553 lines
19 KiB
Markdown
553 lines
19 KiB
Markdown
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---
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title: MongoDB GridFS文件存储
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date: 2021-01-28
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author: ac
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tags:
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- MongoDB
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- GridFS
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- mongofiles
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categories:
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- Database
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---
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> GIS中遥感影像数据可以使用MongoDB的GridFS进行存储。
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<!-- more -->
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### 1 `GridFS` 简介
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`GridFS`文件系统是`MongoDB`存储大文件的一种规范,所有官方的`MongoDB`驱动都遵循该规范。它解决了`BSON`文档大小不能超过**16M**的问题。
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`GridFS`不是将文件存储在单个文档中,而是将文件分成多个数据块,并将每个块存储为单独的文档。默认情况下,`GridFS`使用的默认数据块大小为255 kB;也就是说,除了最后一个数据块外,`GridFS`将一个文件划分为255 kB的小块。
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`GridFS`使用两个集合来存储文件。一个集合存储文件的数据块,另一个集合存储文件元数据,像文件名称、大小、创建日期等。
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当您在使用`GridFS`查询文件时,会根据需要重新组装这些数据块。另外`GridFS`不仅可以存储操过16MB的文件,还可以访问大文件的部分信息而不必将整个文件加载到内存中。
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使用`GridFS`的方式有以下两种:
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- 使用[程序接口](https://docs.mongodb.com/drivers/)的方式,利用`MongoDB`对各程序语言的提供的驱动对文件进行操作。
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
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- 使用`mongofiles`命令行工具。
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### 2 `GridFS` 集合
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` GridFS`将文件存储在两个集合中:
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- `chunks`:存储二进制块
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- `files`:存储文件的元数据
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`GridFS`通过在每个集合前面加上前缀,将这两个集合放在一个公共容器:bucket(命名空间)中。默认情况下,`GridFS`使用两个集合,一个容器名为`fs`:
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- `fs.files`
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- `fs.chunks`
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> 官方的英语文档描述的更加形象:The two collections are in a common bucket and the collection names are prefixed with the bucket name.
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#### 2.1 chunks集合
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```json
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{
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"_id" : <ObjectId>,
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"files_id" : <ObjectId>,
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"n" : <num>,
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"data" : <binary>
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}
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```
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> `ObjectId`: 一种特殊的BSON类型,它保证集合内的唯一性。
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>
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> `ObjectId`值的长度为12个字节,包括: 4 byte 时间戳、5 byte 随机数 、3 byte 增长量
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- chunks._id:数据块的标识
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- chunks.files_id:所属文件的标识
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- chunks.n: 块的序列号。`GridFS`给所有块编号,从0开始。
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- chunks.data :数据块中装载的数据,Binary类型。
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#### 2.2 files集合
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```json
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{
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"_id" : <ObjectId>,
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"length" : <num>,
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"chunkSize" : <num>,
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"uploadDate" : <timestamp>,
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"md5" : <hash>,
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"filename" : <string>,
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"contentType" : <string>,
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"aliases" : <string array>,
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"metadata" : <any>,
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}
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```
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- files._id:文件标识
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- files.length:文件长度
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- files.chunkSize: 每个块的大小(以字节为单位)。GridFS将文档分成大小为chunkSize的块,但最后一个块的大小仅根据需要而定。默认大小是255kb。
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- files. uploadDate : 文件第一次被GridFS存储的日期。该值具有日期类型。
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- files.md5: MD5算法被FIPS 140-2禁止。MongoDB驱动程序已弃用MD5支持,并将在未来版本中删除MD5生成。需要文件摘要的应用程序应该在GridFS之外实现它,并存储在files.metadata中。
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- files.filename: 可读的GridFS文件名称。
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- files.metadata: 可选的。元数据字段可以是任何数据类型,可以保存您想要存储的任何附加信息。
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### 3 `mongofiles`工具
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#### 3.1 `mongofiles`作用
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`mongofiles`工具可以通过命令行操作`MongoDB`实例中`GridFS`对象中存储的文件。它提供了存储在文件系统和`GridFS`中的对象之间的接口。
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> 从`MongoDB`4.4 开始,`mongofiles`从`MongoDB`服务器单独发布,并使用自己的版本控制,初始版本为100.0.0。在此之前,`mongofiles`是与`MongoDB`一起发布的,并使用了匹配的版本控制。
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#### 3.2 安装 `mongofiles`
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[windows环境](https://docs.mongodb.com/database-tools/installation/installation-windows/)
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根据之前安装`MongoDB`实例,选择下载工具的版本。之前`MongoDB`使用的是`zip`免安装的形式,所以这里下载`mongodb-database-tools-windows-x86_64-100.2.zip`。
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
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
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
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
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
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将下载的文件解压到任意位置,再将`mongofiles`工具目录下的`bin`目录添加到系统的`Path`环境变量中。
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[Linux环境(ubuntu)](https://docs.mongodb.com/database-tools/installation/installation-linux/)
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```shell
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qiusj@u20:~$ cat /etc/os-release
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NAME="Pop!_OS"
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VERSION="20.04 LTS"
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ID=pop
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ID_LIKE="ubuntu debian"
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PRETTY_NAME="Pop!_OS 20.04 LTS"
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VERSION_ID="20.04"
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HOME_URL="https://pop.system76.com"
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SUPPORT_URL="https://support.system76.com"
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BUG_REPORT_URL="https://github.com/pop-os/pop/issues"
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PRIVACY_POLICY_URL="https://system76.com/privacy"
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VERSION_CODENAME=focal
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UBUNTU_CODENAME=focal
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LOGO=distributor-logo-pop-os
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#查看Linux内核版本
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qiusj@u20:~$ arch
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x86_64
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```
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下载合适的版本,可以下载后使用`sftp`传输到Linux,也可以使用`curl`命令下载:
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
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```shell
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$ curl -o mongodb-database-tools.tgz https://fastdl.mongodb.org/tools/db/mongodb-database-tools-ubuntu2004-x86_64-100.2.1.tgz
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% Total % Received % Xferd Average Speed Time Time Time Current
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Dload Upload Total Spent Left Speed
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100 64.0M 100 64.0M 0 0 1222k 0 0:00:53 0:00:53 --:--:-- 2106k
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$ ll
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总用量 128560
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drwxr-xr-x 5 qiusj intplanet 4096 1月 28 17:00 ./
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drwxr-xr-x 6 qiusj intplanet 4096 1月 5 09:42 ../
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-rw-r--r-- 1 qiusj intplanet 67211368 1月 28 17:00 mongodb-database-tools.tgz
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#解压
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$ tar -zxvf mongodb-database-tools.tgz
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/LICENSE.md
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/README.md
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/THIRD-PARTY-NOTICES
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/bsondump
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongodump
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongoexport
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongofiles
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongoimport
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongorestore
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongostat
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mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin/mongotop
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#将解压的文件bin目录下的命令复制到/usr/local/bin/目录下
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$ cd mongodb-database-tools-ubuntu2004-x86_64-100.2.1/bin
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$ sudo cp * /usr/local/bin
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$ mongofiles --version
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mongofiles version: 100.2.1
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git version: 0cb6f592fcb425ee5b3d5540341de75531d28dac
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Go version: go1.12.17
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os: linux
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arch: amd64
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compiler: gc
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```
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#### 3.3 基本使用
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`mongofiles`命令的语法格式如下:
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```shell
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mongofiles <options> <connection-string> <command> <filename or _id>
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```
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- `options`主要配置`mongofiles`的一些读写优先级。
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- `connection-string`是连接`mongod/mongos`的配合信息,如host、port、安全认证等相关配置。
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- `command`是`mongofiles`具体的文件操作,如导入、导出、查询等。
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> 对于副本集,`mongofiles`只能从主节点读。
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>
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> 当启动安全认证后,`mongofiles`连接的用户需要有`read`权限(`list`、`earch`、`get`等命令)和`readWrite`权限(`put`、`delete`等命令)
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**常用Options配置项:**
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| options | description |
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| --------- | ------------------------------------------------------------ |
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| --help | 返回 mongofiles 的配置项和使用信息 |
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| --version | 返回 mongofiles 的版本信息 |
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| --uri | 指定MongoDB 的连接信息,如:<br>--uri="mongodb://[username:password@]host1\[:port1]\[,host2[:port2],...\[,hostN\[:portN]]][/\[database][?options]]" |
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| --config | 指定配置文件,以配置文件的形式启动 |
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**Commands: **
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| 命令 | 说明 |
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| -------------------------------------------------- | ------------------------------------------------------------ |
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| list \<prefix> | 列出`GridFS`存储的文件。\<prefix>用于筛选返回列表中以 prefix字符串为前缀的文件。 |
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| search \<string> | 列出`GridFS`中名称与\<string>的任何部分匹配的文件。 |
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| put \<filename1[ filename2] ...> | 将指定的文件从本地文件系统复制到`GridFS`中。多个文件可以指定为空格分隔的列表。 |
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| get \<filename1[ filename2] ...> | 将指定的文件从`GridFS`存储复制到本地文件系统。 |
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| get_id "<_id>" | 将文件(由\<\_id>指定)从`GridFS`中复制到本地文件系统。\<\_id>是该对象在`GridFS`中的扩展JSON \_id。 |
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| get_regex \<regex> --regexOptions \<regex-options> | 将匹配指定的\<regex>表达式的一个或多个文件从`GridFS`复制到本地文件系统。get_regex命令使用Perl兼容的正则表达式(“PCRE”)8.42版本,支持UTF-8。 |
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| delete \<filename> | 从`GridFS`中删除指定的文件 |
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| delete_id "<_id>" | 从`GridFS`中删除由\<\_id>指定的文件。 |
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#### 3.4 示例
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在系统的命令行中运行 `mongofiles`命令:
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```shell
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# 查看本地mongofiles实例执行过的历史命令
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mongofiles -d=records list
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```
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导入文件,下面命令`mongofiles` 实例将连接 `uri`中的数据库,将文件存入`GridFS`中。
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```shell
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$ mongofiles --uri=mongodb://192.168.0.152:27017 put /home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif
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2021-03-04T17:18:06.681+0800 connected to: mongodb://192.168.0.152:27017
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2021-03-04T17:18:06.682+0800 adding gridFile: /home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif
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2021-03-04T17:18:06.824+0800 added gridFile: /home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif
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```
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查看集合:
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```shell
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#连接数据库
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$ /usr/local/mongodb/bin/mongo --host=192.168.0.152 --port=27017
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#查看数据库
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> db
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test
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#查看集合
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> show collections
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fs.chunks
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fs.files
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#查看files集合
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> db.fs.files.find()
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{
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"_id" : ObjectId("6040a5ce6211dcaf818ac9aa"),
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"length" : NumberLong(15838376),
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"chunkSize" : 261120,
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"uploadDate" : ISODate("2021-03-04T09:18:06.824Z"),
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"filename" : "/home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif",
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"metadata" : { }
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}
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```
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查询文件:
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```shell
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$ mongofiles search 'Cho'
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2021-03-04T17:48:10.976+0800 connected to: mongodb://localhost/
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/home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif 15838376
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```
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> 搜索结果:filename length
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>
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> 可以发现mongofiles命令默认连接本地的 mongo 服务,如果不是本地需带上 uri 连接信息。
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获取文件:
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```shell
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$ mongofiles --uri=mongodb://localhost:27017 get /home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif --local=test.tif
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2021-03-04T17:57:34.507+0800 connected to: mongodb://localhost:27017
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2021-03-04T17:57:34.531+0800 finished writing to test.tif
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```
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> get \<filename1[ filename2] ...>命令,当只有一个文件时,可以使用--local参数给文件重新命名。
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>
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> 导出的目录为get命令执行所在的当前目录。
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删除文件:
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```shell
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$ mongofiles delete /home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif
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|||
|
2021-03-04T18:03:23.399+0800 connected to: mongodb://localhost/
|
|||
|
2021-03-04T18:03:23.402+0800 successfully deleted all instances of '/home/qiusj/.local/mongodb/mongofiles/data/shenzhen_CholophyII_2020.tif' from GridFS
|
|||
|
|
|||
|
#再去数据库里查看
|
|||
|
$ /usr/local/mongodb/bin/mongo
|
|||
|
> show collections
|
|||
|
fs.chunks
|
|||
|
fs.files
|
|||
|
> db.fs.files.find()
|
|||
|
>
|
|||
|
```
|
|||
|
|
|||
|
### 4 Springboot中使用GridFS
|
|||
|
|
|||
|
使用一个单实例的未启用认证的`mongodb`作为示例数据库。
|
|||
|
|
|||
|
#### 4.1 导入依赖
|
|||
|
|
|||
|
```groovy
|
|||
|
compile 'org.springframework.boot:spring-boot-starter-data-mongodb'
|
|||
|
testImplementation 'org.springframework.boot:spring-boot-starter-test'
|
|||
|
```
|
|||
|
|
|||
|
#### 4.2 配置文件
|
|||
|
|
|||
|
`application.yml`文件:
|
|||
|
|
|||
|
```yaml
|
|||
|
#如果连接的不是本地的mongo,会比较慢,因为会受到网络传输速度的影响
|
|||
|
spring:
|
|||
|
data:
|
|||
|
mongodb:
|
|||
|
database: files
|
|||
|
host: localhost
|
|||
|
port: 27017
|
|||
|
|
|||
|
#用于测试的本地遥感数据文件
|
|||
|
rsfilepath: "E:\\data\\ShenzhenNDWI_2019_S2L1C.tif"
|
|||
|
```
|
|||
|
|
|||
|
`MongoConfig.java`,在该类中根据配置信息创建`mongo`的客户端实例和`GridFSBucket`实例。
|
|||
|
|
|||
|
> `GridFS`用于存储文件的两个集合都在同一个`bucket`中。集合的前缀为`bucket name`,默认为`fs`。
|
|||
|
|
|||
|
```java
|
|||
|
@Configuration
|
|||
|
public class MongoConfig {
|
|||
|
|
|||
|
@Value("${spring.data.mongodb.host}")
|
|||
|
private String host;
|
|||
|
|
|||
|
@Value("${spring.data.mongodb.port}")
|
|||
|
private int port;
|
|||
|
|
|||
|
@Value("${spring.data.mongodb.database}")
|
|||
|
private String database;
|
|||
|
|
|||
|
@Bean
|
|||
|
public MongoClient getMongoClient(){
|
|||
|
MongoClient mongoClient = MongoClients.create(
|
|||
|
MongoClientSettings.builder()
|
|||
|
.applyToClusterSettings(builder ->
|
|||
|
builder.hosts(Arrays.asList(
|
|||
|
new ServerAddress(host, port)
|
|||
|
)))
|
|||
|
.build());
|
|||
|
return mongoClient;
|
|||
|
}
|
|||
|
|
|||
|
@Bean
|
|||
|
public GridFSBucket getgridFSBucket(MongoClient mongoClient) {
|
|||
|
MongoDatabase mongoDatabase = mongoClient.getDatabase(database);
|
|||
|
//使用默认的fs前缀
|
|||
|
GridFSBucket gridFSBucket = GridFSBuckets.create(mongoDatabase);
|
|||
|
return gridFSBucket;
|
|||
|
}
|
|||
|
}
|
|||
|
```
|
|||
|
|
|||
|
#### 4.3 测试类
|
|||
|
|
|||
|
我们在Test模块下创建一个`GridsApplicationTests.java`测试类,用于测试`GridFSBucket`中的方法:
|
|||
|
|
|||
|

|
|||
|
|
|||
|
```java
|
|||
|
|
|||
|
@SpringBootTest
|
|||
|
class GridfsApplicationTests {
|
|||
|
|
|||
|
@Autowired
|
|||
|
private GridFSService gridFSService;
|
|||
|
|
|||
|
@Value("${rsfilepath}")
|
|||
|
private String rsfilepath;
|
|||
|
|
|||
|
private int chunckSize = 1024;
|
|||
|
|
|||
|
@Autowired
|
|||
|
private GridFSBucket gridFSBucket;
|
|||
|
|
|||
|
/**
|
|||
|
* uploadFromStream()方法
|
|||
|
* 文件导入到GridFS中
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testUploadToGridFS() throws IOException {
|
|||
|
File file = new File(rsfilepath);
|
|||
|
FileInputStream inputStream = new FileInputStream(file);
|
|||
|
|
|||
|
//GridFSUploadOptions配置chunkSize和添加元数据
|
|||
|
GridFSUploadOptions options = new GridFSUploadOptions()
|
|||
|
.chunkSizeBytes(chunckSize)
|
|||
|
.metadata(new Document("k1","v1").append("k2","v2"));
|
|||
|
|
|||
|
//GridFSBucket.InputStream方法读取字节输入流中的内容并将其保存到GridFSBucket中
|
|||
|
ObjectId fileId = gridFSBucket.uploadFromStream("GridFS输入", inputStream, options);
|
|||
|
System.out.println(fileId);
|
|||
|
inputStream.close();
|
|||
|
}
|
|||
|
|
|||
|
/**
|
|||
|
* openUploadStream()方法
|
|||
|
* 返回GridFSUploadStream,作为缓存
|
|||
|
* 文件导入到GridFS中
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testUOpenploadToGridFS() throws IOException {
|
|||
|
byte[] data = Files.readAllBytes(Paths.get(rsfilepath));
|
|||
|
|
|||
|
//GridFSUploadOptions 配置 chunkSize 和添加元数据
|
|||
|
GridFSUploadOptions options = new GridFSUploadOptions()
|
|||
|
.chunkSizeBytes(chunckSize)
|
|||
|
.metadata(new Document("format","tiff").append("SRS","EPSG:3857"));
|
|||
|
|
|||
|
GridFSUploadStream uploadStream = gridFSBucket.openUploadStream("缓冲", options);
|
|||
|
//GridFSUploadStream缓冲数据达到chunckSizeBytes时才进行插入数据块chunks操作
|
|||
|
uploadStream.write(data);
|
|||
|
//当GridFSUploadStream被关闭后,才会将最后一块chunk写入chunks集合和将文件元数据插入files集合
|
|||
|
uploadStream.close();
|
|||
|
String fileId = uploadStream.getObjectId().toString();
|
|||
|
System.out.println(fileId);
|
|||
|
}
|
|||
|
|
|||
|
/**
|
|||
|
* find()方法
|
|||
|
* 查找GridFS中的文件
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testFindFileFromGridFS() throws IOException {
|
|||
|
//查询GridFS中所有的文件
|
|||
|
gridFSBucket.find().forEach(gridFSFile -> {
|
|||
|
System.out.println(gridFSFile.getObjectId()+": "+gridFSFile.getFilename());
|
|||
|
});
|
|||
|
System.out.println("-----------------------");
|
|||
|
gridFSBucket.find(eq("metadata.SRS","EPSG:3857")).forEach(gridFSFile -> {
|
|||
|
System.out.println(gridFSFile.getObjectId()+": "+gridFSFile.getFilename());
|
|||
|
});
|
|||
|
}
|
|||
|
|
|||
|
/**
|
|||
|
* downloadToStream()方法
|
|||
|
* 根据fileId从GridFS中下载文件
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testDownloadToStreamById() throws IOException {
|
|||
|
//需要导出的文件的fileId
|
|||
|
ObjectId fileId = new ObjectId("6049d240efdc5715fc6ecbbe");
|
|||
|
//指定输出目标路径和输出文件名
|
|||
|
File file = new File("E:\\data\\out\\NDWI_2019_S2L1C.tiff");
|
|||
|
if(!file.exists()){
|
|||
|
file.getParentFile().mkdirs();
|
|||
|
file.createNewFile();
|
|||
|
}
|
|||
|
//创建文件字节输出流
|
|||
|
FileOutputStream out = new FileOutputStream(file);
|
|||
|
|
|||
|
gridFSBucket.downloadToStream(fileId, out);
|
|||
|
out.close();
|
|||
|
}
|
|||
|
|
|||
|
/**
|
|||
|
* downloadToStream()方法
|
|||
|
* 根据filename从GridFS中下载文件
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testDownloadToStreamByFilename() throws IOException {
|
|||
|
//创建下载条件对象
|
|||
|
GridFSDownloadOptions downloadOptions = new GridFSDownloadOptions();
|
|||
|
/**
|
|||
|
* 版本控制,默认下载最新的一个版本对象,这里指定为0,选择原始的版本
|
|||
|
* 0 = the original stored file
|
|||
|
* 1 = the first revision
|
|||
|
* 2 = the second revision
|
|||
|
* etc..
|
|||
|
* -2 = the second most recent revision
|
|||
|
* -1 = the most recent revision
|
|||
|
*/
|
|||
|
downloadOptions.revision(0);
|
|||
|
|
|||
|
//指定输出目标路径和输出文件名
|
|||
|
File file = new File("E:\\data\\out\\NDWI2.tiff");
|
|||
|
if(!file.exists()){
|
|||
|
file.getParentFile().mkdirs();
|
|||
|
file.createNewFile();
|
|||
|
}
|
|||
|
//创建文件字节输出流
|
|||
|
FileOutputStream out = new FileOutputStream(file);
|
|||
|
|
|||
|
gridFSBucket.downloadToStream("归一化指数2019",out,downloadOptions);
|
|||
|
out.close();
|
|||
|
}
|
|||
|
|
|||
|
|
|||
|
/**
|
|||
|
* rename,重命名
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testRenameFile(){
|
|||
|
ObjectId fileId = new ObjectId("6049d240efdc5715fc6ecbbe");
|
|||
|
gridFSBucket.rename(fileId,"归一化指数2019");
|
|||
|
}
|
|||
|
|
|||
|
/**
|
|||
|
* delete
|
|||
|
*/
|
|||
|
@Test
|
|||
|
void testDeleteFile(){
|
|||
|
ObjectId fileId = new ObjectId("6049bf658ca88237b95c9952");
|
|||
|
gridFSBucket.delete(fileId);
|
|||
|
}
|
|||
|
}
|
|||
|
|
|||
|
```
|
|||
|
|
|||
|
|
|||
|
|
|||
|
|
|||
|
|
|||
|
### 参考文章
|
|||
|
|
|||
|
[1] `GridFS` https://docs.mongodb.com/manual/core/gridfs/
|
|||
|
|
|||
|
[2] `mongofiles` https://docs.mongodb.com/database-tools/mongofiles
|
|||
|
|
|||
|
[3] `Java Driver Tutorial GridFS` https://mongodb.github.io/mongo-java-driver/4.2/driver/tutorials/gridfs/
|