IQSS · scolapasta · Jul 21, 2020 · May 29, 2020 · May 29, 2020 · Jun 2, 2020
diff --git a/doc/release-notes/6505-zipdownload-service.md b/doc/release-notes/6505-zipdownload-service.md
@@ -0,0 +1,30 @@
+### A multi-file, zipped download optimization
+
+In this release we are offering an experimental optimization for the
+multi-file, download-as-zip functionality. If this option is enabled,
+instead of enforcing size limits, we attempt to serve all the files
+that the user requested (that they are authorized to download), but
+the request is redirected to a standalone zipper service running as a
+cgi executable. Thus moving these potentially long-running jobs
+completely outside the Application Server (Payara); and preventing
+service threads from becoming locked serving them. Since zipping is
+also a CPU-intensive task, it is possible to have this service running
+on a different host system, thus freeing the cycles on the main
+Application Server. (The system running the service needs to have
+access to the database as well as to the storage filesystem, and/or S3
+bucket).
+
+Please consult the scripts/zipdownload/README.md in the Dataverse 5
+source tree.
+
+The components of the standalone "zipper tool" can also be downloaded
+here:
+(my plan is to build the executable and to add it to the v5
+release files on github: - L.A.)
+https://github.com/IQSS/dataverse/releases/download/v5.0/zipper.zip.
+
+## New JVM Options and DB Options
+
+### New DB Option CustomZipDownloadServiceUrl
+
+If defined, this is the URL of the zipping service outside the main Application Service where zip downloads should be directed (instead of /api/access/datafiles/)
diff --git a/doc/sphinx-guides/Makefile b/doc/sphinx-guides/Makefile
@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -W
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build

diff --git a/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml b/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml
@@ -47,7 +47,8 @@ output_file: /tmp/make-data-count-report
 output_format: json
 
 # the name of the platform that goes into your reports
-# FIXME: Change "platform" to the brand of your Dataverse installation.
+# FIXME: Change "platform" to match the name of your Dataverse installation. Examples
+# are "Harvard Dataverse" for Harvard University or "LibraData" for the University of Virginia.
 platform: LibreScholar
 
 # Don't put your api token in here if you're going to commit it, but put in separate secrets.yaml in same

diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst
@@ -2311,6 +2311,8 @@ Place this ``user-add.json`` file in your current directory and run the followin
 
   curl -d @user-add.json -H "Content-type:application/json" "$SERVER_URL/api/builtin-users?password=$NEWUSER_PASSWORD&key=$BUILTIN_USERS_KEY"
 
+Optionally, you may use a third query parameter "sendEmailNotification=false" to explicitly disable sending an email notification to the new user.
+
 Roles
 -----
 

diff --git a/doc/sphinx-guides/source/developers/make-data-count.rst b/doc/sphinx-guides/source/developers/make-data-count.rst
@@ -41,7 +41,7 @@ Next you should run Counter Processor to convert the log into a SUSHI report, wh
 - ``log_name_pattern`` You might want something like ``/usr/local/payara5/glassfish/domains/domain1/logs/counter_(yyyy-mm-dd).log``
 - ``year_month`` You should probably set this to the current month.
 - ``output_file`` This needs to be a directory that the "dataverse" Unix user can read but that the "counter" user can write to. In dev, you can probably get away with "/tmp" as the directory.
-- ``platform`` Out of the box from Counter Processor this is set to ``Dash`` but we're not 100% sure if this should be "Dataverse" or a branch for a Dataverse installation like "LibreScholar".
+- ``platform`` Out of the box from Counter Processor this is set to ``Dash`` but this should be changed to match the name of your Dataverse. Examples are "Harvard Dataverse" for Harvard University or "LibraData" for the University of Virginia.
 - ``upload_to_hub`` This should be "False" unless you are testing sending SUSHI reports to the DataCite hub.
 - ``simulate_date`` You should probably set this to tomorrow.
 

diff --git a/doc/sphinx-guides/source/installation/advanced.rst b/doc/sphinx-guides/source/installation/advanced.rst
@@ -35,3 +35,51 @@ If you have successfully installed multiple app servers behind a load balancer y
 You would repeat the steps above for all of your app servers. If users seem to be having a problem with a particular server, you can ask them to visit https://dataverse.example.edu/host.txt and let you know what they see there (e.g. "server1.example.edu") to help you know which server to troubleshoot.
 
 Please note that :ref:`network-ports` under the Configuration section has more information on fronting your app server with Apache. The :doc:`shibboleth` section talks about the use of ``ProxyPassMatch``.
+
+Optional Components
+-------------------
+
+Standalone "Zipper" Service Tool
+++++++++++++++++++++++++++++++++
+
+As of Dataverse v5.0 we offer an experimental optimization for the
+multi-file, download-as-zip functionality. If this option
+(``:CustomZipDownloadServiceUrl``) is enabled, instead of enforcing
+the size limit on multi-file zipped downloads (as normally specified
+by the option ``:ZipDownloadLimit``), we attempt to serve all the
+files that the user requested (that they are authorized to download),
+but the request is redirected to a standalone zipper service running
+as a cgi-bin executable under Apache. Thus moving these potentially
+long-running jobs completely outside the Application Server (Payara);
+and preventing worker threads from becoming locked serving them. Since
+zipping is also a CPU-intensive task, it is possible to have this
+service running on a different host system, freeing the cycles on the
+main Application Server. (The system running the service needs to have
+access to the database as well as to the storage filesystem, and/or S3
+bucket).
+
+Please consult the scripts/zipdownload/README.md in the Dataverse 5
+source tree for more information. 
+
+To install: You can follow the instructions in the file above to build
+``ZipDownloadService-v1.0.0.jar``. It will also be available, pre-built as part of the Dataverse release on GitHub. Copy it, together with the shell
+script scripts/zipdownload/cgi-bin/zipdownload to the cgi-bin
+directory of the chosen Apache server (/var/www/cgi-bin standard). 
+
+Make sure the shell script (zipdownload) is executable, and edit it to configure the
+database access credentials. Do note that the executable does not need
+access to the entire Dataverse database. A security-conscious admin
+can create a dedicated database user with access to just one table:
+``CUSTOMZIPSERVICEREQUEST``.
+
+You may need to make extra Apache configuration changes to make sure /cgi-bin/zipdownload is accessible from the outside.
+For example, if this is the same Apache that's in front of your Dataverse Payara instance, you will need to add another pass through statement to your configuration:
+
+``ProxyPassMatch ^/cgi-bin/zipdownload !``
+
+Test this by accessing it directly at ``<SERVER URL>/cgi-bin/download``. You should get a ``404 No such download job!``. If instead you are getting an "internal server error", this may be an SELinux issue; try ``setenforce Permissive``. If you are getting a generic Dataverse "not found" page, review the ``ProxyPassMatch`` rule you have added. 
+
+To activate in Dataverse::
+
+   curl -X PUT -d '/cgi-bin/zipdownload' http://localhost:8080/api/admin/settings/:CustomZipDownloadServiceUrl
+
diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
@@ -2134,3 +2134,16 @@ Unlike other facets, those indexed by Date/Year are sorted chronologically by de
 If you don’t want date facets to be sorted chronologically, set:
 
 ``curl -X PUT -d 'false' http://localhost:8080/api/admin/settings/:ChronologicalDateFacets``
+
+:CustomZipDownloadServiceUrl
+++++++++++++++++++++++++++++
+
+The location of the "Standalone Zipper" service. If this option is specified, Dataverse will be redirecing bulk/mutli-file zip download requests to that location, instead of serving them internally. See the "Advanced" section of the Installation guide for information on how to install the external zipper. (This is still an experimental feature, as of v5.0).
+
+To enable redirects to the zipper installed on the same server as the main Dataverse application: 
+
+``curl -X PUT -d '/cgi-bin/zipdownload' http://localhost:8080/api/admin/settings/:CustomZipDownloadServiceUrl``
+
+To enable redirects to the zipper on a different server: 
+
+``curl -X PUT -d 'https://zipper.example.edu/cgi-bin/zipdownload' http://localhost:8080/api/admin/settings/:CustomZipDownloadServiceUrl`` 
diff --git a/doc/sphinx-guides/source/user/account.rst b/doc/sphinx-guides/source/user/account.rst
@@ -158,10 +158,10 @@ Notifications appear in the notifications tab on your account page and are also
 
 You will receive a notification when:
 
-- You've created your account
-- You've created a dataverse or added a dataset
-- Another Dataverse user has requested access to a restricted file in one of your datasets
-- A file in one of your datasets has finished the ingest process
+- You've created your account.
+- You've created a dataverse or added a dataset.
+- Another Dataverse user has requested access to restricted files in a dataset that you published. (If you submitted your dataset for review and it was published by a curator, the curators of the dataverse that contains your dataset will get a notification about requests to access your restricted files.)
+- A file in one of your datasets has finished the ingest process.
 
 Notifications will only be emailed one time even if you haven't read the notification on the Dataverse site.
 

diff --git a/scripts/zipdownload/README.md b/scripts/zipdownload/README.md
@@ -0,0 +1,104 @@
+Work in progress!
+
+to build: 
+
+cd scripts/zipdownload
+mvn clean compile assembly:single
+
+to install: 
+
+install cgi-bin/zipdownload and ZipDownloadService-v1.0.0.jar in your cgi-bin directory (/var/www/cgi-bin standard). 
+
+Edit the config lines in the shell script (zipdownload) as needed. 
+
+You may need to make extra Apache configuration changes to make sure /cgi-bin/zipdownload is accessible from the outside. 
+For example, if this is the same Apache that's in front of your Dataverse Payara instance, you'll need to add another pass through statement to your configuration: 
+
+``ProxyPassMatch ^/cgi-bin/zipdownload !``
+
+(see the "Advanced" section of the Installation Guide for some extra troubleshooting tips)
+
+To activate in Dataverse: 
+
+curl -X PUT -d '/cgi-bin/zipdownload' http://localhost:8080/api/admin/settings/:CustomZipDownloadServiceUrl
+
+How it works:
+=============
+
+(This is an ongoing design discussion - other developers are welcome to contribute)
+
+The goal: to move this potentially long-running task out of the
+Application Server. This is the sole focus of this implementation. It
+does not attempt to make it faster.
+
+The rationale here is a zipped download of a large enough number of
+large enough files will always be slow. Zipping (compressing) itself
+is a fairly CPU-intensive task. This will most frequently be the
+bottleneck of the service. Although with a slow storage location (S3
+or Swift, with a slow link to the share) it may be the speed at which
+the application accesses the raw bytes. The exact location of the
+bottleneck is in a sense irrelevant. On a very fast system, with the
+files stored on a very fast local RAID, the bottleneck for most users
+will likely shift to the speed of their internet connection to the
+server. The bottom line is, downloading this multi-file compressed
+stream will take a long time no matter how you slice it. So this hack
+addresses it by moving the task outside Payara, where it's not going
+to hog any threads. 
+
+A quick, somewhat unrelated note: attempting to download a multi-GB
+stream over http will always have its own inherent risks. If the
+download has to take hours or days to complete, it is very likely that
+it'll break down somewhere in the middle. Do note that for a zipped
+download our users will not be able to utilize `wget --continue`, or
+any similar "resume" functionality - because it's impossible to resume
+generating a zipped stream from a certain offset.
+
+The implementation is a hack. It relies on direct access to everything - storage locations (filesystem or S3) and the database.
+
+There are no network calls between the application (Dataverse) and the zipper (an
+implementation relying on such a call was discussed early
+on). Dataverse issues a "job key" and sends the user's browser to the
+zipper (to, for ex., /cgi-bin/zipdownload?<job key>) instead of
+/api/access/datafiles/<file ids>). To authorize the zipdownload for
+the "job key", and inform the zipper on which files to zip and where
+to find them, the application relies on a database table, that the
+zipper also has access to. In other words, there is a saved state
+information associated with each zipped download request. Zipper may
+be given a limited database access - for example, via a user
+authorized to access that one table only. After serving the files, the
+zipper removes the database entries. Job records in the database have
+time stamps, so on the application side, as an added level of cleanup,
+it automatically deletes any records older than 5 minutes (can be
+further reduced) every time the service adds new records; as an added
+level of cleanup for any records that got stuck in the db because the
+corresponding zipper jobs never completed. A paranoid admin may choose
+to give the zipper read-only access to the database, and rely on a
+cleanup solely on the application side.
+
+I have explored ways to avoid maintaining this state information. A
+potential implementation we discussed early on, where the application
+would make a network call to the zipper before redirecting the user
+there, would NOT solve that problem - the state would need to somehow
+be maintained on the zipper side. The only truly stateless
+implementation would rely on including all the file information WITH
+the redirect itself, with some pre-signed URL mechanism to make it
+secure. Mechanisms for pre-signing requests are readily available and
+simple to implement. We could go with something similar to how S3
+presigns their access URLs. Jim Myers has already speced out how this
+could be done for Dataverse access urls in a design document
+(https://docs.google.com/document/d/1J8GW6zi-vSRKZdtFjLpmYJ2SUIcIkAEwHkP4q1fxL-s/edit#). (Basically,
+you hash the product of your request parameters, the issue timestamp
+AND some "secret" - like the user's API key - and send the resulting
+hash along with the request. Tampering with any of the parameters, or
+trying to extend the life span of the request, becomes impossible,
+because it would invalidate the hash). What stopped me from trying
+something like that was the sheer size of information that would need
+to be included with a request, for a potentially long list of files
+that need to be zipped. When serving a zipped download from a page
+that would be doable - we could javascript together a POST call that
+the browser could make to send all that info to the zipper. But if we
+want to implement something similar in the API, I felt like I really
+wanted to be able to simply issue a quick redirect to a manageable url
+- which with the implementation above is simply
+/cgi-bin/zipdownload?<job key>, with the <job key> being just a 16
+character hex string in the current implementation.
diff --git a/scripts/zipdownload/cgi-bin/zipdownload b/scripts/zipdownload/cgi-bin/zipdownload
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+CLASSPATH=/var/www/cgi-bin; export CLASSPATH
+
+PGHOST="localhost"; export PGHOST
+PGPORT=5432; 	    export PGPORT
+PGUSER="dvnapp";    export PGUSER
+PGDB="dvndb"; 	    export PGDB
+PGPW="xxxxx"; 	    export PGPW
+
+java -Ddb.serverName=$PGHOST -Ddb.portNumber=$PGPORT -Ddb.user=$PGUSER -Ddb.databaseName=$PGDB -Ddb.password=$PGPW -jar ZipDownloadService-v1.0.0.jar
diff --git a/scripts/zipdownload/pom.xml b/scripts/zipdownload/pom.xml
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>ZipDownloadService</groupId>
+    <artifactId>ZipDownloadService</artifactId>
+    <version>1.0.0</version>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+    <pluginRepositories>
+        <pluginRepository>
+            <id>central</id>
+            <name>Central Repository</name>
+            <url>https://repo.maven.apache.org/maven2</url>
+            <layout>default</layout>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+            <releases>
+                <updatePolicy>never</updatePolicy>
+            </releases>
+        </pluginRepository>
+    </pluginRepositories>
+    <repositories>
+        <repository>
+            <id>central-repo</id>
+            <name>Central Repository</name>
+            <url>https://repo1.maven.org/maven2</url>
+            <layout>default</layout>
+        </repository>
+    </repositories>
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>com.amazonaws</groupId>
+                <artifactId>aws-java-sdk-bom</artifactId>
+                <version>1.11.790</version>
+                <type>pom</type>
+                <scope>import</scope>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
+    <dependencies>
+        <!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
+        <dependency>
+            <groupId>org.postgresql</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>42.2.2</version>
+        </dependency>
+        <dependency>
+            <groupId>com.amazonaws</groupId>
+            <artifactId>aws-java-sdk-s3</artifactId>
+        </dependency>
+    </dependencies>
+    <build>
+        <sourceDirectory>src/main/java</sourceDirectory>
+        <plugins>
+            <plugin>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>2.4</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>edu.harvard.iq.dataverse.custom.service.download.ZipDownloadService</mainClass>
+                        </manifest>
+                    </archive>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                    <finalName>${project.artifactId}-v${project.version}</finalName>
+                    <appendAssemblyId>false</appendAssemblyId>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>