenance) - * [4.6 Retrieve and Display Results](#retrieve-and-display-results) - * [4.7 I/O workflows](#i-o-workflows) -- [5. Documentation](#documentation) -- [6. Dependencies](#dependencies) -- [7. License](#license) -- [8. Author](#author) - - -# 1. Project Goals + * [Build from source](#build-from-source) +- [Demo](#demo) +- [Tutorial](#tutorial) +- [Citation](#citation) +- [Dependencies](#dependencies) +- [License](#license) + + +# Software Goals 1) turning large-scale distributed deep network into manageable modernized workflows; @@ -50,23 +48,34 @@ quality of the result maps; 5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series. -# 2. Installation - -## 2.1 Dependencies +# Installation -If you choose "Quick Install", no need to install these dependencies separately. The install scripts will retrieve these dependencies automatically. +## Dependencies Java 1.8+ (OpenJDK 8 or higher) -Tomcat 8.0+ +!(only for install via docker) [Docker](https://docs.docker.com/install/) 18.09.1+ + +!(only for install via docker) [Docker-compose](https://docs.docker.com/compose/install/) 1.23.1+ + +## Quick Install + +(Recommended) + +* Step 1: Download the latest version of [geoweaver.jar](https://github.com/ESIPFed/Geoweaver/releases/download/latest/geoweaver.jar) + +* Step 2: Run the command: + +```shell +java -jar geoweaver.jar +``` -Apache Maven 3.5+ (optional for building from source) +* Step 3: Open browser and enter: http://localhost:8070/Geoweaver/ .That's it! -[Docker](https://docs.docker.com/install/) 18.09.1+ (for install via docker) +## Developer Install -[Docker-compose](https://docs.docker.com/compose/install/) 1.23.1+ (for install via docker) +This section is dedicated for developer users who have better background on web technologies and familiar with MySQL, H2, tomcat, docker, and maven. If you are familiar with neither of them, we strongly suggest you use the "Quick Install" way to install Geoweaver. -## 2.2 Quick Install ### Linux @@ -86,7 +95,7 @@ chmod 755 install-linux.sh ./install-linux.sh ``` -* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.sh`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.sh` @@ -106,7 +115,7 @@ chmod 755 install-mac.sh ./install-mac.sh ``` -* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.sh`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.sh` @@ -125,14 +134,10 @@ cd Geoweaver ./install-windows.bat ``` -* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. +* Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. * Optional: To stop Geoweaver, type: `install/apache-tomcat-9.0.22/bin/shutdown.bat`. To start Geoweaver again, type: `install/apache-tomcat-9.0.22/bin/startup.bat` -## 2.3 Developer Install - -This section is dedicated for high-level users who have better background on web technologies and familiar with MySQL, Tomcat and Docker. If you are not familiar with either of them, we strongly suggest you use the "Quick Install" way to install Geoweaver. - ### Docker We use `docker-compose` to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps. @@ -161,9 +166,9 @@ The address is: http://your-ip:your-port/Geoweaver/web/geoweaver ``` -Replace the `your-ip`, `your-port` with the real domain of your tomcat. For example, `localhost:8080`. +Replace the `your-ip`, `your-port` with the real domain of your tomcat. For example, `localhost:8070`. -Notice: Make sure the local services like mysql and tomcat are shut down before starting `docker-compose`. Otherwise there might be port conflict error on `3306` and `8080`. Or you can change the port to some other free ports in the docker-compose.yml. +Notice: Make sure the local services like mysql and tomcat are shut down before starting `docker-compose`. Otherwise there might be port conflict error on `3306` and `8070`. Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. [docker](https://docs.docker.com/install) [docker-compose](https://docs.docker.com/compose/install/) @@ -198,7 +203,7 @@ nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/cc_secret.properties Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and `WEB-INF/classes/cc_secret.properties` (database username and password: database_user=root database_password=xxxxxxxx). -(**Note: the database must be initiated by the SQL file under the folder Geoweaver/docker/db first.**) +(**Note: the MySQL database must be initiated by the SQL file under the folder Geoweaver/docker/db first. If you are using H2 database, please copy the two files: geoweaver.mv.db and geoweaver.trace.db to your user home directory before you start tomcat. **) ```shell mysql -u root -p < docker/db/gw.sql @@ -236,84 +241,25 @@ To stop Geoweaver, use: docker stop $(docker ps -aq) ``` -## 2.4 Build from source - -Use maven to build. In the command line go to the root folder and execute `mvn install`. After a success build, the Geoweaver war package will be under the directory: `Geoweaver/target/Geoweaver-.war`. - -# 3. Demo - -A live demo site is available in George Mason University: [I am a link, hit me](https://cloud.csiss.gmu.edu/Geoweaver). - -Here is a use case of Geoweaver, using deep neural network like LSTM RNN and SegNet to classify landsat images into agricultural land use maps. In this case, Geoweaver can help stakeholders get crop maps with better accuracy and high temporal resolution by providing a deep-learning-powered and distributed workflow system. - -![Result Demo](demo.png) - -![LSTM-Crop concept](lstm.png) - -Animation demo: - -![AnimationDemo](geoweaver-demo.gif) +## Build from source +Use maven to build. In the command line go to the root folder and execute `mvn install`. After a success build, the Geoweaver jar package will be under the directory: `Geoweaver/target/Geoweaver-.jar`. -# 4. Usage +# Demo -## 4.1 Add A Server +[A live demo site](https://cloud.csiss.gmu.edu/Geoweaver) is available in George Mason University. -Enroll a server to Geoweaver is simple. The server must have SSH server installed and enabled. The server must be accessible from Geoweaver host server. +# Tutorial -![Add a host](addhost.gif) +[Geoweaver Tutorial](https://andrewmagill.github.io/#/) - A beginner tutorial about what Geoweaver can do and how it works -## 4.2 Create A Process +# Citation -Geoweaver supports Bash Shell scripts as processes. You can write bash command lines in the code area. Note: the commands should exist on the target hosts. +If you found Geoweaver helpful in your research, please cite us: -![Add a process](addprocess.gif) +Sun, Ziheng, Liping Di, Annie Burgess, Jason A. Tullis, and Andrew B. Magill. "Geoweaver: Advanced cyberinfrastructure for managing hybrid geoscientific AI workflows." ISPRS International Journal of Geo-Information 9, no. 2 (2020): 119. -## 4.3 Create A Workflow - -Geoweaver can link the processes together to form a workflow. To connect two processes, press `shift` key while dragging from one process to another. - -![Create a workflow](createworkflow.gif) - -## 4.4 Run Workflow - -Geoweaver can run the created workflows on the enlisted servers. During the running, Geoweaver is monitoring the status of each process. The color of process text in their circles indicate the process status. Yellow means running, green means completed, and red means failure. - -![Run a workflow](runworkflow.gif) - -## 4.5 Browse Provenance - -Geoweaver stores all the inputs and outputs of each process run. Users can check the workflow provenance by simply clicking. - -![Check provenance](checkprovenance.gif) - -## 4.6 Retrieve and Display Results - -Geoweaver can retrieve the result files of the executed workflows and visualize them if the format is supported (png, jpg, bmp, etc. The list is expanding. I am on it.). - -![Get result](getresult.gif) - -## 4.7 I/O workflows - -The workflows can be exported and move around and imported back. - -![Export workflow](exportworkflow.gif) - -# 5. Documentation - -[Project Proposal](geoweaver-proposal-revised-v4.pdf) - -[August Report](ESIP-Geoweaver-Report-1.docx) - -[September Report](ESIP-Geoweaver-Report-2.docx) - -[October Report](ESIP-Geoweaver-Report-3.docx) - -[November Report](ESIP-Geoweaver-Report-4.docx) - -[December Report](ESIP-Geoweaver-Report-5.docx) - -# 6. Dependencies +# Dependencies This project is impossible without the support of several fantastic open source libraries. @@ -327,11 +273,8 @@ This project is impossible without the support of several fantastic open source [JQuery Terminal](https://github.com/jcubic/jquery.terminal) - MIT License -# 7. License +# License MIT -# 8. Author - -[developer list](https://github.com/ESIPFed/Geoweaver/graphs/contributors) diff --git a/site/404.html b/site/404.html index 30fa495b2..35c5e5a2f 100644 --- a/site/404.html +++ b/site/404.html @@ -7,17 +7,18 @@ + Geoweaver - + - - - + + + - + @@ -28,6 +29,7 @@
@@ -71,6 +68,7 @@ +
@@ -94,7 +92,7 @@

404

- Built with MkDocs using a theme provided by Read the Docs. + Built with MkDocs using a theme provided by Read the Docs. @@ -104,7 +102,7 @@

404

-
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@@ -114,6 +112,11 @@

404

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@@ -146,6 +81,7 @@ +
@@ -154,40 +90,33 @@

Build Status License Stars Forks Issues Coverage

Geoweaver

2018 ESIP Lab Incubator Project

-

Geoweaver is a web system allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It is a perfect alternative to SSH client (e.g., Putty), FTP client, and scientific workflow software.

+

Geoweaver is a browser-based software allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It provides all-in-one capacity including SSH client (e.g., Putty), FTP client, and scientific workflow software.

+

It can be run from local machines.

+

GeoWeaver is a community effort. Any contribution is welcome and greatly appreciated!

+

Geoweaver Online API

Table of Contents
    -
  • 1. Project Goals
    • -
  • 2. Installation
    • -
  • 2.1 Dependencies
    • -
  • 2.2 Quick Install -

    1. Project Goals

    +

    Software Goals

    1) turning large-scale distributed deep network into manageable modernized workflows;

    2) boosting higher utilization ratio of the existing cyberinfrastructures by separating scientists from tedious technical details;

    @@ -196,15 +125,29 @@

    1. Project Goals

    quality of the result maps;

    5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series.

    -

    2. Installation

    -

    2.1 Dependencies

    -

    If you choose "Quick Install", no need to install these dependencies separately. The install scripts will retrieve these dependencies automatically.

    +

    Installation

    +

    Dependencies

    Java 1.8+ (OpenJDK 8 or higher)

    -

    Tomcat 8.0+

    -

    Apache Maven 3.5+ (optional for building from source)

    -

    Docker 18.09.1+ (for install via docker)

    -

    Docker-compose 1.23.1+ (for install via docker)

    -

    2.2 Quick Install

    +

    !(only for install via docker) Docker 18.09.1+

    +

    !(only for install via docker) Docker-compose 1.23.1+

    +

    Quick Install

    +

    (Recommended)

    +
      +
    • +

      Step 1: Download the latest version of geoweaver.jar

      +
      • +
    • +

      Step 2: Run the command:

      +
      • +
    +
    java -jar geoweaver.jar 
+
    + +
      +
    • Step 3: Open browser and enter: http://localhost:8070/Geoweaver/ .That's it!
      • +
    +

    Developer Install

    +

    This section is dedicated for developer users who have better background on web technologies and familiar with MySQL, H2, tomcat, docker, and maven. If you are familiar with neither of them, we strongly suggest you use the "Quick Install" way to install Geoweaver.

    Linux

    This way works for most linux releases, e.g., Ubuntu, CentOS, RedHat, OpenBSD, etc.

      @@ -223,7 +166,7 @@

      Linux

      • -

        Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it.

        +

        Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it.

      • Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh. To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh

        @@ -246,7 +189,7 @@

        Mac

        • -

          Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it.

          +

          Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it.

        • Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh. To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh

          @@ -268,14 +211,12 @@

          Windows

          • -

            Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it.

            +

            Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it.

          • Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.bat. To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.bat

          -

          2.3 Developer Install

          -

          This section is dedicated for high-level users who have better background on web technologies and familiar with MySQL, Tomcat and Docker. If you are not familiar with either of them, we strongly suggest you use the "Quick Install" way to install Geoweaver.

          Docker

          We use docker-compose to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps.

          Install

          @@ -289,7 +230,7 @@

          Install

        • Enter the repo and create a new folder target. Download a Geoweaver war package from the release page and save it in the created target folder.
        cd Geoweaver && mkdir target && cd target
-wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.0/Geoweaver-0.7.0.war -O Geoweaver.war
+wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war
          @@ -302,8 +243,8 @@

          Install

          http://your-ip:your-port/Geoweaver/web/geoweaver
          -

          Replace the your-ip, your-port with the real domain of your tomcat. For example, localhost:8080.

          -

          Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose. Otherwise there might be port conflict error on 3306 and 8080. Or you can change the port to some other free ports in the docker-compose.yml.

          +

          Replace the your-ip, your-port with the real domain of your tomcat. For example, localhost:8070.

          +

          Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose. Otherwise there might be port conflict error on 3306 and 8070. Or you can change the port to some other free ports in the docker-compose.yml.

          If you don't have docker or docker-compose installed, these documents will help. docker docker-compose

          Shutdown

          To stop Geoweaver, type:

          @@ -316,7 +257,7 @@

          Install

        • Download the latest release war and copy it to the webapps directory of Tomcat (e.g. /usr/local/tomcat). Start Tomcat. 
        
-wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.6.10/Geoweaver-0.6.10.war -O Geoweaver.war
+wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war
 cp Geoweaver.war /usr/local/tomcat/webapps/
 /usr/local/tomcat/bin/startup.sh
 
@@ -330,7 +271,7 @@ 
        Install

        Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and WEB-INF/classes/cc_secret.properties (database username and password: database_user=root database_password=xxxxxxxx).

        -

        (Note: the database must be initiated by the SQL file under the folder Geoweaver/docker/db first.)

        +

        (Note: the MySQL database must be initiated by the SQL file under the folder Geoweaver/docker/db first. If you are using H2 database, please copy the two files: geoweaver.mv.db and geoweaver.trace.db to your user home directory before you start tomcat. )

        mysql -u root -p < docker/db/gw.sql
        @@ -357,55 +298,24 @@

        Shutdown

        docker stop $(docker ps -aq)
        -

        2.4 Build from source

        -

        Use maven to build. In the command line go to the root folder and execute mvn install. After a success build, the Geoweaver war package will be under the directory: Geoweaver/target/Geoweaver-<version>.war.

        -

        3. Demo

        -

        A live demo site is available in George Mason University: I am a link, hit me.

        -

        Here is a use case of Geoweaver, using deep neural network like LSTM RNN and SegNet to classify landsat images into agricultural land use maps. In this case, Geoweaver can help stakeholders get crop maps with better accuracy and high temporal resolution by providing a deep-learning-powered and distributed workflow system.

        -

        Result Demo

        -

        LSTM-Crop concept

        -

        Animation demo:

        -

        AnimationDemo

        -

        4. Usage

        -

        4.1 Add A Server

        -

        Enroll a server to Geoweaver is simple. The server must have SSH server installed and enabled. The server must be accessible from Geoweaver host server.

        -

        Add a host

        -

        4.2 Create A Process

        -

        Geoweaver supports Bash Shell scripts as processes. You can write bash command lines in the code area. Note: the commands should exist on the target hosts.

        -

        Add a process

        -

        4.3 Create A Workflow

        -

        Geoweaver can link the processes together to form a workflow. To connect two processes, press shift key while dragging from one process to another.

        -

        Create a workflow

        -

        4.4 Run Workflow

        -

        Geoweaver can run the created workflows on the enlisted servers. During the running, Geoweaver is monitoring the status of each process. The color of process text in their circles indicate the process status. Yellow means running, green means completed, and red means failure.

        -

        Run a workflow

        -

        4.5 Browse Provenance

        -

        Geoweaver stores all the inputs and outputs of each process run. Users can check the workflow provenance by simply clicking.

        -

        Check provenance

        -

        4.6 Retrieve and Display Results

        -

        Geoweaver can retrieve the result files of the executed workflows and visualize them if the format is supported (png, jpg, bmp, etc. The list is expanding. I am on it.).

        -

        Get result

        -

        4.7 I/O workflows

        -

        The workflows can be exported and move around and imported back.

        -

        Export workflow

        -

        5. Documentation

        -

        Project Proposal

        -

        August Report

        -

        September Report

        -

        October Report

        -

        November Report

        -

        December Report

        -

        6. Dependencies

        +

        Build from source

        +

        Use maven to build. In the command line go to the root folder and execute mvn install. After a success build, the Geoweaver jar package will be under the directory: Geoweaver/target/Geoweaver-<version>.jar.

        +

        Demo

        +

        A live demo site is available in George Mason University.

        +

        Tutorial

        +

        Geoweaver Tutorial - A beginner tutorial about what Geoweaver can do and how it works

        +

        Citation

        +

        If you found Geoweaver helpful in your research, please cite us:

        +

        Sun, Ziheng, Liping Di, Annie Burgess, Jason A. Tullis, and Andrew B. Magill. "Geoweaver: Advanced cyberinfrastructure for managing hybrid geoscientific AI workflows." ISPRS International Journal of Geo-Information 9, no. 2 (2020): 119.

        +

        Dependencies

        This project is impossible without the support of several fantastic open source libraries.

        d3.js - BSD 3-Clause

        graph-creator - MIT License

        bootstrap - MIT License

        CodeMirror - MIT License

        JQuery Terminal - MIT License

        -

        7. License

        +

        License

        MIT

        -

        8. Author

        -

        developer list

@@ -419,7 +329,7 @@

8. Author

- Built with MkDocs using a theme provided by Read the Docs. + Built with MkDocs using a theme provided by Read the Docs. @@ -429,7 +339,7 @@

8. Author

-
+
@@ -439,11 +349,16 @@

8. Author

+ diff --git a/site/js/theme.js b/site/js/theme.js index aecbb8611..68d3ba07f 100644 --- a/site/js/theme.js +++ b/site/js/theme.js @@ -1,105 +1,3 @@ -$( document ).ready(function() { - // Shift nav in mobile when clicking the menu. - $(document).on('click', "[data-toggle='wy-nav-top']", function() { - $("[data-toggle='wy-nav-shift']").toggleClass("shift"); - $("[data-toggle='rst-versions']").toggleClass("shift"); - }); - - // Close menu when you click a link. - $(document).on('click', ".wy-menu-vertical .current ul li a", function() { - $("[data-toggle='wy-nav-shift']").removeClass("shift"); - $("[data-toggle='rst-versions']").toggleClass("shift"); - }); - - // Keyboard navigation - document.addEventListener("keydown", function(e) { - var key = e.which || e.keyCode || window.event && window.event.keyCode; - var page; - switch (key) { - case 78: // n - page = $('[role="navigation"] a:contains(Next):first').prop('href'); - break; - case 80: // p - page = $('[role="navigation"] a:contains(Previous):first').prop('href'); - break; - case 13: // enter - if (e.target === document.getElementById('mkdocs-search-query')) { - e.preventDefault(); - } - break; - default: break; - } - if ($(e.target).is(':input')) { - return true; - } else if (page) { - window.location.href = page; - } - }); - - $(document).on('click', "[data-toggle='rst-current-version']", function() { - $("[data-toggle='rst-versions']").toggleClass("shift-up"); - }); - - // Make tables responsive - $("table.docutils:not(.field-list)").wrap("
"); - - $('table').addClass('docutils'); -}); - -window.SphinxRtdTheme = (function (jquery) { - var stickyNav = (function () { - var navBar, - win, - stickyNavCssClass = 'stickynav', - applyStickNav = function () { - if (navBar.height() <= win.height()) { - navBar.addClass(stickyNavCssClass); - } else { - navBar.removeClass(stickyNavCssClass); - } - }, - enable = function () { - applyStickNav(); - win.on('resize', applyStickNav); - }, - init = function () { - navBar = jquery('nav.wy-nav-side:first'); - win = jquery(window); - }; - jquery(init); - return { - enable : enable - }; - }()); - return { - StickyNav : stickyNav - }; -}($)); - -// The code below is a copy of @seanmadsen code posted Jan 10, 2017 on issue 803. -// https://github.com/mkdocs/mkdocs/issues/803 -// This just incorporates the auto scroll into the theme itself without -// the need for additional custom.js file. -// -$(function() { - $.fn.isFullyWithinViewport = function(){ - var viewport = {}; - viewport.top = $(window).scrollTop(); - viewport.bottom = viewport.top + $(window).height(); - var bounds = {}; - bounds.top = this.offset().top; - bounds.bottom = bounds.top + this.outerHeight(); - return ( ! ( - (bounds.top <= viewport.top) || - (bounds.bottom >= viewport.bottom) - ) ); - }; - if( $('li.toctree-l1.current').length && !$('li.toctree-l1.current').isFullyWithinViewport() ) { - $('.wy-nav-side') - .scrollTop( - $('li.toctree-l1.current').offset().top - - $('.wy-nav-side').offset().top - - 60 - ); - } -}); +/* sphinx_rtd_theme version 0.4.1 | MIT license */ +/* Built 20180727 10:07 */ +require=function n(e,i,t){function o(s,a){if(!i[s]){if(!e[s]){var l="function"==typeof require&&require;if(!a&&l)return l(s,!0);if(r)return r(s,!0);var c=new Error("Cannot find module '"+s+"'");throw c.code="MODULE_NOT_FOUND",c}var u=i[s]={exports:{}};e[s][0].call(u.exports,function(n){var i=e[s][1][n];return o(i||n)},u,u.exports,n,e,i,t)}return i[s].exports}for(var r="function"==typeof require&&require,s=0;s
"),n("table.docutils.footnote").wrap("
"),n("table.docutils.citation").wrap("
"),n(".wy-menu-vertical ul").not(".simple").siblings("a").each(function(){var i=n(this);expand=n(''),expand.on("click",function(n){return e.toggleCurrent(i),n.stopPropagation(),!1}),i.prepend(expand)})},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),i=e.find('[href="'+n+'"]');if(0===i.length){var t=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(i=e.find('[href="#'+t.attr("id")+'"]')).length&&(i=e.find('[href="#"]'))}i.length>0&&($(".wy-menu-vertical .current").removeClass("current"),i.addClass("current"),i.closest("li.toctree-l1").addClass("current"),i.closest("li.toctree-l1").parent().addClass("current"),i.closest("li.toctree-l1").addClass("current"),i.closest("li.toctree-l2").addClass("current"),i.closest("li.toctree-l3").addClass("current"),i.closest("li.toctree-l4").addClass("current"))}catch(o){console.log("Error expanding nav for anchor",o)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,i=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(i),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",function(){this.linkScroll=!1})},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current"),e.siblings().find("li.current").removeClass("current"),e.find("> ul li.current").removeClass("current"),e.toggleClass("current")}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:e.exports.ThemeNav,StickyNav:e.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],i=0;i + Geoweaver - + - - - + + + - + @@ -28,6 +29,7 @@
@@ -71,6 +68,7 @@ +
@@ -101,7 +99,7 @@

Search Results

- Built with MkDocs using a theme provided by Read the Docs. + Built with MkDocs using a theme provided by Read the Docs. @@ -111,7 +109,7 @@

Search Results

-
+
@@ -121,6 +119,11 @@

Search Results

+ diff --git a/site/search/lunr.js b/site/search/lunr.js index c218cc897..c3537658a 100644 --- a/site/search/lunr.js +++ b/site/search/lunr.js @@ -1,6 +1,6 @@ /** - * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.1.6 - * Copyright (C) 2018 Oliver Nightingale + * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.8 + * Copyright (C) 2019 Oliver Nightingale * @license MIT */ @@ -54,14 +54,15 @@ var lunr = function (config) { return builder.build() } -lunr.version = "2.1.6" +lunr.version = "2.3.8" /*! * lunr.utils - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** * A namespace containing utils for the rest of the lunr library + * @namespace lunr.utils */ lunr.utils = {} @@ -69,7 +70,8 @@ lunr.utils = {} * Print a warning message to the console. * * @param {String} message The message to be printed. - * @memberOf Utils + * @memberOf lunr.utils + * @function */ lunr.utils.warn = (function (global) { /* eslint-disable no-console */ @@ -90,7 +92,7 @@ lunr.utils.warn = (function (global) { * * @param {Any} obj The object to convert to a string. * @return {String} string representation of the passed object. - * @memberOf Utils + * @memberOf lunr.utils */ lunr.utils.asString = function (obj) { if (obj === void 0 || obj === null) { @@ -99,6 +101,52 @@ lunr.utils.asString = function (obj) { return obj.toString() } } + +/** + * Clones an object. + * + * Will create a copy of an existing object such that any mutations + * on the copy cannot affect the original. + * + * Only shallow objects are supported, passing a nested object to this + * function will cause a TypeError. + * + * Objects with primitives, and arrays of primitives are supported. + * + * @param {Object} obj The object to clone. + * @return {Object} a clone of the passed object. + * @throws {TypeError} when a nested object is passed. + * @memberOf Utils + */ +lunr.utils.clone = function (obj) { + if (obj === null || obj === undefined) { + return obj + } + + var clone = Object.create(null), + keys = Object.keys(obj) + + for (var i = 0; i < keys.length; i++) { + var key = keys[i], + val = obj[key] + + if (Array.isArray(val)) { + clone[key] = val.slice() + continue + } + + if (typeof val === 'string' || + typeof val === 'number' || + typeof val === 'boolean') { + clone[key] = val + continue + } + + throw new TypeError("clone is not deep and does not support nested objects") + } + + return clone +} lunr.FieldRef = function (docRef, fieldName, stringValue) { this.docRef = docRef this.fieldName = fieldName @@ -127,6 +175,139 @@ lunr.FieldRef.prototype.toString = function () { return this._stringValue } +/*! + * lunr.Set + * Copyright (C) 2019 Oliver Nightingale + */ + +/** + * A lunr set. + * + * @constructor + */ +lunr.Set = function (elements) { + this.elements = Object.create(null) + + if (elements) { + this.length = elements.length + + for (var i = 0; i < this.length; i++) { + this.elements[elements[i]] = true + } + } else { + this.length = 0 + } +} + +/** + * A complete set that contains all elements. + * + * @static + * @readonly + * @type {lunr.Set} + */ +lunr.Set.complete = { + intersect: function (other) { + return other + }, + + union: function (other) { + return other + }, + + contains: function () { + return true + } +} + +/** + * An empty set that contains no elements. + * + * @static + * @readonly + * @type {lunr.Set} + */ +lunr.Set.empty = { + intersect: function () { + return this + }, + + union: function (other) { + return other + }, + + contains: function () { + return false + } +} + +/** + * Returns true if this set contains the specified object. + * + * @param {object} object - Object whose presence in this set is to be tested. + * @returns {boolean} - True if this set contains the specified object. + */ +lunr.Set.prototype.contains = function (object) { + return !!this.elements[object] +} + +/** + * Returns a new set containing only the elements that are present in both + * this set and the specified set. + * + * @param {lunr.Set} other - set to intersect with this set. + * @returns {lunr.Set} a new set that is the intersection of this and the specified set. + */ + +lunr.Set.prototype.intersect = function (other) { + var a, b, elements, intersection = [] + + if (other === lunr.Set.complete) { + return this + } + + if (other === lunr.Set.empty) { + return other + } + + if (this.length < other.length) { + a = this + b = other + } else { + a = other + b = this + } + + elements = Object.keys(a.elements) + + for (var i = 0; i < elements.length; i++) { + var element = elements[i] + if (element in b.elements) { + intersection.push(element) + } + } + + return new lunr.Set (intersection) +} + +/** + * Returns a new set combining the elements of this and the specified set. + * + * @param {lunr.Set} other - set to union with this set. + * @return {lunr.Set} a new set that is the union of this and the specified set. + */ + +lunr.Set.prototype.union = function (other) { + if (other === lunr.Set.complete) { + return lunr.Set.complete + } + + if (other === lunr.Set.empty) { + return this + } + + return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements))) +} /** * A function to calculate the inverse document frequency for * a posting. This is shared between the builder and the index @@ -208,7 +389,7 @@ lunr.Token.prototype.clone = function (fn) { } /*! * lunr.tokenizer - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -220,22 +401,30 @@ lunr.Token.prototype.clone = function (fn) { * then will split this string on the character in `lunr.tokenizer.separator`. * Arrays will have their elements converted to strings and wrapped in a lunr.Token. * + * Optional metadata can be passed to the tokenizer, this metadata will be cloned and + * added as metadata to every token that is created from the object to be tokenized. + * * @static * @param {?(string|object|object[])} obj - The object to convert into tokens + * @param {?object} metadata - Optional metadata to associate with every token * @returns {lunr.Token[]} + * @see {@link lunr.Pipeline} */ -lunr.tokenizer = function (obj) { +lunr.tokenizer = function (obj, metadata) { if (obj == null || obj == undefined) { return [] } if (Array.isArray(obj)) { return obj.map(function (t) { - return new lunr.Token(lunr.utils.asString(t).toLowerCase()) + return new lunr.Token( + lunr.utils.asString(t).toLowerCase(), + lunr.utils.clone(metadata) + ) }) } - var str = obj.toString().trim().toLowerCase(), + var str = obj.toString().toLowerCase(), len = str.length, tokens = [] @@ -246,11 +435,15 @@ lunr.tokenizer = function (obj) { if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) { if (sliceLength > 0) { + var tokenMetadata = lunr.utils.clone(metadata) || {} + tokenMetadata["position"] = [sliceStart, sliceLength] + tokenMetadata["index"] = tokens.length + tokens.push( - new lunr.Token (str.slice(sliceStart, sliceEnd), { - position: [sliceStart, sliceLength], - index: tokens.length - }) + new lunr.Token ( + str.slice(sliceStart, sliceEnd), + tokenMetadata + ) ) } @@ -272,7 +465,7 @@ lunr.tokenizer = function (obj) { lunr.tokenizer.separator = /[\s\-]+/ /*! * lunr.Pipeline - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -316,8 +509,8 @@ lunr.Pipeline.registeredFunctions = Object.create(null) * or mutate (or add) metadata for a given token. * * A pipeline function can indicate that the passed token should be discarded by returning - * null. This token will not be passed to any downstream pipeline functions and will not be - * added to the index. + * null, undefined or an empty string. This token will not be passed to any downstream pipeline + * functions and will not be added to the index. * * Multiple tokens can be returned by returning an array of tokens. Each token will be passed * to any downstream pipeline functions and all will returned tokens will be added to the index. @@ -480,9 +673,9 @@ lunr.Pipeline.prototype.run = function (tokens) { for (var j = 0; j < tokens.length; j++) { var result = fn(tokens[j], j, tokens) - if (result === void 0 || result === '') continue + if (result === null || result === void 0 || result === '') continue - if (result instanceof Array) { + if (Array.isArray(result)) { for (var k = 0; k < result.length; k++) { memo.push(result[k]) } @@ -503,10 +696,12 @@ lunr.Pipeline.prototype.run = function (tokens) { * token and mapping the resulting tokens back to strings. * * @param {string} str - The string to pass through the pipeline. + * @param {?object} metadata - Optional metadata to associate with the token + * passed to the pipeline. * @returns {string[]} */ -lunr.Pipeline.prototype.runString = function (str) { - var token = new lunr.Token (str) +lunr.Pipeline.prototype.runString = function (str, metadata) { + var token = new lunr.Token (str, metadata) return this.run([token]).map(function (t) { return t.toString() @@ -537,7 +732,7 @@ lunr.Pipeline.prototype.toJSON = function () { } /*! * lunr.Vector - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -698,15 +893,14 @@ lunr.Vector.prototype.dot = function (otherVector) { } /** - * Calculates the cosine similarity between this vector and another - * vector. + * Calculates the similarity between this vector and another vector. * * @param {lunr.Vector} otherVector - The other vector to calculate the * similarity with. * @returns {Number} */ lunr.Vector.prototype.similarity = function (otherVector) { - return this.dot(otherVector) / (this.magnitude() * otherVector.magnitude()) + return this.dot(otherVector) / this.magnitude() || 0 } /** @@ -735,7 +929,7 @@ lunr.Vector.prototype.toJSON = function () { /* eslint-disable */ /*! * lunr.stemmer - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt */ @@ -748,6 +942,7 @@ lunr.Vector.prototype.toJSON = function () { * @param {lunr.Token} token - The string to stem * @returns {lunr.Token} * @see {@link lunr.Pipeline} + * @function */ lunr.stemmer = (function(){ var step2list = { @@ -956,7 +1151,7 @@ lunr.stemmer = (function(){ lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer') /*! * lunr.stopWordFilter - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -966,6 +1161,7 @@ lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer') * The built in lunr.stopWordFilter is built using this generator and can be used * to generate custom stopWordFilters for applications or non English languages. * + * @function * @param {Array} token The token to pass through the filter * @returns {lunr.PipelineFunction} * @see lunr.Pipeline @@ -989,6 +1185,7 @@ lunr.generateStopWordFilter = function (stopWords) { * This is intended to be used in the Pipeline. If the token does not pass the * filter then undefined will be returned. * + * @function * @implements {lunr.PipelineFunction} * @params {lunr.Token} token - A token to check for being a stop word. * @returns {lunr.Token} @@ -1119,7 +1316,7 @@ lunr.stopWordFilter = lunr.generateStopWordFilter([ lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter') /*! * lunr.trimmer - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -1146,7 +1343,7 @@ lunr.trimmer = function (token) { lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer') /*! * lunr.TokenSet - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -1263,50 +1460,58 @@ lunr.TokenSet.fromFuzzyString = function (str, editDistance) { if (frame.str.length == 1) { noEditNode.final = true - } else { - stack.push({ - node: noEditNode, - editsRemaining: frame.editsRemaining, - str: frame.str.slice(1) - }) } + + stack.push({ + node: noEditNode, + editsRemaining: frame.editsRemaining, + str: frame.str.slice(1) + }) + } + + if (frame.editsRemaining == 0) { + continue + } + + // insertion + if ("*" in frame.node.edges) { + var insertionNode = frame.node.edges["*"] + } else { + var insertionNode = new lunr.TokenSet + frame.node.edges["*"] = insertionNode } + if (frame.str.length == 0) { + insertionNode.final = true + } + + stack.push({ + node: insertionNode, + editsRemaining: frame.editsRemaining - 1, + str: frame.str + }) + // deletion // can only do a deletion if we have enough edits remaining // and if there are characters left to delete in the string - if (frame.editsRemaining > 0 && frame.str.length > 1) { - var char = frame.str.charAt(1), - deletionNode - - if (char in frame.node.edges) { - deletionNode = frame.node.edges[char] - } else { - deletionNode = new lunr.TokenSet - frame.node.edges[char] = deletionNode - } - - if (frame.str.length <= 2) { - deletionNode.final = true - } else { - stack.push({ - node: deletionNode, - editsRemaining: frame.editsRemaining - 1, - str: frame.str.slice(2) - }) - } + if (frame.str.length > 1) { + stack.push({ + node: frame.node, + editsRemaining: frame.editsRemaining - 1, + str: frame.str.slice(1) + }) } // deletion // just removing the last character from the str - if (frame.editsRemaining > 0 && frame.str.length == 1) { + if (frame.str.length == 1) { frame.node.final = true } // substitution // can only do a substitution if we have enough edits remaining // and if there are characters left to substitute - if (frame.editsRemaining > 0 && frame.str.length >= 1) { + if (frame.str.length >= 1) { if ("*" in frame.node.edges) { var substitutionNode = frame.node.edges["*"] } else { @@ -1316,40 +1521,19 @@ lunr.TokenSet.fromFuzzyString = function (str, editDistance) { if (frame.str.length == 1) { substitutionNode.final = true - } else { - stack.push({ - node: substitutionNode, - editsRemaining: frame.editsRemaining - 1, - str: frame.str.slice(1) - }) } - } - // insertion - // can only do insertion if there are edits remaining - if (frame.editsRemaining > 0) { - if ("*" in frame.node.edges) { - var insertionNode = frame.node.edges["*"] - } else { - var insertionNode = new lunr.TokenSet - frame.node.edges["*"] = insertionNode - } - - if (frame.str.length == 0) { - insertionNode.final = true - } else { - stack.push({ - node: insertionNode, - editsRemaining: frame.editsRemaining - 1, - str: frame.str - }) - } + stack.push({ + node: substitutionNode, + editsRemaining: frame.editsRemaining - 1, + str: frame.str.slice(1) + }) } // transposition // can only do a transposition if there are edits remaining // and there are enough characters to transpose - if (frame.editsRemaining > 0 && frame.str.length > 1) { + if (frame.str.length > 1) { var charA = frame.str.charAt(0), charB = frame.str.charAt(1), transposeNode @@ -1363,13 +1547,13 @@ lunr.TokenSet.fromFuzzyString = function (str, editDistance) { if (frame.str.length == 1) { transposeNode.final = true - } else { - stack.push({ - node: transposeNode, - editsRemaining: frame.editsRemaining - 1, - str: charA + frame.str.slice(2) - }) } + + stack.push({ + node: transposeNode, + editsRemaining: frame.editsRemaining - 1, + str: charA + frame.str.slice(2) + }) } } @@ -1388,14 +1572,13 @@ lunr.TokenSet.fromFuzzyString = function (str, editDistance) { */ lunr.TokenSet.fromString = function (str) { var node = new lunr.TokenSet, - root = node, - wildcardFound = false + root = node /* * Iterates through all characters within the passed string * appending a node for each character. * - * As soon as a wildcard character is found then a self + * When a wildcard character is found then a self * referencing edge is introduced to continually match * any number of any characters. */ @@ -1404,7 +1587,6 @@ lunr.TokenSet.fromString = function (str) { final = (i == len - 1) if (char == "*") { - wildcardFound = true node.edges[char] = node node.final = final @@ -1414,11 +1596,6 @@ lunr.TokenSet.fromString = function (str) { node.edges[char] = next node = next - - // TODO: is this needed anymore? - if (wildcardFound) { - node.edges["*"] = root - } } } @@ -1429,6 +1606,10 @@ lunr.TokenSet.fromString = function (str) { * Converts this TokenSet into an array of strings * contained within the TokenSet. * + * This is not intended to be used on a TokenSet that + * contains wildcards, in these cases the results are + * undefined and are likely to cause an infinite loop. + * * @returns {string[]} */ lunr.TokenSet.prototype.toArray = function () { @@ -1445,6 +1626,11 @@ lunr.TokenSet.prototype.toArray = function () { len = edges.length if (frame.node.final) { + /* In Safari, at this point the prefix is sometimes corrupted, see: + * https://github.com/olivernn/lunr.js/issues/279 Calling any + * String.prototype method forces Safari to "cast" this string to what + * it's supposed to be, fixing the bug. */ + frame.prefix.charAt(0) words.push(frame.prefix) } @@ -1641,7 +1827,7 @@ lunr.TokenSet.Builder.prototype.minimize = function (downTo) { } /*! * lunr.Index - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -1655,7 +1841,7 @@ lunr.TokenSet.Builder.prototype.minimize = function (downTo) { * @constructor * @param {Object} attrs - The attributes of the built search index. * @param {Object} attrs.invertedIndex - An index of term/field to document reference. - * @param {Object} attrs.documentVectors - Document vectors keyed by document reference. + * @param {Object} attrs.fieldVectors - Field vectors * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens. * @param {string[]} attrs.fields - The names of indexed document fields. * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms. @@ -1701,6 +1887,12 @@ lunr.Index = function (attrs) { * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2. * Avoid large values for edit distance to improve query performance. * + * Each term also supports a presence modifier. By default a term's presence in document is optional, however + * this can be changed to either required or prohibited. For a term's presence to be required in a document the + * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and + * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not + * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'. + * * To escape special characters the backslash character '\' can be used, this allows searches to include * characters that would normally be considered modifiers, e.g. `foo\~2` will search for a term "foo~2" instead * of attempting to apply a boost of 2 to the search term "foo". @@ -1716,13 +1908,16 @@ lunr.Index = function (attrs) { * hello^10 * @example term with an edit distance of 2 * hello~2 + * @example terms with presence modifiers + * -foo +bar baz */ /** * Performs a search against the index using lunr query syntax. * * Results will be returned sorted by their score, the most relevant results - * will be returned first. + * will be returned first. For details on how the score is calculated, please see + * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}. * * For more programmatic querying use lunr.Index#query. * @@ -1773,7 +1968,18 @@ lunr.Index.prototype.query = function (fn) { var query = new lunr.Query(this.fields), matchingFields = Object.create(null), queryVectors = Object.create(null), - termFieldCache = Object.create(null) + termFieldCache = Object.create(null), + requiredMatches = Object.create(null), + prohibitedMatches = Object.create(null) + + /* + * To support field level boosts a query vector is created per + * field. An empty vector is eagerly created to support negated + * queries. + */ + for (var i = 0; i < this.fields.length; i++) { + queryVectors[this.fields[i]] = new lunr.Vector + } fn.call(query, query) @@ -1787,10 +1993,13 @@ lunr.Index.prototype.query = function (fn) { * for a single query term. */ var clause = query.clauses[i], - terms = null + terms = null, + clauseMatches = lunr.Set.complete if (clause.usePipeline) { - terms = this.pipeline.runString(clause.term) + terms = this.pipeline.runString(clause.term, { + fields: clause.fields + }) } else { terms = [clause.term] } @@ -1814,6 +2023,21 @@ lunr.Index.prototype.query = function (fn) { var termTokenSet = lunr.TokenSet.fromClause(clause), expandedTerms = this.tokenSet.intersect(termTokenSet).toArray() + /* + * If a term marked as required does not exist in the tokenSet it is + * impossible for the search to return any matches. We set all the field + * scoped required matches set to empty and stop examining any further + * clauses. + */ + if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) { + for (var k = 0; k < clause.fields.length; k++) { + var field = clause.fields[k] + requiredMatches[field] = lunr.Set.empty + } + + break + } + for (var j = 0; j < expandedTerms.length; j++) { /* * For each term get the posting and termIndex, this is required for @@ -1835,26 +2059,50 @@ lunr.Index.prototype.query = function (fn) { var field = clause.fields[k], fieldPosting = posting[field], matchingDocumentRefs = Object.keys(fieldPosting), - termField = expandedTerm + "/" + field + termField = expandedTerm + "/" + field, + matchingDocumentsSet = new lunr.Set(matchingDocumentRefs) /* - * To support field level boosts a query vector is created per - * field. This vector is populated using the termIndex found for - * the term and a unit value with the appropriate boost applied. + * if the presence of this term is required ensure that the matching + * documents are added to the set of required matches for this clause. * - * If the query vector for this field does not exist yet it needs - * to be created. */ - if (queryVectors[field] === undefined) { - queryVectors[field] = new lunr.Vector + if (clause.presence == lunr.Query.presence.REQUIRED) { + clauseMatches = clauseMatches.union(matchingDocumentsSet) + + if (requiredMatches[field] === undefined) { + requiredMatches[field] = lunr.Set.complete + } + } + + /* + * if the presence of this term is prohibited ensure that the matching + * documents are added to the set of prohibited matches for this field, + * creating that set if it does not yet exist. + */ + if (clause.presence == lunr.Query.presence.PROHIBITED) { + if (prohibitedMatches[field] === undefined) { + prohibitedMatches[field] = lunr.Set.empty + } + + prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet) + + /* + * Prohibited matches should not be part of the query vector used for + * similarity scoring and no metadata should be extracted so we continue + * to the next field + */ + continue } /* + * The query field vector is populated using the termIndex found for + * the term and a unit value with the appropriate boost applied. * Using upsert because there could already be an entry in the vector * for the term we are working with. In that case we just add the scores * together. */ - queryVectors[field].upsert(termIndex, 1 * clause.boost, function (a, b) { return a + b }) + queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b }) /** * If we've already seen this term, field combo then we've already collected @@ -1888,12 +2136,65 @@ lunr.Index.prototype.query = function (fn) { } } } + + /** + * If the presence was required we need to update the requiredMatches field sets. + * We do this after all fields for the term have collected their matches because + * the clause terms presence is required in _any_ of the fields not _all_ of the + * fields. + */ + if (clause.presence === lunr.Query.presence.REQUIRED) { + for (var k = 0; k < clause.fields.length; k++) { + var field = clause.fields[k] + requiredMatches[field] = requiredMatches[field].intersect(clauseMatches) + } + } + } + + /** + * Need to combine the field scoped required and prohibited + * matching documents into a global set of required and prohibited + * matches + */ + var allRequiredMatches = lunr.Set.complete, + allProhibitedMatches = lunr.Set.empty + + for (var i = 0; i < this.fields.length; i++) { + var field = this.fields[i] + + if (requiredMatches[field]) { + allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field]) + } + + if (prohibitedMatches[field]) { + allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field]) + } } var matchingFieldRefs = Object.keys(matchingFields), results = [], matches = Object.create(null) + /* + * If the query is negated (contains only prohibited terms) + * we need to get _all_ fieldRefs currently existing in the + * index. This is only done when we know that the query is + * entirely prohibited terms to avoid any cost of getting all + * fieldRefs unnecessarily. + * + * Additionally, blank MatchData must be created to correctly + * populate the results. + */ + if (query.isNegated()) { + matchingFieldRefs = Object.keys(this.fieldVectors) + + for (var i = 0; i < matchingFieldRefs.length; i++) { + var matchingFieldRef = matchingFieldRefs[i] + var fieldRef = lunr.FieldRef.fromString(matchingFieldRef) + matchingFields[matchingFieldRef] = new lunr.MatchData + } + } + for (var i = 0; i < matchingFieldRefs.length; i++) { /* * Currently we have document fields that match the query, but we @@ -1904,8 +2205,17 @@ lunr.Index.prototype.query = function (fn) { * above, and combined into a final document score using addition. */ var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]), - docRef = fieldRef.docRef, - fieldVector = this.fieldVectors[fieldRef], + docRef = fieldRef.docRef + + if (!allRequiredMatches.contains(docRef)) { + continue + } + + if (allProhibitedMatches.contains(docRef)) { + continue + } + + var fieldVector = this.fieldVectors[fieldRef], score = queryVectors[fieldRef.fieldName].similarity(fieldVector), docMatch @@ -1970,7 +2280,7 @@ lunr.Index.load = function (serializedIndex) { var attrs = {}, fieldVectors = {}, serializedVectors = serializedIndex.fieldVectors, - invertedIndex = {}, + invertedIndex = Object.create(null), serializedInvertedIndex = serializedIndex.invertedIndex, tokenSetBuilder = new lunr.TokenSet.Builder, pipeline = lunr.Pipeline.load(serializedIndex.pipeline) @@ -2009,7 +2319,7 @@ lunr.Index.load = function (serializedIndex) { } /*! * lunr.Builder - * Copyright (C) 2018 Oliver Nightingale + * Copyright (C) 2019 Oliver Nightingale */ /** @@ -2038,7 +2348,8 @@ lunr.Index.load = function (serializedIndex) { */ lunr.Builder = function () { this._ref = "id" - this._fields = [] + this._fields = Object.create(null) + this._documents = Object.create(null) this.invertedIndex = Object.create(null) this.fieldTermFrequencies = {} this.fieldLengths = {} @@ -2068,6 +2379,20 @@ lunr.Builder.prototype.ref = function (ref) { this._ref = ref } +/** + * A function that is used to extract a field from a document. + * + * Lunr expects a field to be at the top level of a document, if however the field + * is deeply nested within a document an extractor function can be used to extract + * the right field for indexing. + * + * @callback fieldExtractor + * @param {object} doc - The document being added to the index. + * @returns {?(string|object|object[])} obj - The object that will be indexed for this field. + * @example Extracting a nested field + * function (doc) { return doc.nested.field } + */ + /** * Adds a field to the list of document fields that will be indexed. Every document being * indexed should have this field. Null values for this field in indexed documents will @@ -2076,10 +2401,22 @@ lunr.Builder.prototype.ref = function (ref) { * All fields should be added before adding documents to the index. Adding fields after * a document has been indexed will have no effect on already indexed documents. * - * @param {string} field - The name of a field to index in all documents. + * Fields can be boosted at build time. This allows terms within that field to have more + * importance when ranking search results. Use a field boost to specify that matches within + * one field are more important than other fields. + * + * @param {string} fieldName - The name of a field to index in all documents. + * @param {object} attributes - Optional attributes associated with this field. + * @param {number} [attributes.boost=1] - Boost applied to all terms within this field. + * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document. + * @throws {RangeError} fieldName cannot contain unsupported characters '/' */ -lunr.Builder.prototype.field = function (field) { - this._fields.push(field) +lunr.Builder.prototype.field = function (fieldName, attributes) { + if (/\//.test(fieldName)) { + throw new RangeError ("Field '" + fieldName + "' contains illegal character '/'") + } + + this._fields[fieldName] = attributes || {} } /** @@ -2121,17 +2458,27 @@ lunr.Builder.prototype.k1 = function (number) { * it should have all fields defined for indexing, though null or undefined values will not * cause errors. * + * Entire documents can be boosted at build time. Applying a boost to a document indicates that + * this document should rank higher in search results than other documents. + * * @param {object} doc - The document to add to the index. + * @param {object} attributes - Optional attributes associated with this document. + * @param {number} [attributes.boost=1] - Boost applied to all terms within this document. */ -lunr.Builder.prototype.add = function (doc) { - var docRef = doc[this._ref] +lunr.Builder.prototype.add = function (doc, attributes) { + var docRef = doc[this._ref], + fields = Object.keys(this._fields) + this._documents[docRef] = attributes || {} this.documentCount += 1 - for (var i = 0; i < this._fields.length; i++) { - var fieldName = this._fields[i], - field = doc[fieldName], - tokens = this.tokenizer(field), + for (var i = 0; i < fields.length; i++) { + var fieldName = fields[i], + extractor = this._fields[fieldName].extractor, + field = extractor ? extractor(doc) : doc[fieldName], + tokens = this.tokenizer(field, { + fields: [fieldName] + }), terms = this.pipeline.run(tokens), fieldRef = new lunr.FieldRef (docRef, fieldName), fieldTerms = Object.create(null) @@ -2159,8 +2506,8 @@ lunr.Builder.prototype.add = function (doc) { posting["_index"] = this.termIndex this.termIndex += 1 - for (var k = 0; k < this._fields.length; k++) { - posting[this._fields[k]] = Object.create(null) + for (var k = 0; k < fields.length; k++) { + posting[fields[k]] = Object.create(null) } this.invertedIndex[term] = posting @@ -2211,9 +2558,11 @@ lunr.Builder.prototype.calculateAverageFieldLengths = function () { accumulator[field] += this.fieldLengths[fieldRef] } - for (var i = 0; i < this._fields.length; i++) { - var field = this._fields[i] - accumulator[field] = accumulator[field] / documentsWithField[field] + var fields = Object.keys(this._fields) + + for (var i = 0; i < fields.length; i++) { + var fieldName = fields[i] + accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName] } this.averageFieldLength = accumulator @@ -2232,13 +2581,17 @@ lunr.Builder.prototype.createFieldVectors = function () { for (var i = 0; i < fieldRefsLength; i++) { var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]), - field = fieldRef.fieldName, + fieldName = fieldRef.fieldName, fieldLength = this.fieldLengths[fieldRef], fieldVector = new lunr.Vector, termFrequencies = this.fieldTermFrequencies[fieldRef], terms = Object.keys(termFrequencies), termsLength = terms.length + + var fieldBoost = this._fields[fieldName].boost || 1, + docBoost = this._documents[fieldRef.docRef].boost || 1 + for (var j = 0; j < termsLength; j++) { var term = terms[j], tf = termFrequencies[term], @@ -2252,7 +2605,9 @@ lunr.Builder.prototype.createFieldVectors = function () { idf = termIdfCache[term] } - score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[field])) + tf) + score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf) + score *= fieldBoost + score *= docBoost scoreWithPrecision = Math.round(score * 1000) / 1000 // Converts 1.23456789 to 1.234. // Reducing the precision so that the vectors take up less @@ -2298,7 +2653,7 @@ lunr.Builder.prototype.build = function () { invertedIndex: this.invertedIndex, fieldVectors: this.fieldVectors, tokenSet: this.tokenSet, - fields: this._fields, + fields: Object.keys(this._fields), pipeline: this.searchPipeline }) } @@ -2336,7 +2691,7 @@ lunr.Builder.prototype.use = function (fn) { */ lunr.MatchData = function (term, field, metadata) { var clonedMetadata = Object.create(null), - metadataKeys = Object.keys(metadata) + metadataKeys = Object.keys(metadata || {}) // Cloning the metadata to prevent the original // being mutated during match data combination. @@ -2349,8 +2704,11 @@ lunr.MatchData = function (term, field, metadata) { } this.metadata = Object.create(null) - this.metadata[term] = Object.create(null) - this.metadata[term][field] = clonedMetadata + + if (term !== undefined) { + this.metadata[term] = Object.create(null) + this.metadata[term][field] = clonedMetadata + } } /** @@ -2465,11 +2823,42 @@ lunr.Query = function (allFields) { * wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING * }) */ + lunr.Query.wildcard = new String ("*") lunr.Query.wildcard.NONE = 0 lunr.Query.wildcard.LEADING = 1 lunr.Query.wildcard.TRAILING = 2 +/** + * Constants for indicating what kind of presence a term must have in matching documents. + * + * @constant + * @enum {number} + * @see lunr.Query~Clause + * @see lunr.Query#clause + * @see lunr.Query#term + * @example query term with required presence + * query.term('foo', { presence: lunr.Query.presence.REQUIRED }) + */ +lunr.Query.presence = { + /** + * Term's presence in a document is optional, this is the default value. + */ + OPTIONAL: 1, + + /** + * Term's presence in a document is required, documents that do not contain + * this term will not be returned. + */ + REQUIRED: 2, + + /** + * Term's presence in a document is prohibited, documents that do contain + * this term will not be returned. + */ + PROHIBITED: 3 +} + /** * A single clause in a {@link lunr.Query} contains a term and details on how to * match that term against a {@link lunr.Index}. @@ -2479,7 +2868,8 @@ lunr.Query.wildcard.TRAILING = 2 * @property {number} [boost=1] - Any boost that should be applied when matching this clause. * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be. * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline. - * @property {number} [wildcard=0] - Whether the term should have wildcards appended or prepended. + * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended. + * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents. */ /** @@ -2517,17 +2907,44 @@ lunr.Query.prototype.clause = function (clause) { clause.term = "" + clause.term + "*" } + if (!('presence' in clause)) { + clause.presence = lunr.Query.presence.OPTIONAL + } + this.clauses.push(clause) return this } +/** + * A negated query is one in which every clause has a presence of + * prohibited. These queries require some special processing to return + * the expected results. + * + * @returns boolean + */ +lunr.Query.prototype.isNegated = function () { + for (var i = 0; i < this.clauses.length; i++) { + if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) { + return false + } + } + + return true +} + /** * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause} * to the list of clauses that make up this query. * - * @param {string} term - The term to add to the query. - * @param {Object} [options] - Any additional properties to add to the query clause. + * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion + * to a token or token-like string should be done before calling this method. + * + * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an + * array, each term in the array will share the same options. + * + * @param {object|object[]} term - The term(s) to add to the query. + * @param {object} [options] - Any additional properties to add to the query clause. * @returns {lunr.Query} * @see lunr.Query#clause * @see lunr.Query~Clause @@ -2539,10 +2956,17 @@ lunr.Query.prototype.clause = function (clause) { * boost: 10, * wildcard: lunr.Query.wildcard.TRAILING * }) + * @example using lunr.tokenizer to convert a string to tokens before using them as terms + * query.term(lunr.tokenizer("foo bar")) */ lunr.Query.prototype.term = function (term, options) { + if (Array.isArray(term)) { + term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this) + return this + } + var clause = options || {} - clause.term = term + clause.term = term.toString() this.clause(clause) @@ -2654,6 +3078,7 @@ lunr.QueryLexer.FIELD = 'FIELD' lunr.QueryLexer.TERM = 'TERM' lunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE' lunr.QueryLexer.BOOST = 'BOOST' +lunr.QueryLexer.PRESENCE = 'PRESENCE' lunr.QueryLexer.lexField = function (lexer) { lexer.backup() @@ -2742,6 +3167,22 @@ lunr.QueryLexer.lexText = function (lexer) { return lunr.QueryLexer.lexBoost } + // "+" indicates term presence is required + // checking for length to ensure that only + // leading "+" are considered + if (char == "+" && lexer.width() === 1) { + lexer.emit(lunr.QueryLexer.PRESENCE) + return lunr.QueryLexer.lexText + } + + // "-" indicates term presence is prohibited + // checking for length to ensure that only + // leading "-" are considered + if (char == "-" && lexer.width() === 1) { + lexer.emit(lunr.QueryLexer.PRESENCE) + return lunr.QueryLexer.lexText + } + if (char.match(lunr.QueryLexer.termSeparator)) { return lunr.QueryLexer.lexTerm } @@ -2759,7 +3200,7 @@ lunr.QueryParser.prototype.parse = function () { this.lexer.run() this.lexemes = this.lexer.lexemes - var state = lunr.QueryParser.parseFieldOrTerm + var state = lunr.QueryParser.parseClause while (state) { state = state(this) @@ -2784,7 +3225,7 @@ lunr.QueryParser.prototype.nextClause = function () { this.currentClause = {} } -lunr.QueryParser.parseFieldOrTerm = function (parser) { +lunr.QueryParser.parseClause = function (parser) { var lexeme = parser.peekLexeme() if (lexeme == undefined) { @@ -2792,6 +3233,8 @@ lunr.QueryParser.parseFieldOrTerm = function (parser) { } switch (lexeme.type) { + case lunr.QueryLexer.PRESENCE: + return lunr.QueryParser.parsePresence case lunr.QueryLexer.FIELD: return lunr.QueryParser.parseField case lunr.QueryLexer.TERM: @@ -2807,6 +3250,43 @@ lunr.QueryParser.parseFieldOrTerm = function (parser) { } } +lunr.QueryParser.parsePresence = function (parser) { + var lexeme = parser.consumeLexeme() + + if (lexeme == undefined) { + return + } + + switch (lexeme.str) { + case "-": + parser.currentClause.presence = lunr.Query.presence.PROHIBITED + break + case "+": + parser.currentClause.presence = lunr.Query.presence.REQUIRED + break + default: + var errorMessage = "unrecognised presence operator'" + lexeme.str + "'" + throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end) + } + + var nextLexeme = parser.peekLexeme() + + if (nextLexeme == undefined) { + var errorMessage = "expecting term or field, found nothing" + throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end) + } + + switch (nextLexeme.type) { + case lunr.QueryLexer.FIELD: + return lunr.QueryParser.parseField + case lunr.QueryLexer.TERM: + return lunr.QueryParser.parseTerm + default: + var errorMessage = "expecting term or field, found '" + nextLexeme.type + "'" + throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end) + } +} + lunr.QueryParser.parseField = function (parser) { var lexeme = parser.consumeLexeme() @@ -2870,6 +3350,9 @@ lunr.QueryParser.parseTerm = function (parser) { return lunr.QueryParser.parseEditDistance case lunr.QueryLexer.BOOST: return lunr.QueryParser.parseBoost + case lunr.QueryLexer.PRESENCE: + parser.nextClause() + return lunr.QueryParser.parsePresence default: var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'" throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end) @@ -2910,6 +3393,9 @@ lunr.QueryParser.parseEditDistance = function (parser) { return lunr.QueryParser.parseEditDistance case lunr.QueryLexer.BOOST: return lunr.QueryParser.parseBoost + case lunr.QueryLexer.PRESENCE: + parser.nextClause() + return lunr.QueryParser.parsePresence default: var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'" throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end) @@ -2950,6 +3436,9 @@ lunr.QueryParser.parseBoost = function (parser) { return lunr.QueryParser.parseEditDistance case lunr.QueryLexer.BOOST: return lunr.QueryParser.parseBoost + case lunr.QueryLexer.PRESENCE: + parser.nextClause() + return lunr.QueryParser.parsePresence default: var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'" throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end) diff --git a/site/search/main.js b/site/search/main.js index 0a82ab56a..0e1fc8116 100644 --- a/site/search/main.js +++ b/site/search/main.js @@ -43,7 +43,7 @@ function displayResults (results) { function doSearch () { var query = document.getElementById('mkdocs-search-query').value; - if (query.length > 2) { + if (query.length > min_search_length) { if (!window.Worker) { displayResults(search(query)); } else { @@ -73,6 +73,8 @@ function onWorkerMessage (e) { } else if (e.data.results) { var results = e.data.results; displayResults(results); + } else if (e.data.config) { + min_search_length = e.data.config.min_search_length-1; } } diff --git a/site/search/search_index.json b/site/search/search_index.json index e97e9a661..78f8c854b 100644 --- a/site/search/search_index.json +++ b/site/search/search_index.json @@ -1 +1 @@ -{"config":{"lang":["en"],"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Geoweaver 2018 ESIP Lab Incubator Project Geoweaver is a web system allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It is a perfect alternative to SSH client (e.g., Putty), FTP client, and scientific workflow software. Table of Contents 1. Project Goals 2. Installation 2.1 Dependencies 2.2 Quick Install Linux Mac Windows 2.3 Developer Install Docker Tomcat War Cloud VM Template 2.4 Build from source 3. Demo 4. Usage 4.1 Add A Server 4.2 Create A Process 4.3 Create A Workflow 4.4 Run Workflow 4.5 Browse Provenance 4.6 Retrieve and Display Results 4.7 I/O workflows 5. Documentation 6. Dependencies 7. License 8. Author 1. Project Goals 1) turning large-scale distributed deep network into manageable modernized workflows; 2) boosting higher utilization ratio of the existing cyberinfrastructures by separating scientists from tedious technical details; 3) enhancing the frequency and accuracy of classified land cover land use maps for agricultural purposes; 4) enabling the tracking of provenance by recording the execution logs in structured tables to evaluate the quality of the result maps; 5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series. 2. Installation 2.1 Dependencies If you choose \"Quick Install\", no need to install these dependencies separately. The install scripts will retrieve these dependencies automatically. Java 1.8+ (OpenJDK 8 or higher) Tomcat 8.0+ Apache Maven 3.5+ (optional for building from source) Docker 18.09.1+ (for install via docker) Docker-compose 1.23.1+ (for install via docker) 2.2 Quick Install Linux This way works for most linux releases, e.g., Ubuntu, CentOS, RedHat, OpenBSD, etc. Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-linux.sh ./install-linux.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh Mac Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-mac.sh ./install-mac.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh Windows Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver ./install-windows.bat Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.bat . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.bat 2.3 Developer Install This section is dedicated for high-level users who have better background on web technologies and familiar with MySQL, Tomcat and Docker. If you are not familiar with either of them, we strongly suggest you use the \"Quick Install\" way to install Geoweaver. Docker We use docker-compose to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps. Install Clone this repo to your machine git clone https://github.com/ESIPFed/Geoweaver.git Enter the repo and create a new folder target . Download a Geoweaver war package from the release page and save it in the created target folder. cd Geoweaver && mkdir target && cd target wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.0/Geoweaver-0.7.0.war -O Geoweaver.war Run docker to start rolling. After the command is finished, Geoweaver should be up and running. cd .. && docker-compose up -d The address is: http://your-ip:your-port/Geoweaver/web/geoweaver Replace the your-ip , your-port with the real domain of your tomcat. For example, localhost:8080 . Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose . Otherwise there might be port conflict error on 3306 and 8080 . Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. docker docker-compose Shutdown To stop Geoweaver, type: docker stop $(docker ps -aq) Tomcat War Install Download the latest release war and copy it to the webapps directory of Tomcat (e.g. /usr/local/tomcat). Start Tomcat. wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.6.10/Geoweaver-0.6.10.war -O Geoweaver.war cp Geoweaver.war /usr/local/tomcat/webapps/ /usr/local/tomcat/bin/startup.sh After the tomcat is fully started, configure the database connection. The configuration files are WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/cc_secret.properties Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and WEB-INF/classes/cc_secret.properties (database username and password: database_user=root database_password=xxxxxxxx). ( Note: the database must be initiated by the SQL file under the folder Geoweaver/docker/db first. ) mysql -u root -p < docker/db/gw.sql Enter the following URL into browser address bar to open Geoweaver: http://your-ip:your-port/Geoweaver/web/geoweaver Shutdown To stop Geoweaver, use: /usr/local/tomcat/bin/shutdown.sh Cloud VM Template Install We provide a ready-to-use cloud template for you to install on mainstream cloud platforms like AWS, Google Cloud, Azure, OpenStack and CloudStack. Please go here to download the template (3.1 Gigabytes). The username and password of the instance would be csiss and password respectively. To start Geoweaver, go to directory /home/csiss/Geoweaver and execute docker-compose up -d. With no accident, Geoweaver will be up and running. cd /home/csiss/Geoweaver && docker-compose up -d Shutdown To stop Geoweaver, use: docker stop $(docker ps -aq) 2.4 Build from source Use maven to build. In the command line go to the root folder and execute mvn install . After a success build, the Geoweaver war package will be under the directory: Geoweaver/target/Geoweaver-.war . 3. Demo A live demo site is available in George Mason University: I am a link, hit me . Here is a use case of Geoweaver, using deep neural network like LSTM RNN and SegNet to classify landsat images into agricultural land use maps. In this case, Geoweaver can help stakeholders get crop maps with better accuracy and high temporal resolution by providing a deep-learning-powered and distributed workflow system. Animation demo: 4. Usage 4.1 Add A Server Enroll a server to Geoweaver is simple. The server must have SSH server installed and enabled. The server must be accessible from Geoweaver host server. 4.2 Create A Process Geoweaver supports Bash Shell scripts as processes. You can write bash command lines in the code area. Note: the commands should exist on the target hosts. 4.3 Create A Workflow Geoweaver can link the processes together to form a workflow. To connect two processes, press shift key while dragging from one process to another. 4.4 Run Workflow Geoweaver can run the created workflows on the enlisted servers. During the running, Geoweaver is monitoring the status of each process. The color of process text in their circles indicate the process status. Yellow means running, green means completed, and red means failure. 4.5 Browse Provenance Geoweaver stores all the inputs and outputs of each process run. Users can check the workflow provenance by simply clicking. 4.6 Retrieve and Display Results Geoweaver can retrieve the result files of the executed workflows and visualize them if the format is supported (png, jpg, bmp, etc. The list is expanding. I am on it.). 4.7 I/O workflows The workflows can be exported and move around and imported back. 5. Documentation Project Proposal August Report September Report October Report November Report December Report 6. Dependencies This project is impossible without the support of several fantastic open source libraries. d3.js - BSD 3-Clause graph-creator - MIT License bootstrap - MIT License CodeMirror - MIT License JQuery Terminal - MIT License 7. License MIT 8. Author developer list","title":"Home"},{"location":"#geoweaver","text":"2018 ESIP Lab Incubator Project Geoweaver is a web system allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It is a perfect alternative to SSH client (e.g., Putty), FTP client, and scientific workflow software.","title":"Geoweaver"},{"location":"#table-of-contents","text":"1. Project Goals 2. Installation 2.1 Dependencies 2.2 Quick Install Linux Mac Windows 2.3 Developer Install Docker Tomcat War Cloud VM Template 2.4 Build from source 3. Demo 4. Usage 4.1 Add A Server 4.2 Create A Process 4.3 Create A Workflow 4.4 Run Workflow 4.5 Browse Provenance 4.6 Retrieve and Display Results 4.7 I/O workflows 5. Documentation 6. Dependencies 7. License 8. Author","title":"Table of Contents"},{"location":"#1-project-goals","text":"1) turning large-scale distributed deep network into manageable modernized workflows; 2) boosting higher utilization ratio of the existing cyberinfrastructures by separating scientists from tedious technical details; 3) enhancing the frequency and accuracy of classified land cover land use maps for agricultural purposes; 4) enabling the tracking of provenance by recording the execution logs in structured tables to evaluate the quality of the result maps; 5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series.","title":"1. Project Goals"},{"location":"#2-installation","text":"","title":"2. Installation"},{"location":"#21-dependencies","text":"If you choose \"Quick Install\", no need to install these dependencies separately. The install scripts will retrieve these dependencies automatically. Java 1.8+ (OpenJDK 8 or higher) Tomcat 8.0+ Apache Maven 3.5+ (optional for building from source) Docker 18.09.1+ (for install via docker) Docker-compose 1.23.1+ (for install via docker)","title":"2.1 Dependencies"},{"location":"#22-quick-install","text":"","title":"2.2 Quick Install"},{"location":"#linux","text":"This way works for most linux releases, e.g., Ubuntu, CentOS, RedHat, OpenBSD, etc. Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-linux.sh ./install-linux.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh","title":"Linux"},{"location":"#mac","text":"Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-mac.sh ./install-mac.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh","title":"Mac"},{"location":"#windows","text":"Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver ./install-windows.bat Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8080/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.bat . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.bat","title":"Windows"},{"location":"#23-developer-install","text":"This section is dedicated for high-level users who have better background on web technologies and familiar with MySQL, Tomcat and Docker. If you are not familiar with either of them, we strongly suggest you use the \"Quick Install\" way to install Geoweaver.","title":"2.3 Developer Install"},{"location":"#docker","text":"We use docker-compose to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps.","title":"Docker"},{"location":"#install","text":"Clone this repo to your machine git clone https://github.com/ESIPFed/Geoweaver.git Enter the repo and create a new folder target . Download a Geoweaver war package from the release page and save it in the created target folder. cd Geoweaver && mkdir target && cd target wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.0/Geoweaver-0.7.0.war -O Geoweaver.war Run docker to start rolling. After the command is finished, Geoweaver should be up and running. cd .. && docker-compose up -d The address is: http://your-ip:your-port/Geoweaver/web/geoweaver Replace the your-ip , your-port with the real domain of your tomcat. For example, localhost:8080 . Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose . Otherwise there might be port conflict error on 3306 and 8080 . Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. docker docker-compose","title":"Install"},{"location":"#shutdown","text":"To stop Geoweaver, type: docker stop $(docker ps -aq)","title":"Shutdown"},{"location":"#tomcat-war","text":"","title":"Tomcat War"},{"location":"#install_1","text":"Download the latest release war and copy it to the webapps directory of Tomcat (e.g. /usr/local/tomcat). Start Tomcat. wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.6.10/Geoweaver-0.6.10.war -O Geoweaver.war cp Geoweaver.war /usr/local/tomcat/webapps/ /usr/local/tomcat/bin/startup.sh After the tomcat is fully started, configure the database connection. The configuration files are WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/cc_secret.properties Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and WEB-INF/classes/cc_secret.properties (database username and password: database_user=root database_password=xxxxxxxx). ( Note: the database must be initiated by the SQL file under the folder Geoweaver/docker/db first. ) mysql -u root -p < docker/db/gw.sql Enter the following URL into browser address bar to open Geoweaver: http://your-ip:your-port/Geoweaver/web/geoweaver","title":"Install"},{"location":"#shutdown_1","text":"To stop Geoweaver, use: /usr/local/tomcat/bin/shutdown.sh","title":"Shutdown"},{"location":"#cloud-vm-template","text":"","title":"Cloud VM Template"},{"location":"#install_2","text":"We provide a ready-to-use cloud template for you to install on mainstream cloud platforms like AWS, Google Cloud, Azure, OpenStack and CloudStack. Please go here to download the template (3.1 Gigabytes). The username and password of the instance would be csiss and password respectively. To start Geoweaver, go to directory /home/csiss/Geoweaver and execute docker-compose up -d. With no accident, Geoweaver will be up and running. cd /home/csiss/Geoweaver && docker-compose up -d","title":"Install"},{"location":"#shutdown_2","text":"To stop Geoweaver, use: docker stop $(docker ps -aq)","title":"Shutdown"},{"location":"#24-build-from-source","text":"Use maven to build. In the command line go to the root folder and execute mvn install . After a success build, the Geoweaver war package will be under the directory: Geoweaver/target/Geoweaver-.war .","title":"2.4 Build from source"},{"location":"#3-demo","text":"A live demo site is available in George Mason University: I am a link, hit me . Here is a use case of Geoweaver, using deep neural network like LSTM RNN and SegNet to classify landsat images into agricultural land use maps. In this case, Geoweaver can help stakeholders get crop maps with better accuracy and high temporal resolution by providing a deep-learning-powered and distributed workflow system. Animation demo:","title":"3. Demo"},{"location":"#4-usage","text":"","title":"4. Usage"},{"location":"#41-add-a-server","text":"Enroll a server to Geoweaver is simple. The server must have SSH server installed and enabled. The server must be accessible from Geoweaver host server.","title":"4.1 Add A Server"},{"location":"#42-create-a-process","text":"Geoweaver supports Bash Shell scripts as processes. You can write bash command lines in the code area. Note: the commands should exist on the target hosts.","title":"4.2 Create A Process"},{"location":"#43-create-a-workflow","text":"Geoweaver can link the processes together to form a workflow. To connect two processes, press shift key while dragging from one process to another.","title":"4.3 Create A Workflow"},{"location":"#44-run-workflow","text":"Geoweaver can run the created workflows on the enlisted servers. During the running, Geoweaver is monitoring the status of each process. The color of process text in their circles indicate the process status. Yellow means running, green means completed, and red means failure.","title":"4.4 Run Workflow"},{"location":"#45-browse-provenance","text":"Geoweaver stores all the inputs and outputs of each process run. Users can check the workflow provenance by simply clicking.","title":"4.5 Browse Provenance"},{"location":"#46-retrieve-and-display-results","text":"Geoweaver can retrieve the result files of the executed workflows and visualize them if the format is supported (png, jpg, bmp, etc. The list is expanding. I am on it.).","title":"4.6 Retrieve and Display Results"},{"location":"#47-io-workflows","text":"The workflows can be exported and move around and imported back.","title":"4.7 I/O workflows"},{"location":"#5-documentation","text":"Project Proposal August Report September Report October Report November Report December Report","title":"5. Documentation"},{"location":"#6-dependencies","text":"This project is impossible without the support of several fantastic open source libraries. d3.js - BSD 3-Clause graph-creator - MIT License bootstrap - MIT License CodeMirror - MIT License JQuery Terminal - MIT License","title":"6. Dependencies"},{"location":"#7-license","text":"MIT","title":"7. License"},{"location":"#8-author","text":"developer list","title":"8. Author"}]} \ No newline at end of file +{"config":{"lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Geoweaver 2018 ESIP Lab Incubator Project Geoweaver is a browser-based software allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It provides all-in-one capacity including SSH client (e.g., Putty), FTP client, and scientific workflow software. It can be run from local machines. GeoWeaver is a community effort. Any contribution is welcome and greatly appreciated! Geoweaver Online API Table of Contents Software Goals Installation Dependencies Quick Install (Recommended) Developer Install Linux Mac Windows Docker Tomcat War Cloud VM Template Build from source Demo Tutorial Citation Dependencies License Software Goals 1) turning large-scale distributed deep network into manageable modernized workflows; 2) boosting higher utilization ratio of the existing cyberinfrastructures by separating scientists from tedious technical details; 3) enhancing the frequency and accuracy of classified land cover land use maps for agricultural purposes; 4) enabling the tracking of provenance by recording the execution logs in structured tables to evaluate the quality of the result maps; 5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series. Installation Dependencies Java 1.8+ (OpenJDK 8 or higher) !(only for install via docker) Docker 18.09.1+ !(only for install via docker) Docker-compose 1.23.1+ Quick Install (Recommended) Step 1: Download the latest version of geoweaver.jar Step 2: Run the command: java -jar geoweaver.jar Step 3: Open browser and enter: http://localhost:8070/Geoweaver/ .That's it! Developer Install This section is dedicated for developer users who have better background on web technologies and familiar with MySQL, H2, tomcat, docker, and maven. If you are familiar with neither of them, we strongly suggest you use the \"Quick Install\" way to install Geoweaver. Linux This way works for most linux releases, e.g., Ubuntu, CentOS, RedHat, OpenBSD, etc. Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-linux.sh ./install-linux.sh Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh Mac Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-mac.sh ./install-mac.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh Windows Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver ./install-windows.bat Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.bat . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.bat Docker We use docker-compose to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps. Install Clone this repo to your machine git clone https://github.com/ESIPFed/Geoweaver.git Enter the repo and create a new folder target . Download a Geoweaver war package from the release page and save it in the created target folder. cd Geoweaver && mkdir target && cd target wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war Run docker to start rolling. After the command is finished, Geoweaver should be up and running. cd .. && docker-compose up -d The address is: http://your-ip:your-port/Geoweaver/web/geoweaver Replace the your-ip , your-port with the real domain of your tomcat. For example, localhost:8070 . Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose . Otherwise there might be port conflict error on 3306 and 8070 . Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. docker docker-compose Shutdown To stop Geoweaver, type: docker stop $(docker ps -aq) Tomcat War Install Download the latest release war and copy it to the webapps directory of Tomcat (e.g. /usr/local/tomcat). Start Tomcat. wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war cp Geoweaver.war /usr/local/tomcat/webapps/ /usr/local/tomcat/bin/startup.sh After the tomcat is fully started, configure the database connection. The configuration files are WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/cc_secret.properties Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and WEB-INF/classes/cc_secret.properties (database username and password: database_user=root database_password=xxxxxxxx). ( Note: the MySQL database must be initiated by the SQL file under the folder Geoweaver/docker/db first. If you are using H2 database, please copy the two files: geoweaver.mv.db and geoweaver.trace.db to your user home directory before you start tomcat. ) mysql -u root -p < docker/db/gw.sql Enter the following URL into browser address bar to open Geoweaver: http://your-ip:your-port/Geoweaver/web/geoweaver Shutdown To stop Geoweaver, use: /usr/local/tomcat/bin/shutdown.sh Cloud VM Template Install We provide a ready-to-use cloud template for you to install on mainstream cloud platforms like AWS, Google Cloud, Azure, OpenStack and CloudStack. Please go here to download the template (3.1 Gigabytes). The username and password of the instance would be csiss and password respectively. To start Geoweaver, go to directory /home/csiss/Geoweaver and execute docker-compose up -d. With no accident, Geoweaver will be up and running. cd /home/csiss/Geoweaver && docker-compose up -d Shutdown To stop Geoweaver, use: docker stop $(docker ps -aq) Build from source Use maven to build. In the command line go to the root folder and execute mvn install . After a success build, the Geoweaver jar package will be under the directory: Geoweaver/target/Geoweaver-.jar . Demo A live demo site is available in George Mason University. Tutorial Geoweaver Tutorial - A beginner tutorial about what Geoweaver can do and how it works Citation If you found Geoweaver helpful in your research, please cite us: Sun, Ziheng, Liping Di, Annie Burgess, Jason A. Tullis, and Andrew B. Magill. \"Geoweaver: Advanced cyberinfrastructure for managing hybrid geoscientific AI workflows.\" ISPRS International Journal of Geo-Information 9, no. 2 (2020): 119. Dependencies This project is impossible without the support of several fantastic open source libraries. d3.js - BSD 3-Clause graph-creator - MIT License bootstrap - MIT License CodeMirror - MIT License JQuery Terminal - MIT License License MIT","title":"Home"},{"location":"#geoweaver","text":"2018 ESIP Lab Incubator Project Geoweaver is a browser-based software allowing users to easily compose and execute full-stack deep learning workflows via taking advantage of online spatial data facilities, high-performance computation platforms, and open-source deep learning libraries. It provides all-in-one capacity including SSH client (e.g., Putty), FTP client, and scientific workflow software. It can be run from local machines. GeoWeaver is a community effort. Any contribution is welcome and greatly appreciated! Geoweaver Online API","title":"Geoweaver"},{"location":"#table-of-contents","text":"Software Goals Installation Dependencies Quick Install (Recommended) Developer Install Linux Mac Windows Docker Tomcat War Cloud VM Template Build from source Demo Tutorial Citation Dependencies License","title":"Table of Contents"},{"location":"#software-goals","text":"1) turning large-scale distributed deep network into manageable modernized workflows; 2) boosting higher utilization ratio of the existing cyberinfrastructures by separating scientists from tedious technical details; 3) enhancing the frequency and accuracy of classified land cover land use maps for agricultural purposes; 4) enabling the tracking of provenance by recording the execution logs in structured tables to evaluate the quality of the result maps; 5) proof the effectiveness of operationally using large-scale distributed deep learning models in classifying Landsat image time series.","title":"Software Goals"},{"location":"#installation","text":"","title":"Installation"},{"location":"#dependencies","text":"Java 1.8+ (OpenJDK 8 or higher) !(only for install via docker) Docker 18.09.1+ !(only for install via docker) Docker-compose 1.23.1+","title":"Dependencies"},{"location":"#quick-install","text":"(Recommended) Step 1: Download the latest version of geoweaver.jar Step 2: Run the command: java -jar geoweaver.jar Step 3: Open browser and enter: http://localhost:8070/Geoweaver/ .That's it!","title":"Quick Install"},{"location":"#developer-install","text":"This section is dedicated for developer users who have better background on web technologies and familiar with MySQL, H2, tomcat, docker, and maven. If you are familiar with neither of them, we strongly suggest you use the \"Quick Install\" way to install Geoweaver.","title":"Developer Install"},{"location":"#linux","text":"This way works for most linux releases, e.g., Ubuntu, CentOS, RedHat, OpenBSD, etc. Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-linux.sh ./install-linux.sh Once the script stops, Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh","title":"Linux"},{"location":"#mac","text":"Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver chmod 755 install-mac.sh ./install-mac.sh Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.sh . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.sh","title":"Mac"},{"location":"#windows","text":"Step 1: clone the github repo git clone https://github.com/ESIPFed/Geoweaver.git Step 2: enter the folder and start the install cd Geoweaver ./install-windows.bat Once the script stops, the Geoweaver should already be up and running. Enter URL http://127.0.0.1:8070/Geoweaver/web/geoweaver in browser to open it. Optional: To stop Geoweaver, type: install/apache-tomcat-9.0.22/bin/shutdown.bat . To start Geoweaver again, type: install/apache-tomcat-9.0.22/bin/startup.bat","title":"Windows"},{"location":"#docker","text":"We use docker-compose to establish the containers for Geoweaver. As the DockerHub is not very friendly for docker-compose yaml at present, we only suggest manual to start from GitHub repo. It only has three steps.","title":"Docker"},{"location":"#install","text":"Clone this repo to your machine git clone https://github.com/ESIPFed/Geoweaver.git Enter the repo and create a new folder target . Download a Geoweaver war package from the release page and save it in the created target folder. cd Geoweaver && mkdir target && cd target wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war Run docker to start rolling. After the command is finished, Geoweaver should be up and running. cd .. && docker-compose up -d The address is: http://your-ip:your-port/Geoweaver/web/geoweaver Replace the your-ip , your-port with the real domain of your tomcat. For example, localhost:8070 . Notice: Make sure the local services like mysql and tomcat are shut down before starting docker-compose . Otherwise there might be port conflict error on 3306 and 8070 . Or you can change the port to some other free ports in the docker-compose.yml. If you don't have docker or docker-compose installed, these documents will help. docker docker-compose","title":"Install"},{"location":"#shutdown","text":"To stop Geoweaver, type: docker stop $(docker ps -aq)","title":"Shutdown"},{"location":"#tomcat-war","text":"","title":"Tomcat War"},{"location":"#install_1","text":"Download the latest release war and copy it to the webapps directory of Tomcat (e.g. /usr/local/tomcat). Start Tomcat. wget https://github.com/ESIPFed/Geoweaver/releases/download/v0.7.1/Geoweaver.war -O Geoweaver.war cp Geoweaver.war /usr/local/tomcat/webapps/ /usr/local/tomcat/bin/startup.sh After the tomcat is fully started, configure the database connection. The configuration files are WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/config.properties nano /usr/local/tomcat/webapps/Geoweaver/WEB-INF/classes/cc_secret.properties Fill the fields with correct values. (database url, default: jdbc:mysql://localhost:3306/cyberconnector) and WEB-INF/classes/cc_secret.properties (database username and password: database_user=root database_password=xxxxxxxx). ( Note: the MySQL database must be initiated by the SQL file under the folder Geoweaver/docker/db first. If you are using H2 database, please copy the two files: geoweaver.mv.db and geoweaver.trace.db to your user home directory before you start tomcat. ) mysql -u root -p < docker/db/gw.sql Enter the following URL into browser address bar to open Geoweaver: http://your-ip:your-port/Geoweaver/web/geoweaver","title":"Install"},{"location":"#shutdown_1","text":"To stop Geoweaver, use: /usr/local/tomcat/bin/shutdown.sh","title":"Shutdown"},{"location":"#cloud-vm-template","text":"","title":"Cloud VM Template"},{"location":"#install_2","text":"We provide a ready-to-use cloud template for you to install on mainstream cloud platforms like AWS, Google Cloud, Azure, OpenStack and CloudStack. Please go here to download the template (3.1 Gigabytes). The username and password of the instance would be csiss and password respectively. To start Geoweaver, go to directory /home/csiss/Geoweaver and execute docker-compose up -d. With no accident, Geoweaver will be up and running. cd /home/csiss/Geoweaver && docker-compose up -d","title":"Install"},{"location":"#shutdown_2","text":"To stop Geoweaver, use: docker stop $(docker ps -aq)","title":"Shutdown"},{"location":"#build-from-source","text":"Use maven to build. In the command line go to the root folder and execute mvn install . After a success build, the Geoweaver jar package will be under the directory: Geoweaver/target/Geoweaver-.jar .","title":"Build from source"},{"location":"#demo","text":"A live demo site is available in George Mason University.","title":"Demo"},{"location":"#tutorial","text":"Geoweaver Tutorial - A beginner tutorial about what Geoweaver can do and how it works","title":"Tutorial"},{"location":"#citation","text":"If you found Geoweaver helpful in your research, please cite us: Sun, Ziheng, Liping Di, Annie Burgess, Jason A. Tullis, and Andrew B. Magill. \"Geoweaver: Advanced cyberinfrastructure for managing hybrid geoscientific AI workflows.\" ISPRS International Journal of Geo-Information 9, no. 2 (2020): 119.","title":"Citation"},{"location":"#dependencies_1","text":"This project is impossible without the support of several fantastic open source libraries. d3.js - BSD 3-Clause graph-creator - MIT License bootstrap - MIT License CodeMirror - MIT License JQuery Terminal - MIT License","title":"Dependencies"},{"location":"#license","text":"MIT","title":"License"}]} \ No newline at end of file diff --git a/site/search/worker.js b/site/search/worker.js index a3ccc07f2..9cce2f798 100644 --- a/site/search/worker.js +++ b/site/search/worker.js @@ -58,6 +58,7 @@ function onScriptsLoaded () { if (data.config && data.config.separator && data.config.separator.length) { lunr.tokenizer.separator = new RegExp(data.config.separator); } + if (data.index) { index = lunr.Index.load(data.index); data.docs.forEach(function (doc) { @@ -84,6 +85,7 @@ function onScriptsLoaded () { console.log('Lunr index built, search ready'); } allowSearch = true; + postMessage({config: data.config}); postMessage({allowSearch: allowSearch}); } diff --git a/site/sitemap.xml b/site/sitemap.xml index 83e36c463..d79a43cb2 100644 --- a/site/sitemap.xml +++ b/site/sitemap.xml @@ -1,8 +1,7 @@ - - + None - 2019-08-23 + 2021-03-09 daily \ No newline at end of file diff --git a/site/sitemap.xml.gz b/site/sitemap.xml.gz index d4f2cdcbd..16a4f8f00 100644 Binary files a/site/sitemap.xml.gz and b/site/sitemap.xml.gz differ diff --git a/src/main/java/com/gw/jpa/History.java b/src/main/java/com/gw/jpa/History.java index 684333397..95dc007f5 100644 --- a/src/main/java/com/gw/jpa/History.java +++ b/src/main/java/com/gw/jpa/History.java @@ -5,10 +5,7 @@ import javax.persistence.Column; import javax.persistence.Entity; -import javax.persistence.GeneratedValue; -import javax.persistence.GenerationType; import javax.persistence.Id; -import javax.persistence.Lob; import javax.persistence.Temporal; import javax.persistence.TemporalType; @@ -36,6 +33,10 @@ public class History { @Temporal(TemporalType.TIMESTAMP) private Date history_end_time; + @Column(columnDefinition = "TEXT") + private String history_notes; + + private String history_process; private String host_id; @@ -46,6 +47,16 @@ public class History { /** end of history section **/ /**********************************************/ + + public String getHistory_notes() { + return this.history_notes; + } + + public void setHistory_notes(String history_notes) { + this.history_notes = history_notes; + } + + public String getIndicator() { return indicator; } diff --git a/src/main/java/com/gw/server/Java2JupyterClientEndpoint.java b/src/main/java/com/gw/server/Java2JupyterClientEndpoint.java index ad83e7f87..a6019f759 100644 --- a/src/main/java/com/gw/server/Java2JupyterClientEndpoint.java +++ b/src/main/java/com/gw/server/Java2JupyterClientEndpoint.java @@ -111,7 +111,7 @@ public void afterResponse(HandshakeResponse hr) { public void beforeRequest(Map> nativeheaders) { // headers.put("Cookie", Arrays.asList("JSESSIONID=" + sessionID)); -// logger.debug("Original Native Headers: " + nativeheaders); + logger.debug("Original Native Headers: " + nativeheaders); Map> uppercaseheaders = new HashMap(); @@ -130,7 +130,8 @@ public void beforeRequest(Map> nativeheaders) { List values = mapElement.getValue(); // if("Sec-WebSocket-Key".equals(newkey)) { - if("Host".equals(newkey) || "Origin".equals(newkey) || "Sec-WebSocket-Key".equals(newkey)) { + // if("Host".equals(newkey) || "Origin".equals(newkey) ) { + if("Host".equals(newkey) || "Origin".equals(newkey) || "Sec-WebSocket-Key".equals(newkey)) { continue; diff --git a/src/main/java/com/gw/server/JupyterHubRedirectServlet.java b/src/main/java/com/gw/server/JupyterHubRedirectServlet.java index e5769c5d1..eba73083f 100644 --- a/src/main/java/com/gw/server/JupyterHubRedirectServlet.java +++ b/src/main/java/com/gw/server/JupyterHubRedirectServlet.java @@ -244,9 +244,11 @@ public void open(Session session, String wsprotocol = "ws"; - String trueurl = wsprotocol + "://"+hh[1]+":"+hh[2]+"/api/kernels/"+uuid1+"/channels?" + session.getQueryString(); + String trueurl = wsprotocol + "://" + hh[1] + ":" + hh[2] + "/user/" + username + + + "/api/kernels/"+uuid1+"/channels?" + session.getQueryString(); -// logger.debug("Query String: " + trueurl); + logger.debug("Query String: " + trueurl); // this.wsSession = session; diff --git a/src/main/java/com/gw/server/Test2SocketServlet.java b/src/main/java/com/gw/server/Test2SocketServlet.java new file mode 100644 index 000000000..f7f3e35ba --- /dev/null +++ b/src/main/java/com/gw/server/Test2SocketServlet.java @@ -0,0 +1,48 @@ +package com.gw.server; + +import javax.websocket.EndpointConfig; +import javax.websocket.OnClose; +import javax.websocket.OnError; +import javax.websocket.OnMessage; +import javax.websocket.OnOpen; +import javax.websocket.Session; +import javax.websocket.server.PathParam; +import javax.websocket.server.ServerEndpoint; + +@ServerEndpoint(value = "/test-socket2/{hostid}/api/kernels/{uuid1}/channels") +public class Test2SocketServlet { + + public Test2SocketServlet() { + + System.out.println("Test2 websocket servlet is created!"); + + } + + @OnOpen + public void open(Session session, + @PathParam("hostid") String hostid, + @PathParam("uuid1") String uuid1, + EndpointConfig config) { + + + } + + @OnError + public void error(final Session session, final Throwable throwable) throws Throwable { + + + } + + @OnMessage(maxMessageSize = 10000000) + public void echo(String message, @PathParam("uuid1") String uuid1, Session session) { + + + } + + @OnClose + public void close(final Session session) { + + + } + +} diff --git a/src/main/java/com/gw/server/TestSocketServlet.java b/src/main/java/com/gw/server/TestSocketServlet.java new file mode 100644 index 000000000..7ce75b139 --- /dev/null +++ b/src/main/java/com/gw/server/TestSocketServlet.java @@ -0,0 +1,228 @@ +package com.gw.server; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import javax.websocket.EndpointConfig; +import javax.websocket.OnClose; +import javax.websocket.OnError; +import javax.websocket.OnMessage; +import javax.websocket.OnOpen; +import javax.websocket.Session; +import javax.websocket.server.ServerEndpoint; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + + +//ws://geoweaver2.eastus.cloudapp.azure.com:8000/user/zsun/api/kernels/eaa5f686-0df2-4f39-ae95-d6715d9f7fc5/channels?session_id=f7550de984274d3785f246b3e9eb1c0a +@ServerEndpoint(value = "/xyz-socket") +public class TestSocketServlet { + +// public TestSocketServlet() { +// super(); +// +// System.out.println("Test websocket servlet is created!"); +// +// +// } + + +// @OnOpen +// public void open(Session session, +//// @PathParam("hostid") String hostid, +//// @PathParam("uname") String username, +//// @PathParam("uuid1") String uuid1, +// EndpointConfig config) { +// +// +// } +// +// @OnError +// public void error(final Session session, final Throwable throwable) throws Throwable { +// +// +// } +// +// @OnMessage(maxMessageSize = 10000000) +// public void echo(String message, +//// @PathParam("uuid1") String uuid1, +// Session session) { +// +// System.out.println("onMessage::From=" + session.getId() + " Message=" + message); +// +// try { +// session.getBasicRemote().sendText("Hello Client " + session.getId() + "!"); +// } catch (IOException e) { +// e.printStackTrace(); +// } +// +// } +// +// @OnClose +// public void close(final Session session) { +// +// +// } + + + Logger logger = LoggerFactory.getLogger(getClass()); + + /** + * WebSocket Session between the client and Geoweaver + */ + private Session wsSession; + + private List logoutCommands = Arrays.asList(new String[]{"logout", "quit"}); + + static Map peers = new HashMap(); + +// private HttpSession httpSession; + + @OnOpen + public void open(Session session, EndpointConfig config) { + + try { + + logger.debug("websocket channel openned"); + +// this.wsSession = session; +// +// WsSession wss = (WsSession) session; + +// logger.debug("Web Socket Session ID:" + wss.getHttpSessionId()); + +// peers.put(wss.getHttpSessionId(), session); + + } catch (Exception e) { + + e.printStackTrace(); + + } + + } + + @OnError + public void error(final Session session, final Throwable throwable) throws Throwable { + + logger.error("websocket channel error" + throwable.getLocalizedMessage()); + + throw throwable; + + } + + @OnMessage + public void echo(String message, Session session) { + + try { + + logger.debug("Received message: " + message); + + logger.debug(" Session ID: " + session.getQueryString()); + + logger.debug("Transfer message to Jupyter Notebook server.."); + +// session.getBasicRemote().sendText("Message received and Geoweaver Shell Socket Send back: " + message); + +// SSHSession sshSession = GeoweaverController.sessionManager.sshSessionByToken.get(session.getId()); +// +// if (sshSession == null) { +// +// logger.debug("linking " + session.getId() + message); +// +// // TODO is there a better way to do this? +// // Can the client send the websocket session id and username in a REST call to link them up? +// sshSession = GeoweaverController.sessionManager.sshSessionByToken.get(message); +// +//// if(sshSession!=null&&sshSession.getSSHInput().ready()) { +// if(sshSession!=null) { +// +//// sshSession.setWebSocketSession(session); +// +// GeoweaverController.sessionManager.sshSessionByToken.put(session.getId(), sshSession); +// +//// GeoweaverController.sessionManager.sshSessionByToken.remove(messageText); //remove session, a token can only be used once +// +// }else { +// +// if(session.isOpen()) { +// +// session.getAsyncRemote().sendText("No SSH connection is active"); +// +// } +// +//// session.close(); +// +// } +// +// } else { +// +// logger.debug("message in " + session.getId() + message); +// +// sshSession.getSSHOutput().write((message + '\n').getBytes()); +// +// sshSession.getSSHOutput().flush(); +// +//// //send Ctrl + C command to the SSH to close the connection +//// +//// cmd.getOutputStream().write(3); +//// +//// cmd.getOutputStream().flush(); +// +// // if we receive a valid logout command, then close the websocket session. +// // the system will logout and tidy itself up... +// +// if (logoutCommands.contains(message.trim().toLowerCase())) { +// +// logger.debug("valid logout command received " + message); +// +// sshSession.logout(); +// +//// session.close(); //close WebSocket session. Notice: the SSHSession will continue to run. +// +// } +// +// } + + }catch(Exception e) { + + e.printStackTrace(); + + } + + } + + @OnClose + public void close(final Session session) { + + try { + + logger.debug("Geoweaver Shell Channel closed."); + + logger.debug("websocket session closed:" + session.getId()); + + //close SSH session +// if(GeoweaverController.sessionManager!=null) { +// +// SSHSession sshSession = GeoweaverController.sessionManager.sshSessionByToken.get(session.getId()); +// if (sshSession != null && sshSession.isTerminal()) { //only close when it is shell +// sshSession.logout(); +// } +// GeoweaverController.sessionManager.sshSessionByToken.remove(session.getId()); +// +// } +// peers.remove(session.getId()); + + } catch (Exception e) { + + e.printStackTrace(); + + } + + } + + + +} diff --git a/src/main/java/com/gw/server/WebSocketConfig.java b/src/main/java/com/gw/server/WebSocketConfig.java index 7e90d01f3..53e41b338 100644 --- a/src/main/java/com/gw/server/WebSocketConfig.java +++ b/src/main/java/com/gw/server/WebSocketConfig.java @@ -20,6 +20,12 @@ public CommandServlet callCommandWebSocketController() return new CommandServlet(); } +// @Bean +// public TestSocketServlet callTestWebSocketController() +// { +// return new TestSocketServlet(); +// } + @Bean public TerminalServlet callTerminalWebSocketController() { @@ -39,5 +45,12 @@ public JupyterRedirectServlet callJupyterWebSocketController() { } + @Bean + public JupyterHubRedirectServlet callJupyterHubWebSocketController() { + + return new JupyterHubRedirectServlet(); + + } + } diff --git a/src/main/java/com/gw/tools/HistoryTool.java b/src/main/java/com/gw/tools/HistoryTool.java index 9a251f798..1ff5d7414 100644 --- a/src/main/java/com/gw/tools/HistoryTool.java +++ b/src/main/java/com/gw/tools/HistoryTool.java @@ -4,8 +4,9 @@ import java.sql.SQLException; import java.util.List; import java.util.Optional; - +import java.util.Collection; import javax.annotation.PostConstruct; +import java.util.Iterator; import org.apache.log4j.Logger; import org.springframework.beans.factory.annotation.Autowired; @@ -398,7 +399,102 @@ public String process_all_history(String pid) { // return resp.toString(); } + + public String deleteAllHistoryByHost(String hostid){ + + String resp = null; + + try{ + + Collection historylist = historyrepository.findRecentHistory(hostid, 1000); + + Iterator hisint = historylist.iterator(); + + StringBuffer idlist = new StringBuffer(); + + while(hisint.hasNext()) { + + History h = hisint.next(); + + idlist.append(h.getHistory_id()).append(","); + + historyrepository.delete(h); + + } + + resp = "{ \"removed_history_ids\": \"" + idlist.toString() + "\""; + + }catch(Exception e){ + + e.printStackTrace(); + + } + + return resp; + + } + + public String deleteNoNotesHistoryByHost(String hostid){ + + String resp = null; + + try{ + + Collection historylist = historyrepository.findRecentHistory(hostid, 1000); + + Iterator hisint = historylist.iterator(); + + StringBuffer idlist = new StringBuffer(); + + while(hisint.hasNext()) { + + History h = hisint.next(); + + if(bt.isNull(h.getHistory_notes())){ + + idlist.append(h.getHistory_id()).append(","); + + historyrepository.delete(h); + + } + + } + + resp = "{ \"removed_history_ids\": \"" + idlist.toString() + "\""; + + }catch(Exception e){ + + e.printStackTrace(); + + } + + return resp; + + } + /** + * Update the notes of a history + */ + public void updateNotes(String hisid, String notes){ + + try{ + + logger.info("Updating history: " + hisid + " - " + notes); + + History h = this.getHistoryById(hisid); + + h.setHistory_notes(notes); + + this.saveHistory(h); + + }catch(Exception e){ + + e.printStackTrace(); + + } + + } + /** * Save Jupyter Notebook Checkpoints into the GW database */ diff --git a/src/main/java/com/gw/tools/HostTool.java b/src/main/java/com/gw/tools/HostTool.java index b72419f19..92fab84ed 100644 --- a/src/main/java/com/gw/tools/HostTool.java +++ b/src/main/java/com/gw/tools/HostTool.java @@ -153,6 +153,8 @@ public String recent(String hostid, int limit) { resp.append("\"name\": \"").append(h.getHistory_process()).append("\", "); resp.append("\"end_time\": \"").append(h.getHistory_end_time()).append("\", "); + + resp.append("\"notes\": \"").append(h.getHistory_notes()).append("\", "); resp.append("\"status\": \"").append(h.getIndicator()).append("\", "); diff --git a/src/main/java/com/gw/tools/ProcessTool.java b/src/main/java/com/gw/tools/ProcessTool.java index 12501ee80..67d13c22d 100644 --- a/src/main/java/com/gw/tools/ProcessTool.java +++ b/src/main/java/com/gw/tools/ProcessTool.java @@ -879,7 +879,9 @@ public String recent(int limit) { resp.append("{ \"id\": \"").append(process_obj[0]).append("\", "); - resp.append("\"name\": \"").append(process_obj[11]).append("\", "); + resp.append("\"name\": \"").append(process_obj[12]).append("\", "); + + resp.append("\"notes\": \"").append(process_obj[8]).append("\", "); resp.append("\"end_time\": \"").append(process_obj[2]).append("\", "); @@ -901,7 +903,27 @@ public String recent(int limit) { } - + public String removeClob(String clob) { + + int fn = clob.indexOf("STRINGDECODE('"); + + String substr = clob; + + if(fn!=-1) { + + fn += 14; + + substr = clob.substring(fn); + + substr = substr.substring(0, substr.length()-2); + + logger.info(substr); + + } + + return substr; + + } /** * get all details of one history @@ -930,15 +952,21 @@ public String one_history(String hid) { resp.append("\"id\": \"").append(first_obj[5]).append("\", "); - resp.append("\"name\": \"").append(first_obj[11]).append("\", "); + resp.append("\"name\": \"").append(first_obj[12]).append("\", "); + + resp.append("\"notes\": \"").append(first_obj[8]).append("\", "); resp.append("\"begin_time\":\"").append(first_obj[1]).append("\", "); resp.append("\"end_time\":\"").append(first_obj[2]).append("\", "); - resp.append("\"input\":\"").append(escape(String.valueOf(first_obj[3]))).append("\", "); + String input_code = escape(String.valueOf(first_obj[3])); + + resp.append("\"input\":\"").append(removeClob(input_code)).append("\", "); - resp.append("\"output\":\"").append(escape(String.valueOf(first_obj[4]))).append("\", "); + String output_code = escape(String.valueOf(first_obj[4])); + + resp.append("\"output\":\"").append(removeClob(output_code)).append("\", "); resp.append("\"category\":\"").append(escape(String.valueOf(first_obj[7]))).append("\", "); @@ -1000,6 +1028,8 @@ public String all_active_process() { resp.append("\", \"status\": \"").append(escape(String.valueOf(row[4]))); + resp.append("\", \"notes\": \"").append(escape(String.valueOf(row[8]))); + resp.append("\", \"host\": \"").append(escape(String.valueOf(row[5]))); resp.append("\"}"); diff --git a/src/main/java/com/gw/utils/BaseTool.java b/src/main/java/com/gw/utils/BaseTool.java index 49b0ab244..62dba8735 100644 --- a/src/main/java/com/gw/utils/BaseTool.java +++ b/src/main/java/com/gw/utils/BaseTool.java @@ -20,6 +20,8 @@ import java.net.URL; import java.net.URLConnection; import java.net.URLDecoder; +import java.net.URLEncoder; +import java.nio.charset.StandardCharsets; import java.nio.file.Path; import java.nio.file.Paths; import java.text.ParseException; @@ -116,7 +118,16 @@ public String removeLob(String lob) { } - + public String encodeValue(String value) { + + try { + value = URLEncoder.encode(value, StandardCharsets.UTF_8.toString()); + } catch (UnsupportedEncodingException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + return value; + } /** * Get the temp folder for file transfer diff --git a/src/main/java/com/gw/utils/LoggingRequestInterceptor.java b/src/main/java/com/gw/utils/LoggingRequestInterceptor.java new file mode 100644 index 000000000..5ac9078c4 --- /dev/null +++ b/src/main/java/com/gw/utils/LoggingRequestInterceptor.java @@ -0,0 +1,52 @@ +package com.gw.utils; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.http.HttpRequest; +import org.springframework.http.client.ClientHttpRequestExecution; +import org.springframework.http.client.ClientHttpRequestInterceptor; +import org.springframework.http.client.ClientHttpResponse; + +public class LoggingRequestInterceptor implements ClientHttpRequestInterceptor { + + final static Logger log = LoggerFactory.getLogger(LoggingRequestInterceptor.class); + + @Override + public ClientHttpResponse intercept(HttpRequest request, byte[] body, ClientHttpRequestExecution execution) throws IOException { + traceRequest(request, body); + ClientHttpResponse response = execution.execute(request, body); + traceResponse(response); + return response; + } + + private void traceRequest(HttpRequest request, byte[] body) throws IOException { + log.info("===========================request begin================================================"); + log.info("URI : {}", request.getURI()); + log.info("Method : {}", request.getMethod()); + log.info("Headers : {}", request.getHeaders() ); + log.info("Request body: {}", new String(body, "UTF-8")); + log.info("==========================request end================================================"); + } + + private void traceResponse(ClientHttpResponse response) throws IOException { + StringBuilder inputStringBuilder = new StringBuilder(); + BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(response.getBody(), "UTF-8")); + String line = bufferedReader.readLine(); + while (line != null) { + inputStringBuilder.append(line); + inputStringBuilder.append('\n'); + line = bufferedReader.readLine(); + } + log.info("============================response begin=========================================="); + log.info("Status code : {}", response.getStatusCode()); + log.info("Status text : {}", response.getStatusText()); + log.info("Headers : {}", response.getHeaders()); + log.info("Response body: {}", inputStringBuilder.toString()); + log.info("=======================response end================================================="); + } + +} diff --git a/src/main/java/com/gw/web/GeoweaverController.java b/src/main/java/com/gw/web/GeoweaverController.java index 5d2341274..7e7421977 100644 --- a/src/main/java/com/gw/web/GeoweaverController.java +++ b/src/main/java/com/gw/web/GeoweaverController.java @@ -11,17 +11,29 @@ import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpSession; +import com.gw.search.GWSearchTool; +import com.gw.ssh.RSAEncryptTool; +import com.gw.ssh.SSHSession; +import com.gw.tools.FileTool; +import com.gw.tools.HistoryTool; +import com.gw.tools.HostTool; +import com.gw.tools.ProcessTool; +import com.gw.tools.SessionManager; +import com.gw.tools.WorkflowTool; +import com.gw.utils.BaseTool; +import com.gw.utils.RandomString; + import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; -import org.springframework.core.io.FileSystemResource; import org.springframework.core.io.InputStreamResource; import org.springframework.core.io.Resource; import org.springframework.http.HttpHeaders; import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; import org.springframework.stereotype.Controller; +import org.springframework.stereotype.Repository; import org.springframework.ui.Model; import org.springframework.ui.ModelMap; import org.springframework.web.bind.annotation.PathVariable; @@ -31,18 +43,6 @@ import org.springframework.web.bind.support.SessionStatus; import org.springframework.web.context.request.WebRequest; -import com.gw.search.GWSearchTool; -import com.gw.ssh.RSAEncryptTool; -import com.gw.ssh.SSHSession; -import com.gw.tools.FileTool; -import com.gw.tools.HistoryTool; -import com.gw.tools.HostTool; -import com.gw.tools.ProcessTool; -import com.gw.tools.SessionManager; -import com.gw.tools.WorkflowTool; -import com.gw.utils.BaseTool; -import com.gw.utils.RandomString; - /** * * Controller for SSH related activities, including all the handlers for Geoweaver. @@ -104,6 +104,48 @@ public void destroy() { sessionManager.closeAll(); } + + @RequestMapping(value="/delAllHistory", method= RequestMethod.POST) + public @ResponseBody String delAllHistory(ModelMap model, WebRequest request){ + + String resp = null; + + try{ + + String hostid = request.getParameter("id"); + + resp = hist.deleteAllHistoryByHost(hostid); + + }catch(Exception e){ + + throw new RuntimeException("failed " + e.getLocalizedMessage()); + + } + + return resp; + + } + + @RequestMapping(value="/delNoNotesHistory", method = RequestMethod.POST) + public @ResponseBody String delNoNotesHistory(ModelMap model, WebRequest request){ + + String resp = null; + + try{ + + String hostid = request.getParameter("id"); + + resp = hist.deleteNoNotesHistoryByHost(hostid); + + }catch(Exception e){ + + throw new RuntimeException("failed " + e.getLocalizedMessage()); + + } + + return resp; + + } @RequestMapping(value = "/del", method = RequestMethod.POST) public @ResponseBody String del(ModelMap model, WebRequest request){ @@ -898,6 +940,16 @@ public ResponseEntity fileGetter(ModelMap model, @PathVariable(value=" resp = "{\"id\" : \"" + wid + "\"}"; + }else if(type.equals("history")){ + + String hisid = request.getParameter("id"); + + String notes = request.getParameter("notes"); + + hist.updateNotes(hisid, notes); + + resp = "{\"id\" : \"" + hisid + "\"}"; + } }catch(Exception e) { diff --git a/src/main/java/com/gw/web/JupyterController.java b/src/main/java/com/gw/web/JupyterController.java index 760ce3f2e..f249a0b9f 100644 --- a/src/main/java/com/gw/web/JupyterController.java +++ b/src/main/java/com/gw/web/JupyterController.java @@ -4,6 +4,7 @@ import java.net.URI; import java.net.URISyntaxException; import java.net.URLDecoder; +import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.Map; @@ -31,7 +32,10 @@ import org.springframework.http.MediaType; import org.springframework.http.RequestEntity; import org.springframework.http.ResponseEntity; +import org.springframework.http.client.BufferingClientHttpRequestFactory; +import org.springframework.http.client.ClientHttpRequestInterceptor; import org.springframework.http.client.HttpComponentsClientHttpRequestFactory; +import org.springframework.http.client.SimpleClientHttpRequestFactory; import org.springframework.stereotype.Controller; import org.springframework.ui.ModelMap; import org.springframework.util.LinkedMultiValueMap; @@ -49,6 +53,7 @@ import com.gw.tools.HistoryTool; import com.gw.tools.HostTool; import com.gw.utils.BaseTool; +import com.gw.utils.LoggingRequestInterceptor; @Controller //@RequestMapping("/Geoweaver/web") @@ -869,7 +874,8 @@ private ResponseEntity processGET(RequestEntity reqentity, HttpMethod met String contenttype = getHeaderProperty(responseEntity.getHeaders(), "Content-Type"); // - if(bt.isNull(newbody)||(!bt.isNull(contenttype)&&(contenttype.contains("image")||contenttype.contains("font")))) { + if(bt.isNull(newbody)|| ( !bt.isNull(contenttype) && (contenttype.contains("image") + || contenttype.contains("font")) )) { // HttpHeaders headers = updateHeader(responseEntity.getHeaders(), newbody, hostid); // @@ -966,7 +972,11 @@ HttpHeaders updateHeader(HttpHeaders oldheaders, String returnbody, String hosti newheaders.set(key, "/Geoweaver/jupyter-proxy/" + hostid + value.get(0)); - }else if (key.toLowerCase().equals("content-length")){ + }else if(key.toLowerCase().equals("transfer-encoding") && value.get(0).equals("chunked")){ + + logger.info("skip the header property of transfer encoding and value is chunked"); + + }else if (key.toLowerCase().equals("content-length")){ // logger.debug("Old Content Length: " + value); @@ -1153,6 +1163,15 @@ public ResponseEntity jupyterhub_login( HttpMethod method, @PathVariable("hostid } + /** + * Login Jupyter Notebook + * @param method + * @param hostid + * @param httpheaders + * @param request + * @return + * @throws URISyntaxException + */ @RequestMapping(value="/jupyter-proxy/{hostid}/login", method = RequestMethod.POST) public ResponseEntity jupyter_login( HttpMethod method, @PathVariable("hostid") String hostid, @RequestHeader HttpHeaders httpheaders, HttpServletRequest request) throws URISyntaxException @@ -1174,11 +1193,11 @@ public ResponseEntity jupyter_login( HttpMethod method, @PathVariable("hostid") logger.debug("Request URI: " + request.getRequestURI()); -// logger.info("Query String: " + request.getQueryString()); + logger.info("Query String: " + request.getQueryString()); -// logger.info("Original Request String: " + request.getParameterMap()); + logger.info("Original Request String: " + request.getParameterMap()); -// logger.info("Old Headers: " + httpheaders); + logger.info("Old Headers: " + httpheaders); // String realurl = this.getRealRequestURL(request.getRequestURI()); // @@ -1192,11 +1211,11 @@ public ResponseEntity jupyter_login( HttpMethod method, @PathVariable("hostid") // // logger.info("URL: " + uri.toString()); // -// logger.info("HTTP Method: " + method.toString()); + logger.info("HTTP Method: " + method.toString()); HttpHeaders newheaders = getHeaders(httpheaders, method, request, hostid); - MultiValueMap map= new LinkedMultiValueMap(); +// MultiValueMap map= new LinkedMultiValueMap(); Iterator hmIterator = request.getParameterMap().entrySet().iterator(); @@ -1208,28 +1227,42 @@ public ResponseEntity jupyter_login( HttpMethod method, @PathVariable("hostid") Map.Entry mapElement = (Map.Entry)hmIterator.next(); - map.add((String)mapElement.getKey(), ((String[])(mapElement.getValue()))[0]); - - if(!bt.isNull(reqstr.toString())) { + String key = (String)mapElement.getKey(); + + String value = (((String[])(mapElement.getValue()))[0]); + + if(!bt.isNull(reqstr.toString())) { reqstr.append("&"); } - - reqstr.append((String)mapElement.getKey()).append("=").append(((String[])(mapElement.getValue()))[0]); + + if(key.equals("_xsrf")) { + + newheaders.set("cookie", "_xsrf="+value); + + logger.info("Cookie XSRF: " + value); + + } + + reqstr.append(key).append("=").append(value); } - - + // HttpHeaders newheaders = this.updateHeaderReferer(httpheaders, h, realurl, request.getQueryString()); HttpEntity requestentity = new HttpEntity(reqstr.toString(), newheaders); -// logger.info("Body: " + requestentity.getBody()); + logger.info("Body: " + requestentity.getBody()); + + logger.info("New Headers: " + requestentity.getHeaders()); -// logger.info("New Headers: " + requestentity.getHeaders()); + RestTemplate restTemplate1 = new RestTemplate(new BufferingClientHttpRequestFactory(new SimpleClientHttpRequestFactory())); + List interceptors = new ArrayList<>(); + interceptors.add(new LoggingRequestInterceptor()); + restTemplate1.setInterceptors(interceptors); - ResponseEntity responseEntity = restTemplate.exchange(getRealTargetURL(newheaders.get("referer").get(0)), method, requestentity, String.class); + ResponseEntity responseEntity = restTemplate1.exchange(getRealTargetURL(newheaders.get("referer").get(0)), method, requestentity, String.class); HttpHeaders respheaders = responseEntity.getHeaders(); @@ -1273,7 +1306,7 @@ public ResponseEntity jupyter_login( HttpMethod method, @PathVariable("hostid") // Set ent = respheaders.entrySet(); -// logger.info(respheaders.toString()); + logger.info(respheaders.toString()); }else if(responseEntity.getStatusCode()==HttpStatus.UNAUTHORIZED) { diff --git a/src/main/resources/static/css/demo.css b/src/main/resources/static/css/demo.css index 6e9351c4e..ba92b83f7 100644 --- a/src/main/resources/static/css/demo.css +++ b/src/main/resources/static/css/demo.css @@ -139,4 +139,37 @@ a{ .no-csstransforms3d .support-note span.no-csstransforms3d, .no-csstransitions .support-note span.no-csstransitions{ display: block; -} \ No newline at end of file +} + +.my-input-class { + padding: 3px 6px; + border: 1px solid #ccc; + border-radius: 4px; +} + +.my-confirm-class { + padding: 3px 6px; + font-size: 12px; + color: white; + text-align: center; + vertical-align: middle; + border-radius: 4px; + background-color: #337ab7; + text-decoration: none; +} + +.my-cancel-class { + padding: 3px 6px; + font-size: 12px; + color: white; + text-align: center; + vertical-align: middle; + border-radius: 4px; + background-color: #a94442; + text-decoration: none; +} + +.error { + border: solid 1px; + border-color: #a94442; +} diff --git a/src/main/resources/static/css/jquery.dataTables.min.css b/src/main/resources/static/css/jquery.dataTables.min.css new file mode 100644 index 000000000..9ec6ca31f --- /dev/null +++ b/src/main/resources/static/css/jquery.dataTables.min.css @@ -0,0 +1 @@ +table.dataTable{width:100%;margin:0 auto;clear:both;border-collapse:separate;border-spacing:0}table.dataTable thead th,table.dataTable tfoot th{font-weight:bold}table.dataTable thead th,table.dataTable thead td{padding:10px 18px;border-bottom:1px solid #111}table.dataTable thead th:active,table.dataTable thead td:active{outline:none}table.dataTable tfoot th,table.dataTable tfoot td{padding:10px 18px 6px 18px;border-top:1px solid #111}table.dataTable thead .sorting,table.dataTable thead .sorting_asc,table.dataTable thead .sorting_desc{cursor:pointer;*cursor:hand}table.dataTable thead .sorting,table.dataTable thead .sorting_asc,table.dataTable thead .sorting_desc,table.dataTable thead .sorting_asc_disabled,table.dataTable thead .sorting_desc_disabled{background-repeat:no-repeat;background-position:center right}table.dataTable thead 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.dataTables_filter{float:none;text-align:center}.dataTables_wrapper .dataTables_filter{margin-top:0.5em}} diff --git a/src/main/resources/static/js/dataTables.cellEdit.js b/src/main/resources/static/js/dataTables.cellEdit.js new file mode 100644 index 000000000..974810c3f --- /dev/null +++ b/src/main/resources/static/js/dataTables.cellEdit.js @@ -0,0 +1,264 @@ +/*! CellEdit 1.0.19 + * ©2016 Elliott Beaty - datatables.net/license + */ + +/** + * @summary CellEdit + * @description Make a cell editable when clicked upon + * @version 1.0.19 + * @file dataTables.editCell.js + * @author Elliott Beaty + * @contact elliott@elliottbeaty.com + * @copyright Copyright 2016 Elliott Beaty + * + * This source file is free software, available under the following license: + * MIT license - http://datatables.net/license/mit + * + * This source file is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + * or FITNESS FOR A PARTICULAR PURPOSE. See the license files for details. + * + * For details please refer to: http://www.datatables.net + */ + +jQuery.fn.dataTable.Api.register('MakeCellsEditable()', function (settings) { + var table = this.table(); + + jQuery.fn.extend({ + // UPDATE + updateEditableCell: function (callingElement) { + // Need to redeclare table here for situations where we have more than one datatable on the page. See issue6 on github + var table = $(callingElement).closest("table").DataTable().table(); + var row = table.row($(callingElement).parents('tr')); + var cell = table.cell($(callingElement).parents('td, th')); + var columnIndex = cell.index().column; + var inputField =getInputField(callingElement); + + // Update + var newValue = inputField.val(); + if (!newValue && ((settings.allowNulls) && settings.allowNulls != true)) { + // If columns specified + if (settings.allowNulls.columns) { + // If current column allows nulls + if (settings.allowNulls.columns.indexOf(columnIndex) > -1) { + _update(newValue); + } else { + _addValidationCss(); + } + // No columns allow null + } else if (!newValue) { + _addValidationCss(); + } + //All columns allow null + } else if (newValue && settings.onValidate) { + if (settings.onValidate(cell, row, newValue)) { + _update(newValue); + } else { + _addValidationCss(); + } + } + else { + _update(newValue); + } + function _addValidationCss() { + // Show validation error + if (settings.allowNulls.errorClass) { + $(inputField).addClass(settings.allowNulls.errorClass); + } else { + $(inputField).css({ "border": "red solid 1px" }); + } + } + function _update(newValue) { + var oldValue = cell.data(); + cell.data(newValue); + //Return cell & row. + settings.onUpdate(cell, row, oldValue); + } + // Get current page + var currentPageIndex = table.page.info().page; + + //Redraw table + table.page(currentPageIndex).draw(false); + }, + // CANCEL + cancelEditableCell: function (callingElement) { + var table = $(callingElement.closest("table")).DataTable().table(); + var cell = table.cell($(callingElement).parents('td, th')); + // Set cell to it's original value + cell.data(cell.data()); + + // Redraw table + table.draw(); + } + }); + + // Destroy + if (settings === "destroy") { + $(table.body()).off("click", "td"); + table = null; + } + + if (table != null) { + // On cell click + $(table.body()).on('click', 'td', function () { + + var currentColumnIndex = table.cell(this).index().column; + + // DETERMINE WHAT COLUMNS CAN BE EDITED + if ((settings.columns && settings.columns.indexOf(currentColumnIndex) > -1) || (!settings.columns)) { + var row = table.row($(this).parents('tr')); + editableCellsRow = row; + + var cell = table.cell(this).node(); + var oldValue = table.cell(this).data(); + // Sanitize value + oldValue = sanitizeCellValue(oldValue); + + // Show input + if (!$(cell).find('input').length && !$(cell).find('select').length && !$(cell).find('textarea').length) { + // Input CSS + var input = getInputHtml(currentColumnIndex, settings, oldValue); + $(cell).html(input.html); + if (input.focus) { + $('#ejbeatycelledit').focus(); + } + } + } + }); + } + +}); + +function getInputHtml(currentColumnIndex, settings, oldValue) { + var inputSetting, inputType, input, inputCss, confirmCss, cancelCss, startWrapperHtml = '', endWrapperHtml = '', listenToKeys = false; + + input = {"focus":true,"html":null}; + + if(settings.inputTypes){ + $.each(settings.inputTypes, function (index, setting) { + if (setting.column == currentColumnIndex) { + inputSetting = setting; + inputType = inputSetting.type.toLowerCase(); + } + }); + } + + if (settings.inputCss) { inputCss = settings.inputCss; } + if (settings.wrapperHtml) { + var elements = settings.wrapperHtml.split('{content}'); + if (elements.length === 2) { + startWrapperHtml = elements[0]; + endWrapperHtml = elements[1]; + } + } + + if (settings.confirmationButton) { + if (settings.confirmationButton.listenToKeys) { listenToKeys = settings.confirmationButton.listenToKeys; } + confirmCss = settings.confirmationButton.confirmCss; + cancelCss = settings.confirmationButton.cancelCss; + inputType = inputType + "-confirm"; + } + switch (inputType) { + case "list": + input.html = startWrapperHtml + "" + endWrapperHtml; + input.focus = false; + break; + case "list-confirm": // List w/ confirm + input.html = startWrapperHtml + " Confirm Cancel" + endWrapperHtml; + input.focus = false; + break; + case "datepicker": //Both datepicker options work best when confirming the values + case "datepicker-confirm": + // Makesure jQuery UI is loaded on the page + if (typeof jQuery.ui == 'undefined') { + alert("jQuery UI is required for the DatePicker control but it is not loaded on the page!"); + break; + } + jQuery(".datepick").datepicker("destroy"); + input.html = startWrapperHtml + "  Confirm Cancel" + endWrapperHtml; + setTimeout(function () { //Set timeout to allow the script to write the input.html before triggering the datepicker + var icon = "http://jqueryui.com/resources/demos/datepicker/images/calendar.gif"; + // Allow the user to provide icon + if (typeof inputSetting.options !== 'undefined' && typeof inputSetting.options.icon !== 'undefined') { + icon = inputSetting.options.icon; + } + var self = jQuery('.datepick').datepicker( + { + showOn: "button", + buttonImage: icon, + buttonImageOnly: true, + buttonText: "Select date" + }); + },100); + break; + case "text-confirm": // text input w/ confirm + input.html = startWrapperHtml + " Confirm Cancel" + endWrapperHtml; + break; + case "undefined-confirm": // text input w/ confirm + input.html = startWrapperHtml + " Confirm Cancel" + endWrapperHtml; + break; + case "textarea": + input.html = startWrapperHtml + "" + endWrapperHtml; + break; + case "textarea-confirm": + input.html = startWrapperHtml + "Confirm Cancel" + endWrapperHtml; + break; + case "number-confirm" : + input.html = startWrapperHtml + " Confirm Cancel" + endWrapperHtml; + break; + default: // text input + input.html = startWrapperHtml + "" + endWrapperHtml; + break; + } + return input; +} + +function getInputField(callingElement) { + // Update datatables cell value + var inputField; + switch ($(callingElement).prop('nodeName').toLowerCase()) { + case 'a': // This means they're using confirmation buttons + if ($(callingElement).siblings('input').length > 0) { + inputField = $(callingElement).siblings('input'); + } + if ($(callingElement).siblings('select').length > 0) { + inputField = $(callingElement).siblings('select'); + } + if ($(callingElement).siblings('textarea').length > 0) { + inputField = $(callingElement).siblings('textarea'); + } + break; + default: + inputField = $(callingElement); + } + return inputField; +} + +function sanitizeCellValue(cellValue) { + if (typeof (cellValue) === 'undefined' || cellValue === null || cellValue.length < 1) { + return ""; + } + + // If not a number + if (isNaN(cellValue)) { + // escape single quote + cellValue = cellValue.replace(/'/g, "'"); + } + return cellValue; +} diff --git a/src/main/resources/static/js/gw.history.js b/src/main/resources/static/js/gw.history.js new file mode 100644 index 000000000..058835f66 --- /dev/null +++ b/src/main/resources/static/js/gw.history.js @@ -0,0 +1,88 @@ +/** + * + * author: Z.S. + * date: Mar 12 2021 + * + */ + +GW.history = { + + deleteAllJupyter: function(hostid, callback){ + + if(confirm("WARNING: Are you sure to remove all the history? This is permanent and cannot be recovered.")){ + + $.ajax({ + + url: "delAllHistory", + + method: "POST", + + data: { id: hostid} + + }).done(function(msg){ + + console.log("All the history has been deleted, refresh the history table"); + + callback(hostid); + + }).fail(function(jxr, status){ + + console.error(status + " failed to update notes, the server may lose connection. Try again. "); + + }); + + } + + }, + + deleteNoNotesJupyter: function(hostid, callback){ + + if(confirm("WARNING: Are you sure to remove all the history without notes? This is permanent and cannot be recovered.")){ + + $.ajax({ + + url: "delNoNotesHistory", + + method: "POST", + + data: { id: hostid} + + }).done(function(msg){ + + console.log("history without notes are deleted, refresh the history table"); + + callback(hostid); + + }).fail(function(jxr, status){ + + console.error(status + " failed to update notes, the server may lose connection. Try again. "); + + }); + + } + + }, + + updateNotesOfAHistory: function(hisid, notes){ + + $.ajax({ + + url: "edit", + + method: "POST", + + data: { type: "history", id: hisid, notes: notes} + + }).done(function(msg){ + + console.log("notes is updated"); + + }).fail(function(jxr, status){ + + console.error(status + " failed to update notes, the server may lose connection. Try again. "); + + }); + }, + + +} diff --git a/src/main/resources/static/js/gw.host.js b/src/main/resources/static/js/gw.host.js index 9ffd28d5b..c5021702e 100644 --- a/src/main/resources/static/js/gw.host.js +++ b/src/main/resources/static/js/gw.host.js @@ -1337,6 +1337,7 @@ GW.host = { }, + deleteSelectedJupyter: function(){ if(confirm("Are you sure to remove all the selected history? This is permanent.")){ @@ -1459,6 +1460,27 @@ GW.host = { }, + historyTableCellUpdateCallBack: function(updatedCell, updatedRow, oldValue){ + + console.log("The new value for the cell is: " + updatedCell.data()); + console.log("The old value for that cell was: " + oldValue); + console.log("The values for each cell in that row are: " + updatedRow.data()); + + // The values for each cell in that row are: ,http://localhost:8888/api/contents/work/GMU%20workspace/COVID/covid_win_laptop.ipynb,xyz,2021-03-03 22:00:32.913,View Download Delete + + var thecheckbox = updatedRow.data()[0] + + var hisid = $(thecheckbox).attr("id").substring(9) + + console.log("history id: " + hisid) + + var newvalue = updatedRow.data()[2] + + GW.history.updateNotesOfAHistory(hisid, newvalue); + + }, + + recent: function(hid){ console.log("Show the history of all previously executed scripts/jupyter notebok"); @@ -1486,15 +1508,18 @@ GW.host = { var content = "

Recent History

"+ "
"+ - " "+ + "
"+ + " "+ + " "+ " "+ - " "+ + "
"+ - " "+ + "
"+ " "+ " "+ " "+ " "+ + " "+ " "+ // " "+ " "+ @@ -1512,8 +1537,9 @@ GW.host = { msg[i].id+"')\">Delete "; content += " "+ - " "+ + " "+ " "+ + " "+ " "+ // status_col + detailbtn + @@ -1525,6 +1551,29 @@ GW.host = { $("#host-history-browser").html(content); + // initialize the tab with editable cells + + var table = $('.host_history_table').DataTable(); + + table.MakeCellsEditable({ + "onUpdate": GW.host.historyTableCellUpdateCallBack, + "columns": [2], + "allowNulls": { + "columns": [2], + "errorClass": 'error' + }, + "confirmationButton": { // could also be true + "confirmCss": 'my-confirm-class', + "cancelCss": 'my-cancel-class' + }, + "inputTypes": [ + { + "column": 2, + "type": "text", + "options": null + }] + }); + // $("#all-selected").on("click", function(){}); $('#all-selected').change(function(){ @@ -1550,6 +1599,18 @@ GW.host = { }); + $("#deleteHostHistoryNoNoteBtn").on("click", function(){ + + GW.history.deleteNoNotesJupyter(hid, GW.host.recent); + + }) + + $("#deleteHostHistoryAllBtn").on("click", function(){ + + GW.history.deleteAllJupyter(hid, GW.host.recent); + + }) + $("#compareHistoryBtn").on("click", function(){ GW.comparison.show(); diff --git a/src/main/resources/static/js/gw.main.js b/src/main/resources/static/js/gw.main.js index 76ebf2455..7c2899ed5 100644 --- a/src/main/resources/static/js/gw.main.js +++ b/src/main/resources/static/js/gw.main.js @@ -24,6 +24,36 @@ GW.main = { return jsId; }, + test_websocket: function(){ + + var test1_url = GW.ssh.getWsPrefixURL() + "test-socket/xxxx/user/zsun/api/kernels/2eee232rsdfsweroeiwr/channels" + + var test1 = new WebSocket(test1_url); + + test1.onopen = function(e) { GW.ssh.ws_onopen(e) }; + + test1.onclose = function(e) { GW.ssh.ws_onclose(e) }; + + test1.onmessage = function(e) { GW.ssh.ws_onmessage(e) }; + + test1.onerror = function(e) { GW.ssh.ws_onerror(e) }; + + var test2_url = GW.ssh.getWsPrefixURL() + "test-socket" + + var test2 = new WebSocket(test2_url); + + test2.onopen = function(e) { GW.ssh.ws_onopen(e) }; + + test2.onclose = function(e) { GW.ssh.ws_onclose(e) }; + + test2.onmessage = function(e) { GW.ssh.ws_onmessage(e) }; + + test2.onerror = function(e) { GW.ssh.ws_onerror(e) }; + + + + }, + init: function(){ $("#menuheader").val("Geoweaver v" + GW.version); @@ -40,6 +70,8 @@ GW.main = { introJs().start(); +// this.test_websocket() + } }; diff --git a/src/main/resources/templates/geoweaver.html b/src/main/resources/templates/geoweaver.html index c4e1a07d1..6278e005a 100644 --- a/src/main/resources/templates/geoweaver.html +++ b/src/main/resources/templates/geoweaver.html @@ -7,7 +7,7 @@ - + @@ -109,6 +109,10 @@ + + + +
ProcessNotes (Click to Edit)Begin TimeStatusAction
"+msg[i].name+""+msg[i].notes+""+msg[i].begin_time+"