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7025 orcid public #2

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809643a
allow changes to file metadata via API #6962
pdurbin Jun 5, 2020
508e95c
allow file metadata changes if passing existing path/name #6962
pdurbin Jun 8, 2020
9954220
allow changes if dir exists and label passed, formatting #6962
pdurbin Jun 9, 2020
e5ec9bc
avoid dir1 + file1 == dir + 1file1 (add "/") #6962
pdurbin Jun 9, 2020
491caff
eliminate code we don't need, handled elsewhere #6962
pdurbin Jun 9, 2020
9673e82
Refactor ConfirmEmailService to offer verification checking and start…
poikilotherm May 28, 2020
45cb9a7
Add a very basic first implementation of the mail domain group infras…
poikilotherm May 28, 2020
1a6b680
Make domain comparison use lowercase. Add some more JavaDocs. #6936
poikilotherm May 29, 2020
0d7379c
Add tests for MailDomainGroup and MailDomainGroupProvider. #6936
poikilotherm May 29, 2020
39075d9
Add generator for MailDomainGroups during testing. #6936
poikilotherm May 29, 2020
fa2a544
Make MailDomainGroupServiceBean more testable by making the mail bise…
poikilotherm May 29, 2020
1b5e0e1
Add test for MailDomainGroupServiceBean and fix error when filtering …
poikilotherm May 29, 2020
69a485f
Wire the new mail domain group in the GroupServiceBean, so it will be…
poikilotherm May 29, 2020
8d2b9cb
Make MailDomainGroup and its test usable from other packages (for JSO…
poikilotherm May 29, 2020
8aaab61
Add JSON parser and printer for MailDomainGroup, to be used for REST …
poikilotherm May 29, 2020
dc0da65
Add persistence handling to create and update MailDomainGroups to the…
poikilotherm Jun 8, 2020
7c72ed5
Add first REST endpoints to get, create and update MailDomainGroups. …
poikilotherm Jun 8, 2020
694ee50
Extend exception handling at REST endpoints. Does now provide a catch…
poikilotherm Jun 9, 2020
389324b
Remove try-catch-boilerplate for mail domain group creation by using …
poikilotherm Jun 9, 2020
09c7f64
Make JsonParser fail on empty (maybe filtered invalid) domains array …
poikilotherm Jun 9, 2020
bd0f685
Add deletion endpoint for MailDomainGroup and make consistent use of …
poikilotherm Jun 9, 2020
a34d7c1
ensure passing "" as directoryLabel doesn't cause problems #6962
pdurbin Jun 10, 2020
30c6fe1
Add btn-explore class to tool link under access dataset btn [ref #6938]
mheppler Jun 12, 2020
9e2c697
#6982 allow newer java versions (LTS and current), correct login cond…
Jun 12, 2020
6b65788
Add db migration for MailDomainGroups as PersistedGlobalGroup uses SI…
poikilotherm Jun 15, 2020
2debed2
simply conflict-checking code #6962
pdurbin Jun 15, 2020
76ae927
Add docs for mail domain groups only, without refactoring to a groups…
poikilotherm Jun 15, 2020
a820869
#6982 stick to LTS OpenJDK releases. next one will be 17.
Jun 15, 2020
7b2f424
Revised click selectors to track dropdown menu option clicks [ref #6938]
mheppler Jun 16, 2020
8ad74b9
Merge branch 'develop' into 6938-analytics-new-buttons
sekmiller Jun 16, 2020
23342bc
#6927 add glassfish_request_timeout setting
Jun 17, 2020
396e467
#6927 move http-listener settings together, drop timeout to 30mins pe…
Jun 17, 2020
61bfb4e
Cleaned up format warnings when building sphinx-guides [ref #6997]
mheppler Jun 17, 2020
c29163d
#6927 break out ApplicationServerSettings, provide real value in example
Jun 18, 2020
0012013
#6927 resolve merge conflicts
Jun 18, 2020
cf7fcb9
Added new button styles to Style Guide, Patterns pg [ref #6940]
mheppler Jun 22, 2020
c3b5982
fix "WARNING: download file not readable" #6997
pdurbin Jun 22, 2020
23a5827
fix formatting around solr #6997
pdurbin Jun 22, 2020
c8a2302
fix formating around minio, s3 #6997
pdurbin Jun 22, 2020
aed68ea
updating release notes file to .md
djbrooke Jun 23, 2020
92f416f
Create 6938-analytics-reload
djbrooke Jun 23, 2020
1da6cc6
#7009 Removed one of the redundant encoding functions.
JingMa87 Jun 23, 2020
6575273
Solves #7011. Add render logic for signup link on login page dependin…
poikilotherm Jun 24, 2020
b72fb31
#6948 check file labels on new draft
sekmiller Jun 24, 2020
7457736
adding release note or tabular downloads
djbrooke Jun 24, 2020
dcb8100
Code cleanup for new button UI [ref #6938]
mheppler Jun 24, 2020
048bb5d
only iterate over current files in latest published version
qqmyers Jun 24, 2020
83de579
#6927 add GLASSFISH_REQUEST_TIMEOUT to interactive.config
Jun 24, 2020
d954ae6
#6927 correct entries in interactive.config
Jun 25, 2020
d15feb7
Added new primary access and more option btns to patterns pg in style…
mheppler Jun 25, 2020
f6d336b
#7023 Replace xml response substring in logging with URL parameters. …
JingMa87 Jun 25, 2020
a4a3911
updates per review
qqmyers Jun 26, 2020
c07a695
#7034 point Jenkinsfile at GlobalDataverseCommunityConsortium/dataver…
Jun 29, 2020
04d09cd
#7017 bump to payara-5.2020.2 per @scolapasta, remove JSF patch
Jun 29, 2020
6f8c054
#7017 5.2020.0 should be 5.2020.2, typo
Jun 29, 2020
5b92433
#7038 ansible repo has moved to GDCC org
Jun 30, 2020
4790996
adding note about ansible and previewer moves
djbrooke Jun 30, 2020
0a4ba60
Merge pull request #6996 from OdumInstitute/6927_download_timeout
kcondon Jun 30, 2020
8bbc7ce
Merge pull request #7035 from OdumInstitute/7034_update_Jenkinsfile
kcondon Jun 30, 2020
fc37fac
Merge pull request #7039 from OdumInstitute/7038_ansible_to_GDCC
kcondon Jun 30, 2020
f00d711
Merge remote-tracking branch 'upstream/develop' into 7017_payara_2020
Jun 30, 2020
ce86fed
Merge pull request #7036 from OdumInstitute/7017_payara_2020
kcondon Jun 30, 2020
18d16f1
UI and accessibility clean up on dataverse, dataset and file pgs [ref…
mheppler Jul 1, 2020
c79ce40
Merge pull request #6974 from poikilotherm/6936-domaingroups
kcondon Jul 1, 2020
79c5dfa
Merge remote-tracking branch 'upstream/develop' into 6982_install_py_…
Jul 1, 2020
bc06fe6
Merge pull request #6968 from IQSS/6962-bugfix
kcondon Jul 1, 2020
95510a3
Merge pull request #6983 from OdumInstitute/6982_install_py_java_check
kcondon Jul 1, 2020
070cda0
Merge pull request #7041 from IQSS/7040-related-project-moves
kcondon Jul 1, 2020
6bc6795
Merge pull request #7007 from IQSS/6940-style-guide-new-buttons
kcondon Jul 1, 2020
7492e77
Merge branch 'develop' into 6997-guides-clean-up
mheppler Jul 1, 2020
4eda5a1
Merge pull request #6998 from IQSS/6997-guides-clean-up
kcondon Jul 1, 2020
ee810fc
Delete asadmin-setup.sh
poikilotherm Jul 1, 2020
c29ce7f
Merge pull request #7008 from IQSS/6938-analytics-new-buttons
kcondon Jul 1, 2020
7de1c5b
Merge pull request #7042 from IQSS/6684-additional-ui-cleanup
kcondon Jul 2, 2020
e20c094
Merge pull request #7012 from poikilotherm/7011-render-signup
kcondon Jul 2, 2020
bd736d2
Merge pull request #7010 from JingMa87/7009-double-set-name-encoding
kcondon Jul 2, 2020
2f193c1
Merge pull request #7016 from IQSS/6948-duplicate-file-name
kcondon Jul 2, 2020
c5c2236
Merge pull request #7024 from JingMa87/7023-replace-xml-with-url
kcondon Jul 2, 2020
98bff8f
Merge pull request #7015 from QualitativeDataRepository/IQSS/7014_cur…
kcondon Jul 2, 2020
6daf219
Merge pull request #7049 from poikilotherm/cleanup-scripts
kcondon Jul 2, 2020
8063067
Merge branch 'develop' into orcid-public-api
poikilotherm Jul 8, 2020
5a98e64
Refactor userEndpoint checks for Public ORCID scope. #7025
poikilotherm Jul 8, 2020
9475838
Convert ORCID OAuth2 provider test from JUnit4 to JUnit5. #7025
poikilotherm Jul 8, 2020
d588210
Add test case for public ORCID API endpoint to result in scope /authe…
poikilotherm Jul 8, 2020
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2 changes: 1 addition & 1 deletion Vagrantfile
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
puts "https://github.com/IQSS/dataverse/issues/6849"
puts
puts "You can also try the Vagrant environment at"
puts "https://github.com/IQSS/dataverse-ansible"
puts "https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible"
exit 1

config.vm.provider "virtualbox" do |vbox|
Expand Down
5 changes: 5 additions & 0 deletions doc/release-notes/6938-analytics-reload
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
### Custom Analytics Code Changes

You should update your custom analytics code to implement necessary changes for tracking updated dataset and file buttons. There was also a fix to the analytics code that will now properly track downloads for tabular files.

We have updated the documentation and sample analytics code snippet provided in [Installation Guide > Configuration > Web Analytics Code](http://guides.dataverse.org/en/latest/installation/config.html#web-analytics-code) to reflect the changes implemented in this version (#6938/#6684).
8 changes: 8 additions & 0 deletions doc/release-notes/7040-project-moves.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
## Notes for Dataverse Installation Administrators

### Location Changes for Related Projects

The dataverse-ansible and dataverse-previewers repositories have been moved to the GDCC Organization on GitHub. If you have been referencing the dataverse-ansible repository from IQSS and the dataverse-previewers from QDR, please instead use them from their new locations:

<https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible>
<https://github.com/GlobalDataverseCommunityConsortium/dataverse-previewers>
61 changes: 61 additions & 0 deletions doc/sphinx-guides/source/_static/docsdataverse_org.css
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,67 @@ div.code-example .messagePanel .glyphicon {
div.code-example span.glyphicon-question-sign.tooltip-icon {color: #99bcdb !important;}
div.code-example span.glyphicon-question-sign.tooltip-icon:hover {color: #337AB7 !important;}

div.code-example .btn-group .btn-link {font-size:2em !important;}
div.code-example .btn-group .btn.btn-link.bootstrap-button-tooltip span.caret {margin-left: 6px;}

div.code-example .btn.btn-default.btn-access {background-color: #fff;background-image:none;}
div.code-example .btn.btn-default.btn-access:focus, div.code-example .btn.btn-default.btn-access:hover, div.code-example .btn.btn-default.btn-access:active {background-color: #e6e6e6;background-image:none;}

/* Dropdown submenu */
div.code-example .dropdown-submenu {
position: relative;
}
div.code-example .dropdown-submenu.pull-left {
width: 100%;
}
div.code-example .dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
-webkit-border-radius: 0 6px 6px 6px;
-moz-border-radius: 0 6px 6px;
border-radius: 0 6px 6px 6px;
}
div.code-example .dropdown-submenu.pull-left>.dropdown-menu {
float: right;
min-width: 100%;
}

div.code-example .dropdown-submenu:hover>.dropdown-menu {
display: block;
}

div.code-example .dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #ccc;
margin-top: 5px;
margin-right: -10px;
}

div.code-example .dropdown-submenu:hover>a:after {
border-left-color: #fff;
}

div.code-example .dropdown-submenu.pull-left {
float: none;
}

div.code-example .dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
-webkit-border-radius: 6px 0 6px 6px;
-moz-border-radius: 6px 0 6px 6px;
border-radius: 6px 0 6px 6px;
}

#breadcrumbNavBlock {margin-top:.5em;}
#breadcrumbNavBlock .breadcrumbBlock {float:left; position:relative;}
#breadcrumbNavBlock .breadcrumbActive {font-weight:bold;}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@

function enableAnalyticsEventCapture() {
// Download button
$(document).on("click", ".btn-download", function() {
$(document).on("click", ".btn-download, .btn-download.dropdown-toggle + ul.dropdown-menu li a", function() {
var category = $(this).text();
var label = getFileId($(this));
gtag('event', 'Download',{'event_category' : category,
Expand All @@ -26,23 +26,23 @@
});

// Explore button
$(document).on("click", ".btn-explore + ul.dropdown-menu li a", function() {
$(document).on("click", ".btn-explore, .btn-explore.dropdown-toggle + ul.dropdown-menu li a", function() {
var category = $(this).text();
var label = getFileId($(this));
gtag('event', 'Explore', {'event_category' : category,
'event_label' : label});
});

// Compute button
$(document).on("click", ".btn-compute", function() {
$(document).on("click", ".btn-compute, .btn-compute.dropdown-toggle + ul.dropdown-menu li a", function() {
var category = $(this).text();
var label = getFileId($(this));
gtag('event', 'Compute', {'event_category' : category,
'event_label' : label});
});

// Preview button
$(document).on("click", ".btn-preview", function() {
$(document).on("click", ".btn-preview, .btn-preview.dropdown-toggle + ul.dropdown-menu li a", function() {
var category = $(this).text();
var label = getFileId($(this));
gtag('event', 'Preview', {'event_category' : category,
Expand Down Expand Up @@ -110,7 +110,7 @@

function getFileId(target) {
var label = 'Unknown';
if(target.parents('th').length>0) {
if(target.parents('th, #actionButtonBlock .btn-access-dataset + ul.dropdown-menu').length>0) {
//Special case - the Download button that downloads all selected files in the dataset
label = 'file(s) from ' + stripId($('#datasetForm').attr('action'));
} else {
Expand Down
1 change: 1 addition & 0 deletions doc/sphinx-guides/source/admin/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ This guide documents the functionality only available to superusers (such as "da
dataverses-datasets
solr-search-index
ip-groups
mail-groups
monitoring
reporting-tools-and-queries
maintenance
Expand Down
82 changes: 82 additions & 0 deletions doc/sphinx-guides/source/admin/mail-groups.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,82 @@
Mail Domain Groups
==================

Groups can be defined based on the domain part of users (verified) email addresses. Email addresses that match
one or more groups configuration will add the user to them.

Within the scientific community, in many cases users will use a institutional email address for their account in a
Dataverse installation. This might offer a simple solution for building groups of people, as the domain part can be
seen as a selector for group membership.

Some use cases: installations that like to avoid Shibboleth, enable self sign up, offer multi-tenancy or can't use
:doc:`ip-groups` plus many more.

.. hint:: Please be aware that non-verified mail addresses will exclude the user even if matching. This is to avoid
privilege escalation.

Listing Mail Domain Groups
--------------------------

Mail Domain Groups can be listed with the following curl command:

``curl http://localhost:8080/api/admin/groups/domain``

Listing a specific Mail Domain Group
------------------------------------

Let's say you used "domainGroup1" as the alias of the Mail Domain Group you created below.
To list just that Mail Domain Group, you can include the alias in the curl command like this:

``curl http://localhost:8080/api/admin/groups/domain/domainGroup1``


Creating a Mail Domain Group
----------------------------

Mail Domain Groups can be created with a simple JSON file:

.. code-block:: json
:caption: domainGroup1.json
:name: domainGroup1.json
{
"name": "Users from @example.org",
"alias": "exampleorg",
"description": "Any verified user from Example Org will be included in this group.",
"domains": ["example.org"]
}
Giving a ``description`` is optional. The ``name`` will be visible in the permission UI, so be sure to pick a sensible
value.

The ``domains`` field is mandatory to be an array. This enables creation of multi-domain groups, too.

Obviously you can create as many of these groups you might like, as long as the ``alias`` is unique.

To load it into your Dataverse installation, either use a ``POST`` or ``PUT`` request (see below):

``curl -X POST -H 'Content-type: application/json' http://localhost:8080/api/admin/groups/domain --upload-file domainGroup1.json``

Updating a Mail Domain Group
----------------------------

Editing a group is done by replacing it. Grab your group definition like the :ref:`above example <domainGroup1.json>`,
change it as you like and ``PUT`` it into your installation:

``curl -X PUT -H 'Content-type: application/json' http://localhost:8080/api/admin/groups/domain/domainGroup1 --upload-file domainGroup1.json``

Please make sure that the alias of the group you want to change is included in the path. You also need to ensure
that this alias matches with the one given in your JSON file.

.. hint:: This is an idempotent call, so it will create the group given if not present.

Deleting a Mail Domain Group
----------------------------

To delete a Mail Domain Group with an alias of "domainGroup1", use the curl command below:

``curl -X DELETE http://localhost:8080/api/admin/groups/domain/domainGroup1``

Please note: it is not recommended to delete a Mail Domain Group that has been assigned roles. If you want to delete
a Mail Domain Group, you should first remove its permissions.

2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/admin/troubleshooting.rst
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ There are several types of dataset locks. Locks can be managed using the locks A

It's normal for the ingest process described in the :doc:`/user/tabulardataingest/ingestprocess` section of the User Guide to take some time but if hours or days have passed and the dataset is still locked, you might want to inspect the locks and consider deleting some or all of them. It is recommended to restart the application server if you are deleting an ingest lock, to make sure the ingest job is no longer running in the background. Ingest locks are idetified by the label ``Ingest`` in the ``reason`` column of the ``DatasetLock`` table in the database.

A dataset is locked with a lock of type ``finalizePublication`` while the persistent identifiers for the datafiles in the dataset are registered or updated, and/or while the physical files are being validated by recalculating the checksums and verifying them against the values stored in the database, before the publication process can be completed (Note that either of the two tasks can be disabled via database options - see :doc:`config`). If a dataset has been in this state for a long period of time, for hours or longer, it is somewhat safe to assume that it is stuck (for example, the process may have been interrupted by an application server restart, or a system crash), so you may want to remove the lock (to be safe, do restart the application server, to ensure that the job is no longer running in the background) and advise the user to try publishing again. See :doc:`dataverses-datasets` for more information on publishing.
A dataset is locked with a lock of type ``finalizePublication`` while the persistent identifiers for the datafiles in the dataset are registered or updated, and/or while the physical files are being validated by recalculating the checksums and verifying them against the values stored in the database, before the publication process can be completed (Note that either of the two tasks can be disabled via database options - see :doc:`/installation/config`). If a dataset has been in this state for a long period of time, for hours or longer, it is somewhat safe to assume that it is stuck (for example, the process may have been interrupted by an application server restart, or a system crash), so you may want to remove the lock (to be safe, do restart the application server, to ensure that the job is no longer running in the background) and advise the user to try publishing again. See :doc:`dataverses-datasets` for more information on publishing.

If any files in the dataset fail the validation above the dataset will be left locked with a ``DatasetLock.Reason=FileValidationFailed``. The user will be notified that they need to contact their Dataverse support in order to address the issue before another attempt to publish can be made. The admin will have to address and fix the underlying problems (by either restoring the missing or corrupted files, or by purging the affected files from the dataset) before deleting the lock and advising the user to try to publish again. The goal of the validation framework is to catch these types of conditions while the dataset is still in DRAFT.

Expand Down
2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/api/apps.rst
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Apps
====

The introduction of Dataverse APIs has fostered the development of a variety of software applications that are listed in the :doc:`/admin/integrations`, :doc:`/admin/external-tools`, and :doc:`/admin/reporting-tools` sections of the Admin Guide.
The introduction of Dataverse APIs has fostered the development of a variety of software applications that are listed in the :doc:`/admin/integrations`, :doc:`/admin/external-tools`, and :doc:`/admin/reporting-tools-and-queries` sections of the Admin Guide.

The apps below are open source and demonstrate how to use Dataverse APIs. Some of these apps are built on :doc:`/api/client-libraries` that are available for Dataverse APIs in Python, Javascript, R, and Java.

Expand Down
2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/api/external-tools.rst
Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ If you've thought to yourself that there ought to be an app store for Dataverse
Demoing Your External Tool
++++++++++++++++++++++++++

https://demo.dataverse.org is the place to play around with Dataverse and your tool can be included. Please email support@dataverse.org to start the conversation about adding your tool. Additionally, you are welcome to open an issue at https://github.com/IQSS/dataverse-ansible which already includes a number of the tools listed above.
https://demo.dataverse.org is the place to play around with Dataverse and your tool can be included. Please email support@dataverse.org to start the conversation about adding your tool. Additionally, you are welcome to open an issue at https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible which already includes a number of the tools listed above.

Announcing Your External Tool
+++++++++++++++++++++++++++++
Expand Down
6 changes: 3 additions & 3 deletions doc/sphinx-guides/source/developers/deployment.rst
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ If you are having trouble configuring the files manually as described above, see
Configure Ansible File (Optional)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In order to configure Dataverse settings such as the password of the dataverseAdmin user, download https://raw.githubusercontent.com/IQSS/dataverse-ansible/master/defaults/main.yml and edit the file to your liking.
In order to configure Dataverse settings such as the password of the dataverseAdmin user, download https://raw.githubusercontent.com/GlobalDataverseCommunityConsortium/dataverse-ansible/master/defaults/main.yml and edit the file to your liking.

You can skip this step if you're fine with the values in the "main.yml" file in the link above.

Expand All @@ -82,9 +82,9 @@ Download and Run the "Create Instance" Script

Once you have done the configuration above, you are ready to try running the "ec2-create-instance.sh" script to spin up Dataverse in AWS.

Download :download:`ec2-create-instance.sh<https://raw.githubusercontent.com/IQSS/dataverse-ansible/master/ec2/ec2-create-instance.sh>` and put it somewhere reasonable. For the purpose of these instructions we'll assume it's in the "Downloads" directory in your home directory.
Download :download:`ec2-create-instance.sh<https://raw.githubusercontent.com/GlobalDataverseCommunityConsortium/dataverse-ansible/master/ec2/ec2-create-instance.sh>` and put it somewhere reasonable. For the purpose of these instructions we'll assume it's in the "Downloads" directory in your home directory.

To run it with default values you just need the script, but you may also want a current copy of the ansible :download:`group vars<https://raw.githubusercontent.com/IQSS/dataverse-ansible/master/defaults/main.yml>`_ file.
To run it with default values you just need the script, but you may also want a current copy of the ansible :download:`group vars<https://raw.githubusercontent.com/GlobalDataverseCommunityConsortium/dataverse-ansible/master/defaults/main.yml>`_ file.

ec2-create-instance accepts a number of command-line switches, including:

Expand Down
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