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Initial commit
This commit is contained in:
3
.gitattributes
vendored
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3
.gitattributes
vendored
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@ -0,0 +1,3 @@
|
|||||||
|
/gradlew text eol=lf
|
||||||
|
*.bat text eol=crlf
|
||||||
|
*.jar binary
|
||||||
40
.gitignore
vendored
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40
.gitignore
vendored
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@ -0,0 +1,40 @@
|
|||||||
|
HELP.md
|
||||||
|
.gradle
|
||||||
|
build/
|
||||||
|
!gradle/wrapper/gradle-wrapper.jar
|
||||||
|
!**/src/main/**/build/
|
||||||
|
!**/src/test/**/build/
|
||||||
|
|
||||||
|
### STS ###
|
||||||
|
.apt_generated
|
||||||
|
.classpath
|
||||||
|
.factorypath
|
||||||
|
.project
|
||||||
|
.settings
|
||||||
|
.springBeans
|
||||||
|
.sts4-cache
|
||||||
|
bin/
|
||||||
|
!**/src/main/**/bin/
|
||||||
|
!**/src/test/**/bin/
|
||||||
|
|
||||||
|
### IntelliJ IDEA ###
|
||||||
|
.idea
|
||||||
|
*.iws
|
||||||
|
*.iml
|
||||||
|
*.ipr
|
||||||
|
out/
|
||||||
|
!**/src/main/**/out/
|
||||||
|
!**/src/test/**/out/
|
||||||
|
|
||||||
|
### NetBeans ###
|
||||||
|
/nbproject/private/
|
||||||
|
/nbbuild/
|
||||||
|
/dist/
|
||||||
|
/nbdist/
|
||||||
|
/.nb-gradle/
|
||||||
|
|
||||||
|
### VS Code ###
|
||||||
|
.vscode/
|
||||||
|
|
||||||
|
### Kotlin ###
|
||||||
|
.kotlin
|
||||||
661
LICENSE.txt
Normal file
661
LICENSE.txt
Normal file
@ -0,0 +1,661 @@
|
|||||||
|
GNU AFFERO GENERAL PUBLIC LICENSE
|
||||||
|
Version 3, 19 November 2007
|
||||||
|
|
||||||
|
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
|
||||||
|
Everyone is permitted to copy and distribute verbatim copies
|
||||||
|
of this license document, but changing it is not allowed.
|
||||||
|
|
||||||
|
Preamble
|
||||||
|
|
||||||
|
The GNU Affero General Public License is a free, copyleft license for
|
||||||
|
software and other kinds of works, specifically designed to ensure
|
||||||
|
cooperation with the community in the case of network server software.
|
||||||
|
|
||||||
|
The licenses for most software and other practical works are designed
|
||||||
|
to take away your freedom to share and change the works. By contrast,
|
||||||
|
our General Public Licenses are intended to guarantee your freedom to
|
||||||
|
share and change all versions of a program--to make sure it remains free
|
||||||
|
software for all its users.
|
||||||
|
|
||||||
|
When we speak of free software, we are referring to freedom, not
|
||||||
|
price. Our General Public Licenses are designed to make sure that you
|
||||||
|
have the freedom to distribute copies of free software (and charge for
|
||||||
|
them if you wish), that you receive source code or can get it if you
|
||||||
|
want it, that you can change the software or use pieces of it in new
|
||||||
|
free programs, and that you know you can do these things.
|
||||||
|
|
||||||
|
Developers that use our General Public Licenses protect your rights
|
||||||
|
with two steps: (1) assert copyright on the software, and (2) offer
|
||||||
|
you this License which gives you legal permission to copy, distribute
|
||||||
|
and/or modify the software.
|
||||||
|
|
||||||
|
A secondary benefit of defending all users' freedom is that
|
||||||
|
improvements made in alternate versions of the program, if they
|
||||||
|
receive widespread use, become available for other developers to
|
||||||
|
incorporate. Many developers of free software are heartened and
|
||||||
|
encouraged by the resulting cooperation. However, in the case of
|
||||||
|
software used on network servers, this result may fail to come about.
|
||||||
|
The GNU General Public License permits making a modified version and
|
||||||
|
letting the public access it on a server without ever releasing its
|
||||||
|
source code to the public.
|
||||||
|
|
||||||
|
The GNU Affero General Public License is designed specifically to
|
||||||
|
ensure that, in such cases, the modified source code becomes available
|
||||||
|
to the community. It requires the operator of a network server to
|
||||||
|
provide the source code of the modified version running there to the
|
||||||
|
users of that server. Therefore, public use of a modified version, on
|
||||||
|
a publicly accessible server, gives the public access to the source
|
||||||
|
code of the modified version.
|
||||||
|
|
||||||
|
An older license, called the Affero General Public License and
|
||||||
|
published by Affero, was designed to accomplish similar goals. This is
|
||||||
|
a different license, not a version of the Affero GPL, but Affero has
|
||||||
|
released a new version of the Affero GPL which permits relicensing under
|
||||||
|
this license.
|
||||||
|
|
||||||
|
The precise terms and conditions for copying, distribution and
|
||||||
|
modification follow.
|
||||||
|
|
||||||
|
TERMS AND CONDITIONS
|
||||||
|
|
||||||
|
0. Definitions.
|
||||||
|
|
||||||
|
"This License" refers to version 3 of the GNU Affero General Public License.
|
||||||
|
|
||||||
|
"Copyright" also means copyright-like laws that apply to other kinds of
|
||||||
|
works, such as semiconductor masks.
|
||||||
|
|
||||||
|
"The Program" refers to any copyrightable work licensed under this
|
||||||
|
License. Each licensee is addressed as "you". "Licensees" and
|
||||||
|
"recipients" may be individuals or organizations.
|
||||||
|
|
||||||
|
To "modify" a work means to copy from or adapt all or part of the work
|
||||||
|
in a fashion requiring copyright permission, other than the making of an
|
||||||
|
exact copy. The resulting work is called a "modified version" of the
|
||||||
|
earlier work or a work "based on" the earlier work.
|
||||||
|
|
||||||
|
A "covered work" means either the unmodified Program or a work based
|
||||||
|
on the Program.
|
||||||
|
|
||||||
|
To "propagate" a work means to do anything with it that, without
|
||||||
|
permission, would make you directly or secondarily liable for
|
||||||
|
infringement under applicable copyright law, except executing it on a
|
||||||
|
computer or modifying a private copy. Propagation includes copying,
|
||||||
|
distribution (with or without modification), making available to the
|
||||||
|
public, and in some countries other activities as well.
|
||||||
|
|
||||||
|
To "convey" a work means any kind of propagation that enables other
|
||||||
|
parties to make or receive copies. Mere interaction with a user through
|
||||||
|
a computer network, with no transfer of a copy, is not conveying.
|
||||||
|
|
||||||
|
An interactive user interface displays "Appropriate Legal Notices"
|
||||||
|
to the extent that it includes a convenient and prominently visible
|
||||||
|
feature that (1) displays an appropriate copyright notice, and (2)
|
||||||
|
tells the user that there is no warranty for the work (except to the
|
||||||
|
extent that warranties are provided), that licensees may convey the
|
||||||
|
work under this License, and how to view a copy of this License. If
|
||||||
|
the interface presents a list of user commands or options, such as a
|
||||||
|
menu, a prominent item in the list meets this criterion.
|
||||||
|
|
||||||
|
1. Source Code.
|
||||||
|
|
||||||
|
The "source code" for a work means the preferred form of the work
|
||||||
|
for making modifications to it. "Object code" means any non-source
|
||||||
|
form of a work.
|
||||||
|
|
||||||
|
A "Standard Interface" means an interface that either is an official
|
||||||
|
standard defined by a recognized standards body, or, in the case of
|
||||||
|
interfaces specified for a particular programming language, one that
|
||||||
|
is widely used among developers working in that language.
|
||||||
|
|
||||||
|
The "System Libraries" of an executable work include anything, other
|
||||||
|
than the work as a whole, that (a) is included in the normal form of
|
||||||
|
packaging a Major Component, but which is not part of that Major
|
||||||
|
Component, and (b) serves only to enable use of the work with that
|
||||||
|
Major Component, or to implement a Standard Interface for which an
|
||||||
|
implementation is available to the public in source code form. A
|
||||||
|
"Major Component", in this context, means a major essential component
|
||||||
|
(kernel, window system, and so on) of the specific operating system
|
||||||
|
(if any) on which the executable work runs, or a compiler used to
|
||||||
|
produce the work, or an object code interpreter used to run it.
|
||||||
|
|
||||||
|
The "Corresponding Source" for a work in object code form means all
|
||||||
|
the source code needed to generate, install, and (for an executable
|
||||||
|
work) run the object code and to modify the work, including scripts to
|
||||||
|
control those activities. However, it does not include the work's
|
||||||
|
System Libraries, or general-purpose tools or generally available free
|
||||||
|
programs which are used unmodified in performing those activities but
|
||||||
|
which are not part of the work. For example, Corresponding Source
|
||||||
|
includes interface definition files associated with source files for
|
||||||
|
the work, and the source code for shared libraries and dynamically
|
||||||
|
linked subprograms that the work is specifically designed to require,
|
||||||
|
such as by intimate data communication or control flow between those
|
||||||
|
subprograms and other parts of the work.
|
||||||
|
|
||||||
|
The Corresponding Source need not include anything that users
|
||||||
|
can regenerate automatically from other parts of the Corresponding
|
||||||
|
Source.
|
||||||
|
|
||||||
|
The Corresponding Source for a work in source code form is that
|
||||||
|
same work.
|
||||||
|
|
||||||
|
2. Basic Permissions.
|
||||||
|
|
||||||
|
All rights granted under this License are granted for the term of
|
||||||
|
copyright on the Program, and are irrevocable provided the stated
|
||||||
|
conditions are met. This License explicitly affirms your unlimited
|
||||||
|
permission to run the unmodified Program. The output from running a
|
||||||
|
covered work is covered by this License only if the output, given its
|
||||||
|
content, constitutes a covered work. This License acknowledges your
|
||||||
|
rights of fair use or other equivalent, as provided by copyright law.
|
||||||
|
|
||||||
|
You may make, run and propagate covered works that you do not
|
||||||
|
convey, without conditions so long as your license otherwise remains
|
||||||
|
in force. You may convey covered works to others for the sole purpose
|
||||||
|
of having them make modifications exclusively for you, or provide you
|
||||||
|
with facilities for running those works, provided that you comply with
|
||||||
|
the terms of this License in conveying all material for which you do
|
||||||
|
not control copyright. Those thus making or running the covered works
|
||||||
|
for you must do so exclusively on your behalf, under your direction
|
||||||
|
and control, on terms that prohibit them from making any copies of
|
||||||
|
your copyrighted material outside their relationship with you.
|
||||||
|
|
||||||
|
Conveying under any other circumstances is permitted solely under
|
||||||
|
the conditions stated below. Sublicensing is not allowed; section 10
|
||||||
|
makes it unnecessary.
|
||||||
|
|
||||||
|
3. Protecting Users' Legal Rights From Anti-Circumvention Law.
|
||||||
|
|
||||||
|
No covered work shall be deemed part of an effective technological
|
||||||
|
measure under any applicable law fulfilling obligations under article
|
||||||
|
11 of the WIPO copyright treaty adopted on 20 December 1996, or
|
||||||
|
similar laws prohibiting or restricting circumvention of such
|
||||||
|
measures.
|
||||||
|
|
||||||
|
When you convey a covered work, you waive any legal power to forbid
|
||||||
|
circumvention of technological measures to the extent such circumvention
|
||||||
|
is effected by exercising rights under this License with respect to
|
||||||
|
the covered work, and you disclaim any intention to limit operation or
|
||||||
|
modification of the work as a means of enforcing, against the work's
|
||||||
|
users, your or third parties' legal rights to forbid circumvention of
|
||||||
|
technological measures.
|
||||||
|
|
||||||
|
4. Conveying Verbatim Copies.
|
||||||
|
|
||||||
|
You may convey verbatim copies of the Program's source code as you
|
||||||
|
receive it, in any medium, provided that you conspicuously and
|
||||||
|
appropriately publish on each copy an appropriate copyright notice;
|
||||||
|
keep intact all notices stating that this License and any
|
||||||
|
non-permissive terms added in accord with section 7 apply to the code;
|
||||||
|
keep intact all notices of the absence of any warranty; and give all
|
||||||
|
recipients a copy of this License along with the Program.
|
||||||
|
|
||||||
|
You may charge any price or no price for each copy that you convey,
|
||||||
|
and you may offer support or warranty protection for a fee.
|
||||||
|
|
||||||
|
5. Conveying Modified Source Versions.
|
||||||
|
|
||||||
|
You may convey a work based on the Program, or the modifications to
|
||||||
|
produce it from the Program, in the form of source code under the
|
||||||
|
terms of section 4, provided that you also meet all of these conditions:
|
||||||
|
|
||||||
|
a) The work must carry prominent notices stating that you modified
|
||||||
|
it, and giving a relevant date.
|
||||||
|
|
||||||
|
b) The work must carry prominent notices stating that it is
|
||||||
|
released under this License and any conditions added under section
|
||||||
|
7. This requirement modifies the requirement in section 4 to
|
||||||
|
"keep intact all notices".
|
||||||
|
|
||||||
|
c) You must license the entire work, as a whole, under this
|
||||||
|
License to anyone who comes into possession of a copy. This
|
||||||
|
License will therefore apply, along with any applicable section 7
|
||||||
|
additional terms, to the whole of the work, and all its parts,
|
||||||
|
regardless of how they are packaged. This License gives no
|
||||||
|
permission to license the work in any other way, but it does not
|
||||||
|
invalidate such permission if you have separately received it.
|
||||||
|
|
||||||
|
d) If the work has interactive user interfaces, each must display
|
||||||
|
Appropriate Legal Notices; however, if the Program has interactive
|
||||||
|
interfaces that do not display Appropriate Legal Notices, your
|
||||||
|
work need not make them do so.
|
||||||
|
|
||||||
|
A compilation of a covered work with other separate and independent
|
||||||
|
works, which are not by their nature extensions of the covered work,
|
||||||
|
and which are not combined with it such as to form a larger program,
|
||||||
|
in or on a volume of a storage or distribution medium, is called an
|
||||||
|
"aggregate" if the compilation and its resulting copyright are not
|
||||||
|
used to limit the access or legal rights of the compilation's users
|
||||||
|
beyond what the individual works permit. Inclusion of a covered work
|
||||||
|
in an aggregate does not cause this License to apply to the other
|
||||||
|
parts of the aggregate.
|
||||||
|
|
||||||
|
6. Conveying Non-Source Forms.
|
||||||
|
|
||||||
|
You may convey a covered work in object code form under the terms
|
||||||
|
of sections 4 and 5, provided that you also convey the
|
||||||
|
machine-readable Corresponding Source under the terms of this License,
|
||||||
|
in one of these ways:
|
||||||
|
|
||||||
|
a) Convey the object code in, or embodied in, a physical product
|
||||||
|
(including a physical distribution medium), accompanied by the
|
||||||
|
Corresponding Source fixed on a durable physical medium
|
||||||
|
customarily used for software interchange.
|
||||||
|
|
||||||
|
b) Convey the object code in, or embodied in, a physical product
|
||||||
|
(including a physical distribution medium), accompanied by a
|
||||||
|
written offer, valid for at least three years and valid for as
|
||||||
|
long as you offer spare parts or customer support for that product
|
||||||
|
model, to give anyone who possesses the object code either (1) a
|
||||||
|
copy of the Corresponding Source for all the software in the
|
||||||
|
product that is covered by this License, on a durable physical
|
||||||
|
medium customarily used for software interchange, for a price no
|
||||||
|
more than your reasonable cost of physically performing this
|
||||||
|
conveying of source, or (2) access to copy the
|
||||||
|
Corresponding Source from a network server at no charge.
|
||||||
|
|
||||||
|
c) Convey individual copies of the object code with a copy of the
|
||||||
|
written offer to provide the Corresponding Source. This
|
||||||
|
alternative is allowed only occasionally and noncommercially, and
|
||||||
|
only if you received the object code with such an offer, in accord
|
||||||
|
with subsection 6b.
|
||||||
|
|
||||||
|
d) Convey the object code by offering access from a designated
|
||||||
|
place (gratis or for a charge), and offer equivalent access to the
|
||||||
|
Corresponding Source in the same way through the same place at no
|
||||||
|
further charge. You need not require recipients to copy the
|
||||||
|
Corresponding Source along with the object code. If the place to
|
||||||
|
copy the object code is a network server, the Corresponding Source
|
||||||
|
may be on a different server (operated by you or a third party)
|
||||||
|
that supports equivalent copying facilities, provided you maintain
|
||||||
|
clear directions next to the object code saying where to find the
|
||||||
|
Corresponding Source. Regardless of what server hosts the
|
||||||
|
Corresponding Source, you remain obligated to ensure that it is
|
||||||
|
available for as long as needed to satisfy these requirements.
|
||||||
|
|
||||||
|
e) Convey the object code using peer-to-peer transmission, provided
|
||||||
|
you inform other peers where the object code and Corresponding
|
||||||
|
Source of the work are being offered to the general public at no
|
||||||
|
charge under subsection 6d.
|
||||||
|
|
||||||
|
A separable portion of the object code, whose source code is excluded
|
||||||
|
from the Corresponding Source as a System Library, need not be
|
||||||
|
included in conveying the object code work.
|
||||||
|
|
||||||
|
A "User Product" is either (1) a "consumer product", which means any
|
||||||
|
tangible personal property which is normally used for personal, family,
|
||||||
|
or household purposes, or (2) anything designed or sold for incorporation
|
||||||
|
into a dwelling. In determining whether a product is a consumer product,
|
||||||
|
doubtful cases shall be resolved in favor of coverage. For a particular
|
||||||
|
product received by a particular user, "normally used" refers to a
|
||||||
|
typical or common use of that class of product, regardless of the status
|
||||||
|
of the particular user or of the way in which the particular user
|
||||||
|
actually uses, or expects or is expected to use, the product. A product
|
||||||
|
is a consumer product regardless of whether the product has substantial
|
||||||
|
commercial, industrial or non-consumer uses, unless such uses represent
|
||||||
|
the only significant mode of use of the product.
|
||||||
|
|
||||||
|
"Installation Information" for a User Product means any methods,
|
||||||
|
procedures, authorization keys, or other information required to install
|
||||||
|
and execute modified versions of a covered work in that User Product from
|
||||||
|
a modified version of its Corresponding Source. The information must
|
||||||
|
suffice to ensure that the continued functioning of the modified object
|
||||||
|
code is in no case prevented or interfered with solely because
|
||||||
|
modification has been made.
|
||||||
|
|
||||||
|
If you convey an object code work under this section in, or with, or
|
||||||
|
specifically for use in, a User Product, and the conveying occurs as
|
||||||
|
part of a transaction in which the right of possession and use of the
|
||||||
|
User Product is transferred to the recipient in perpetuity or for a
|
||||||
|
fixed term (regardless of how the transaction is characterized), the
|
||||||
|
Corresponding Source conveyed under this section must be accompanied
|
||||||
|
by the Installation Information. But this requirement does not apply
|
||||||
|
if neither you nor any third party retains the ability to install
|
||||||
|
modified object code on the User Product (for example, the work has
|
||||||
|
been installed in ROM).
|
||||||
|
|
||||||
|
The requirement to provide Installation Information does not include a
|
||||||
|
requirement to continue to provide support service, warranty, or updates
|
||||||
|
for a work that has been modified or installed by the recipient, or for
|
||||||
|
the User Product in which it has been modified or installed. Access to a
|
||||||
|
network may be denied when the modification itself materially and
|
||||||
|
adversely affects the operation of the network or violates the rules and
|
||||||
|
protocols for communication across the network.
|
||||||
|
|
||||||
|
Corresponding Source conveyed, and Installation Information provided,
|
||||||
|
in accord with this section must be in a format that is publicly
|
||||||
|
documented (and with an implementation available to the public in
|
||||||
|
source code form), and must require no special password or key for
|
||||||
|
unpacking, reading or copying.
|
||||||
|
|
||||||
|
7. Additional Terms.
|
||||||
|
|
||||||
|
"Additional permissions" are terms that supplement the terms of this
|
||||||
|
License by making exceptions from one or more of its conditions.
|
||||||
|
Additional permissions that are applicable to the entire Program shall
|
||||||
|
be treated as though they were included in this License, to the extent
|
||||||
|
that they are valid under applicable law. If additional permissions
|
||||||
|
apply only to part of the Program, that part may be used separately
|
||||||
|
under those permissions, but the entire Program remains governed by
|
||||||
|
this License without regard to the additional permissions.
|
||||||
|
|
||||||
|
When you convey a copy of a covered work, you may at your option
|
||||||
|
remove any additional permissions from that copy, or from any part of
|
||||||
|
it. (Additional permissions may be written to require their own
|
||||||
|
removal in certain cases when you modify the work.) You may place
|
||||||
|
additional permissions on material, added by you to a covered work,
|
||||||
|
for which you have or can give appropriate copyright permission.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, for material you
|
||||||
|
add to a covered work, you may (if authorized by the copyright holders of
|
||||||
|
that material) supplement the terms of this License with terms:
|
||||||
|
|
||||||
|
a) Disclaiming warranty or limiting liability differently from the
|
||||||
|
terms of sections 15 and 16 of this License; or
|
||||||
|
|
||||||
|
b) Requiring preservation of specified reasonable legal notices or
|
||||||
|
author attributions in that material or in the Appropriate Legal
|
||||||
|
Notices displayed by works containing it; or
|
||||||
|
|
||||||
|
c) Prohibiting misrepresentation of the origin of that material, or
|
||||||
|
requiring that modified versions of such material be marked in
|
||||||
|
reasonable ways as different from the original version; or
|
||||||
|
|
||||||
|
d) Limiting the use for publicity purposes of names of licensors or
|
||||||
|
authors of the material; or
|
||||||
|
|
||||||
|
e) Declining to grant rights under trademark law for use of some
|
||||||
|
trade names, trademarks, or service marks; or
|
||||||
|
|
||||||
|
f) Requiring indemnification of licensors and authors of that
|
||||||
|
material by anyone who conveys the material (or modified versions of
|
||||||
|
it) with contractual assumptions of liability to the recipient, for
|
||||||
|
any liability that these contractual assumptions directly impose on
|
||||||
|
those licensors and authors.
|
||||||
|
|
||||||
|
All other non-permissive additional terms are considered "further
|
||||||
|
restrictions" within the meaning of section 10. If the Program as you
|
||||||
|
received it, or any part of it, contains a notice stating that it is
|
||||||
|
governed by this License along with a term that is a further
|
||||||
|
restriction, you may remove that term. If a license document contains
|
||||||
|
a further restriction but permits relicensing or conveying under this
|
||||||
|
License, you may add to a covered work material governed by the terms
|
||||||
|
of that license document, provided that the further restriction does
|
||||||
|
not survive such relicensing or conveying.
|
||||||
|
|
||||||
|
If you add terms to a covered work in accord with this section, you
|
||||||
|
must place, in the relevant source files, a statement of the
|
||||||
|
additional terms that apply to those files, or a notice indicating
|
||||||
|
where to find the applicable terms.
|
||||||
|
|
||||||
|
Additional terms, permissive or non-permissive, may be stated in the
|
||||||
|
form of a separately written license, or stated as exceptions;
|
||||||
|
the above requirements apply either way.
|
||||||
|
|
||||||
|
8. Termination.
|
||||||
|
|
||||||
|
You may not propagate or modify a covered work except as expressly
|
||||||
|
provided under this License. Any attempt otherwise to propagate or
|
||||||
|
modify it is void, and will automatically terminate your rights under
|
||||||
|
this License (including any patent licenses granted under the third
|
||||||
|
paragraph of section 11).
|
||||||
|
|
||||||
|
However, if you cease all violation of this License, then your
|
||||||
|
license from a particular copyright holder is reinstated (a)
|
||||||
|
provisionally, unless and until the copyright holder explicitly and
|
||||||
|
finally terminates your license, and (b) permanently, if the copyright
|
||||||
|
holder fails to notify you of the violation by some reasonable means
|
||||||
|
prior to 60 days after the cessation.
|
||||||
|
|
||||||
|
Moreover, your license from a particular copyright holder is
|
||||||
|
reinstated permanently if the copyright holder notifies you of the
|
||||||
|
violation by some reasonable means, this is the first time you have
|
||||||
|
received notice of violation of this License (for any work) from that
|
||||||
|
copyright holder, and you cure the violation prior to 30 days after
|
||||||
|
your receipt of the notice.
|
||||||
|
|
||||||
|
Termination of your rights under this section does not terminate the
|
||||||
|
licenses of parties who have received copies or rights from you under
|
||||||
|
this License. If your rights have been terminated and not permanently
|
||||||
|
reinstated, you do not qualify to receive new licenses for the same
|
||||||
|
material under section 10.
|
||||||
|
|
||||||
|
9. Acceptance Not Required for Having Copies.
|
||||||
|
|
||||||
|
You are not required to accept this License in order to receive or
|
||||||
|
run a copy of the Program. Ancillary propagation of a covered work
|
||||||
|
occurring solely as a consequence of using peer-to-peer transmission
|
||||||
|
to receive a copy likewise does not require acceptance. However,
|
||||||
|
nothing other than this License grants you permission to propagate or
|
||||||
|
modify any covered work. These actions infringe copyright if you do
|
||||||
|
not accept this License. Therefore, by modifying or propagating a
|
||||||
|
covered work, you indicate your acceptance of this License to do so.
|
||||||
|
|
||||||
|
10. Automatic Licensing of Downstream Recipients.
|
||||||
|
|
||||||
|
Each time you convey a covered work, the recipient automatically
|
||||||
|
receives a license from the original licensors, to run, modify and
|
||||||
|
propagate that work, subject to this License. You are not responsible
|
||||||
|
for enforcing compliance by third parties with this License.
|
||||||
|
|
||||||
|
An "entity transaction" is a transaction transferring control of an
|
||||||
|
organization, or substantially all assets of one, or subdividing an
|
||||||
|
organization, or merging organizations. If propagation of a covered
|
||||||
|
work results from an entity transaction, each party to that
|
||||||
|
transaction who receives a copy of the work also receives whatever
|
||||||
|
licenses to the work the party's predecessor in interest had or could
|
||||||
|
give under the previous paragraph, plus a right to possession of the
|
||||||
|
Corresponding Source of the work from the predecessor in interest, if
|
||||||
|
the predecessor has it or can get it with reasonable efforts.
|
||||||
|
|
||||||
|
You may not impose any further restrictions on the exercise of the
|
||||||
|
rights granted or affirmed under this License. For example, you may
|
||||||
|
not impose a license fee, royalty, or other charge for exercise of
|
||||||
|
rights granted under this License, and you may not initiate litigation
|
||||||
|
(including a cross-claim or counterclaim in a lawsuit) alleging that
|
||||||
|
any patent claim is infringed by making, using, selling, offering for
|
||||||
|
sale, or importing the Program or any portion of it.
|
||||||
|
|
||||||
|
11. Patents.
|
||||||
|
|
||||||
|
A "contributor" is a copyright holder who authorizes use under this
|
||||||
|
License of the Program or a work on which the Program is based. The
|
||||||
|
work thus licensed is called the contributor's "contributor version".
|
||||||
|
|
||||||
|
A contributor's "essential patent claims" are all patent claims
|
||||||
|
owned or controlled by the contributor, whether already acquired or
|
||||||
|
hereafter acquired, that would be infringed by some manner, permitted
|
||||||
|
by this License, of making, using, or selling its contributor version,
|
||||||
|
but do not include claims that would be infringed only as a
|
||||||
|
consequence of further modification of the contributor version. For
|
||||||
|
purposes of this definition, "control" includes the right to grant
|
||||||
|
patent sublicenses in a manner consistent with the requirements of
|
||||||
|
this License.
|
||||||
|
|
||||||
|
Each contributor grants you a non-exclusive, worldwide, royalty-free
|
||||||
|
patent license under the contributor's essential patent claims, to
|
||||||
|
make, use, sell, offer for sale, import and otherwise run, modify and
|
||||||
|
propagate the contents of its contributor version.
|
||||||
|
|
||||||
|
In the following three paragraphs, a "patent license" is any express
|
||||||
|
agreement or commitment, however denominated, not to enforce a patent
|
||||||
|
(such as an express permission to practice a patent or covenant not to
|
||||||
|
sue for patent infringement). To "grant" such a patent license to a
|
||||||
|
party means to make such an agreement or commitment not to enforce a
|
||||||
|
patent against the party.
|
||||||
|
|
||||||
|
If you convey a covered work, knowingly relying on a patent license,
|
||||||
|
and the Corresponding Source of the work is not available for anyone
|
||||||
|
to copy, free of charge and under the terms of this License, through a
|
||||||
|
publicly available network server or other readily accessible means,
|
||||||
|
then you must either (1) cause the Corresponding Source to be so
|
||||||
|
available, or (2) arrange to deprive yourself of the benefit of the
|
||||||
|
patent license for this particular work, or (3) arrange, in a manner
|
||||||
|
consistent with the requirements of this License, to extend the patent
|
||||||
|
license to downstream recipients. "Knowingly relying" means you have
|
||||||
|
actual knowledge that, but for the patent license, your conveying the
|
||||||
|
covered work in a country, or your recipient's use of the covered work
|
||||||
|
in a country, would infringe one or more identifiable patents in that
|
||||||
|
country that you have reason to believe are valid.
|
||||||
|
|
||||||
|
If, pursuant to or in connection with a single transaction or
|
||||||
|
arrangement, you convey, or propagate by procuring conveyance of, a
|
||||||
|
covered work, and grant a patent license to some of the parties
|
||||||
|
receiving the covered work authorizing them to use, propagate, modify
|
||||||
|
or convey a specific copy of the covered work, then the patent license
|
||||||
|
you grant is automatically extended to all recipients of the covered
|
||||||
|
work and works based on it.
|
||||||
|
|
||||||
|
A patent license is "discriminatory" if it does not include within
|
||||||
|
the scope of its coverage, prohibits the exercise of, or is
|
||||||
|
conditioned on the non-exercise of one or more of the rights that are
|
||||||
|
specifically granted under this License. You may not convey a covered
|
||||||
|
work if you are a party to an arrangement with a third party that is
|
||||||
|
in the business of distributing software, under which you make payment
|
||||||
|
to the third party based on the extent of your activity of conveying
|
||||||
|
the work, and under which the third party grants, to any of the
|
||||||
|
parties who would receive the covered work from you, a discriminatory
|
||||||
|
patent license (a) in connection with copies of the covered work
|
||||||
|
conveyed by you (or copies made from those copies), or (b) primarily
|
||||||
|
for and in connection with specific products or compilations that
|
||||||
|
contain the covered work, unless you entered into that arrangement,
|
||||||
|
or that patent license was granted, prior to 28 March 2007.
|
||||||
|
|
||||||
|
Nothing in this License shall be construed as excluding or limiting
|
||||||
|
any implied license or other defenses to infringement that may
|
||||||
|
otherwise be available to you under applicable patent law.
|
||||||
|
|
||||||
|
12. No Surrender of Others' Freedom.
|
||||||
|
|
||||||
|
If conditions are imposed on you (whether by court order, agreement or
|
||||||
|
otherwise) that contradict the conditions of this License, they do not
|
||||||
|
excuse you from the conditions of this License. If you cannot convey a
|
||||||
|
covered work so as to satisfy simultaneously your obligations under this
|
||||||
|
License and any other pertinent obligations, then as a consequence you may
|
||||||
|
not convey it at all. For example, if you agree to terms that obligate you
|
||||||
|
to collect a royalty for further conveying from those to whom you convey
|
||||||
|
the Program, the only way you could satisfy both those terms and this
|
||||||
|
License would be to refrain entirely from conveying the Program.
|
||||||
|
|
||||||
|
13. Remote Network Interaction; Use with the GNU General Public License.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, if you modify the
|
||||||
|
Program, your modified version must prominently offer all users
|
||||||
|
interacting with it remotely through a computer network (if your version
|
||||||
|
supports such interaction) an opportunity to receive the Corresponding
|
||||||
|
Source of your version by providing access to the Corresponding Source
|
||||||
|
from a network server at no charge, through some standard or customary
|
||||||
|
means of facilitating copying of software. This Corresponding Source
|
||||||
|
shall include the Corresponding Source for any work covered by version 3
|
||||||
|
of the GNU General Public License that is incorporated pursuant to the
|
||||||
|
following paragraph.
|
||||||
|
|
||||||
|
Notwithstanding any other provision of this License, you have
|
||||||
|
permission to link or combine any covered work with a work licensed
|
||||||
|
under version 3 of the GNU General Public License into a single
|
||||||
|
combined work, and to convey the resulting work. The terms of this
|
||||||
|
License will continue to apply to the part which is the covered work,
|
||||||
|
but the work with which it is combined will remain governed by version
|
||||||
|
3 of the GNU General Public License.
|
||||||
|
|
||||||
|
14. Revised Versions of this License.
|
||||||
|
|
||||||
|
The Free Software Foundation may publish revised and/or new versions of
|
||||||
|
the GNU Affero General Public License from time to time. Such new versions
|
||||||
|
will be similar in spirit to the present version, but may differ in detail to
|
||||||
|
address new problems or concerns.
|
||||||
|
|
||||||
|
Each version is given a distinguishing version number. If the
|
||||||
|
Program specifies that a certain numbered version of the GNU Affero General
|
||||||
|
Public License "or any later version" applies to it, you have the
|
||||||
|
option of following the terms and conditions either of that numbered
|
||||||
|
version or of any later version published by the Free Software
|
||||||
|
Foundation. If the Program does not specify a version number of the
|
||||||
|
GNU Affero General Public License, you may choose any version ever published
|
||||||
|
by the Free Software Foundation.
|
||||||
|
|
||||||
|
If the Program specifies that a proxy can decide which future
|
||||||
|
versions of the GNU Affero General Public License can be used, that proxy's
|
||||||
|
public statement of acceptance of a version permanently authorizes you
|
||||||
|
to choose that version for the Program.
|
||||||
|
|
||||||
|
Later license versions may give you additional or different
|
||||||
|
permissions. However, no additional obligations are imposed on any
|
||||||
|
author or copyright holder as a result of your choosing to follow a
|
||||||
|
later version.
|
||||||
|
|
||||||
|
15. Disclaimer of Warranty.
|
||||||
|
|
||||||
|
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
|
||||||
|
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
|
||||||
|
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
|
||||||
|
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
|
||||||
|
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
|
||||||
|
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
|
||||||
|
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
|
||||||
|
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
|
||||||
|
|
||||||
|
16. Limitation of Liability.
|
||||||
|
|
||||||
|
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
|
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
|
||||||
|
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
|
||||||
|
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
|
||||||
|
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
|
||||||
|
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
|
||||||
|
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
|
||||||
|
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
|
||||||
|
SUCH DAMAGES.
|
||||||
|
|
||||||
|
17. Interpretation of Sections 15 and 16.
|
||||||
|
|
||||||
|
If the disclaimer of warranty and limitation of liability provided
|
||||||
|
above cannot be given local legal effect according to their terms,
|
||||||
|
reviewing courts shall apply local law that most closely approximates
|
||||||
|
an absolute waiver of all civil liability in connection with the
|
||||||
|
Program, unless a warranty or assumption of liability accompanies a
|
||||||
|
copy of the Program in return for a fee.
|
||||||
|
|
||||||
|
END OF TERMS AND CONDITIONS
|
||||||
|
|
||||||
|
How to Apply These Terms to Your New Programs
|
||||||
|
|
||||||
|
If you develop a new program, and you want it to be of the greatest
|
||||||
|
possible use to the public, the best way to achieve this is to make it
|
||||||
|
free software which everyone can redistribute and change under these terms.
|
||||||
|
|
||||||
|
To do so, attach the following notices to the program. It is safest
|
||||||
|
to attach them to the start of each source file to most effectively
|
||||||
|
state the exclusion of warranty; and each file should have at least
|
||||||
|
the "copyright" line and a pointer to where the full notice is found.
|
||||||
|
|
||||||
|
<one line to give the program's name and a brief idea of what it does.>
|
||||||
|
Copyright (C) <year> <name of author>
|
||||||
|
|
||||||
|
This program is free software: you can redistribute it and/or modify
|
||||||
|
it under the terms of the GNU Affero General Public License as published
|
||||||
|
by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
(at your option) any later version.
|
||||||
|
|
||||||
|
This program 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
|
||||||
|
GNU Affero General Public License for more details.
|
||||||
|
|
||||||
|
You should have received a copy of the GNU Affero General Public License
|
||||||
|
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
|
||||||
|
Also add information on how to contact you by electronic and paper mail.
|
||||||
|
|
||||||
|
If your software can interact with users remotely through a computer
|
||||||
|
network, you should also make sure that it provides a way for users to
|
||||||
|
get its source. For example, if your program is a web application, its
|
||||||
|
interface could display a "Source" link that leads users to an archive
|
||||||
|
of the code. There are many ways you could offer source, and different
|
||||||
|
solutions will be better for different programs; see section 13 for the
|
||||||
|
specific requirements.
|
||||||
|
|
||||||
|
You should also get your employer (if you work as a programmer) or school,
|
||||||
|
if any, to sign a "copyright disclaimer" for the program, if necessary.
|
||||||
|
For more information on this, and how to apply and follow the GNU AGPL, see
|
||||||
|
<https://www.gnu.org/licenses/>.
|
||||||
3
README.md
Normal file
3
README.md
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
GRZ-Metadata-Procoessor
|
||||||
|
|
||||||
|
Anwendung zur Erfassung der Metadaten GRZ für das Modellvorhaben Genomsequenzierung gemäß §64e SGB V.
|
||||||
53
build.gradle.kts
Normal file
53
build.gradle.kts
Normal file
@ -0,0 +1,53 @@
|
|||||||
|
plugins {
|
||||||
|
kotlin("jvm") version "2.1.21"
|
||||||
|
kotlin("plugin.spring") version "2.1.21"
|
||||||
|
id("org.springframework.boot") version "3.5.0"
|
||||||
|
id("io.spring.dependency-management") version "1.1.7"
|
||||||
|
}
|
||||||
|
|
||||||
|
group = "dev.pcvolkmer.onco"
|
||||||
|
version = "0.1.0-SNAPSHOT"
|
||||||
|
|
||||||
|
java {
|
||||||
|
toolchain {
|
||||||
|
languageVersion = JavaLanguageVersion.of(21)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
configurations {
|
||||||
|
compileOnly {
|
||||||
|
extendsFrom(configurations.annotationProcessor.get())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
repositories {
|
||||||
|
mavenCentral()
|
||||||
|
}
|
||||||
|
|
||||||
|
dependencies {
|
||||||
|
implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
|
||||||
|
implementation("org.springframework.boot:spring-boot-starter-thymeleaf")
|
||||||
|
implementation("org.springframework.boot:spring-boot-starter-web")
|
||||||
|
implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
|
||||||
|
implementation("org.jetbrains.kotlin:kotlin-reflect")
|
||||||
|
implementation("org.flywaydb:flyway-database-postgresql")
|
||||||
|
implementation("org.flywaydb:flyway-mysql")
|
||||||
|
developmentOnly("org.springframework.boot:spring-boot-devtools")
|
||||||
|
developmentOnly("org.springframework.boot:spring-boot-docker-compose")
|
||||||
|
runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
|
||||||
|
runtimeOnly("org.postgresql:postgresql")
|
||||||
|
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
|
||||||
|
testImplementation("org.springframework.boot:spring-boot-starter-test")
|
||||||
|
testImplementation("org.jetbrains.kotlin:kotlin-test-junit5")
|
||||||
|
testRuntimeOnly("org.junit.platform:junit-platform-launcher")
|
||||||
|
}
|
||||||
|
|
||||||
|
kotlin {
|
||||||
|
compilerOptions {
|
||||||
|
freeCompilerArgs.addAll("-Xjsr305=strict")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
tasks.withType<Test> {
|
||||||
|
useJUnitPlatform()
|
||||||
|
}
|
||||||
18
compose-dev.yml
Normal file
18
compose-dev.yml
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
services:
|
||||||
|
mariadb:
|
||||||
|
image: 'mariadb:latest'
|
||||||
|
environment:
|
||||||
|
- 'MARIADB_DATABASE=grzmetadata'
|
||||||
|
- 'MARIADB_PASSWORD=devpass'
|
||||||
|
- 'MARIADB_ROOT_PASSWORD=devpass'
|
||||||
|
- 'MARIADB_USER=dev'
|
||||||
|
ports:
|
||||||
|
- '3306:3306'
|
||||||
|
# postgres:
|
||||||
|
# image: 'postgres:latest'
|
||||||
|
# environment:
|
||||||
|
# - 'POSTGRES_DB=grzmetadata'
|
||||||
|
# - 'POSTGRES_PASSWORD=devpass'
|
||||||
|
# - 'POSTGRES_USER=dev'
|
||||||
|
# ports:
|
||||||
|
# - '5432:5432'
|
||||||
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
Binary file not shown.
7
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
7
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
@ -0,0 +1,7 @@
|
|||||||
|
distributionBase=GRADLE_USER_HOME
|
||||||
|
distributionPath=wrapper/dists
|
||||||
|
distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
|
||||||
|
networkTimeout=10000
|
||||||
|
validateDistributionUrl=true
|
||||||
|
zipStoreBase=GRADLE_USER_HOME
|
||||||
|
zipStorePath=wrapper/dists
|
||||||
251
gradlew
vendored
Executable file
251
gradlew
vendored
Executable file
@ -0,0 +1,251 @@
|
|||||||
|
#!/bin/sh
|
||||||
|
|
||||||
|
#
|
||||||
|
# Copyright © 2015-2021 the original authors.
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# https://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
#
|
||||||
|
# SPDX-License-Identifier: Apache-2.0
|
||||||
|
#
|
||||||
|
|
||||||
|
##############################################################################
|
||||||
|
#
|
||||||
|
# Gradle start up script for POSIX generated by Gradle.
|
||||||
|
#
|
||||||
|
# Important for running:
|
||||||
|
#
|
||||||
|
# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
|
||||||
|
# noncompliant, but you have some other compliant shell such as ksh or
|
||||||
|
# bash, then to run this script, type that shell name before the whole
|
||||||
|
# command line, like:
|
||||||
|
#
|
||||||
|
# ksh Gradle
|
||||||
|
#
|
||||||
|
# Busybox and similar reduced shells will NOT work, because this script
|
||||||
|
# requires all of these POSIX shell features:
|
||||||
|
# * functions;
|
||||||
|
# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
|
||||||
|
# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
|
||||||
|
# * compound commands having a testable exit status, especially «case»;
|
||||||
|
# * various built-in commands including «command», «set», and «ulimit».
|
||||||
|
#
|
||||||
|
# Important for patching:
|
||||||
|
#
|
||||||
|
# (2) This script targets any POSIX shell, so it avoids extensions provided
|
||||||
|
# by Bash, Ksh, etc; in particular arrays are avoided.
|
||||||
|
#
|
||||||
|
# The "traditional" practice of packing multiple parameters into a
|
||||||
|
# space-separated string is a well documented source of bugs and security
|
||||||
|
# problems, so this is (mostly) avoided, by progressively accumulating
|
||||||
|
# options in "$@", and eventually passing that to Java.
|
||||||
|
#
|
||||||
|
# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
|
||||||
|
# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
|
||||||
|
# see the in-line comments for details.
|
||||||
|
#
|
||||||
|
# There are tweaks for specific operating systems such as AIX, CygWin,
|
||||||
|
# Darwin, MinGW, and NonStop.
|
||||||
|
#
|
||||||
|
# (3) This script is generated from the Groovy template
|
||||||
|
# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
|
||||||
|
# within the Gradle project.
|
||||||
|
#
|
||||||
|
# You can find Gradle at https://github.com/gradle/gradle/.
|
||||||
|
#
|
||||||
|
##############################################################################
|
||||||
|
|
||||||
|
# Attempt to set APP_HOME
|
||||||
|
|
||||||
|
# Resolve links: $0 may be a link
|
||||||
|
app_path=$0
|
||||||
|
|
||||||
|
# Need this for daisy-chained symlinks.
|
||||||
|
while
|
||||||
|
APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
|
||||||
|
[ -h "$app_path" ]
|
||||||
|
do
|
||||||
|
ls=$( ls -ld "$app_path" )
|
||||||
|
link=${ls#*' -> '}
|
||||||
|
case $link in #(
|
||||||
|
/*) app_path=$link ;; #(
|
||||||
|
*) app_path=$APP_HOME$link ;;
|
||||||
|
esac
|
||||||
|
done
|
||||||
|
|
||||||
|
# This is normally unused
|
||||||
|
# shellcheck disable=SC2034
|
||||||
|
APP_BASE_NAME=${0##*/}
|
||||||
|
# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
|
||||||
|
APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit
|
||||||
|
|
||||||
|
# Use the maximum available, or set MAX_FD != -1 to use that value.
|
||||||
|
MAX_FD=maximum
|
||||||
|
|
||||||
|
warn () {
|
||||||
|
echo "$*"
|
||||||
|
} >&2
|
||||||
|
|
||||||
|
die () {
|
||||||
|
echo
|
||||||
|
echo "$*"
|
||||||
|
echo
|
||||||
|
exit 1
|
||||||
|
} >&2
|
||||||
|
|
||||||
|
# OS specific support (must be 'true' or 'false').
|
||||||
|
cygwin=false
|
||||||
|
msys=false
|
||||||
|
darwin=false
|
||||||
|
nonstop=false
|
||||||
|
case "$( uname )" in #(
|
||||||
|
CYGWIN* ) cygwin=true ;; #(
|
||||||
|
Darwin* ) darwin=true ;; #(
|
||||||
|
MSYS* | MINGW* ) msys=true ;; #(
|
||||||
|
NONSTOP* ) nonstop=true ;;
|
||||||
|
esac
|
||||||
|
|
||||||
|
CLASSPATH="\\\"\\\""
|
||||||
|
|
||||||
|
|
||||||
|
# Determine the Java command to use to start the JVM.
|
||||||
|
if [ -n "$JAVA_HOME" ] ; then
|
||||||
|
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
|
||||||
|
# IBM's JDK on AIX uses strange locations for the executables
|
||||||
|
JAVACMD=$JAVA_HOME/jre/sh/java
|
||||||
|
else
|
||||||
|
JAVACMD=$JAVA_HOME/bin/java
|
||||||
|
fi
|
||||||
|
if [ ! -x "$JAVACMD" ] ; then
|
||||||
|
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
JAVACMD=java
|
||||||
|
if ! command -v java >/dev/null 2>&1
|
||||||
|
then
|
||||||
|
die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Increase the maximum file descriptors if we can.
|
||||||
|
if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
|
||||||
|
case $MAX_FD in #(
|
||||||
|
max*)
|
||||||
|
# In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
|
||||||
|
# shellcheck disable=SC2039,SC3045
|
||||||
|
MAX_FD=$( ulimit -H -n ) ||
|
||||||
|
warn "Could not query maximum file descriptor limit"
|
||||||
|
esac
|
||||||
|
case $MAX_FD in #(
|
||||||
|
'' | soft) :;; #(
|
||||||
|
*)
|
||||||
|
# In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
|
||||||
|
# shellcheck disable=SC2039,SC3045
|
||||||
|
ulimit -n "$MAX_FD" ||
|
||||||
|
warn "Could not set maximum file descriptor limit to $MAX_FD"
|
||||||
|
esac
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Collect all arguments for the java command, stacking in reverse order:
|
||||||
|
# * args from the command line
|
||||||
|
# * the main class name
|
||||||
|
# * -classpath
|
||||||
|
# * -D...appname settings
|
||||||
|
# * --module-path (only if needed)
|
||||||
|
# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
|
||||||
|
|
||||||
|
# For Cygwin or MSYS, switch paths to Windows format before running java
|
||||||
|
if "$cygwin" || "$msys" ; then
|
||||||
|
APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
|
||||||
|
CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
|
||||||
|
|
||||||
|
JAVACMD=$( cygpath --unix "$JAVACMD" )
|
||||||
|
|
||||||
|
# Now convert the arguments - kludge to limit ourselves to /bin/sh
|
||||||
|
for arg do
|
||||||
|
if
|
||||||
|
case $arg in #(
|
||||||
|
-*) false ;; # don't mess with options #(
|
||||||
|
/?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
|
||||||
|
[ -e "$t" ] ;; #(
|
||||||
|
*) false ;;
|
||||||
|
esac
|
||||||
|
then
|
||||||
|
arg=$( cygpath --path --ignore --mixed "$arg" )
|
||||||
|
fi
|
||||||
|
# Roll the args list around exactly as many times as the number of
|
||||||
|
# args, so each arg winds up back in the position where it started, but
|
||||||
|
# possibly modified.
|
||||||
|
#
|
||||||
|
# NB: a `for` loop captures its iteration list before it begins, so
|
||||||
|
# changing the positional parameters here affects neither the number of
|
||||||
|
# iterations, nor the values presented in `arg`.
|
||||||
|
shift # remove old arg
|
||||||
|
set -- "$@" "$arg" # push replacement arg
|
||||||
|
done
|
||||||
|
fi
|
||||||
|
|
||||||
|
|
||||||
|
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
|
||||||
|
|
||||||
|
# Collect all arguments for the java command:
|
||||||
|
# * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
|
||||||
|
# and any embedded shellness will be escaped.
|
||||||
|
# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
|
||||||
|
# treated as '${Hostname}' itself on the command line.
|
||||||
|
|
||||||
|
set -- \
|
||||||
|
"-Dorg.gradle.appname=$APP_BASE_NAME" \
|
||||||
|
-classpath "$CLASSPATH" \
|
||||||
|
-jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
|
||||||
|
"$@"
|
||||||
|
|
||||||
|
# Stop when "xargs" is not available.
|
||||||
|
if ! command -v xargs >/dev/null 2>&1
|
||||||
|
then
|
||||||
|
die "xargs is not available"
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Use "xargs" to parse quoted args.
|
||||||
|
#
|
||||||
|
# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
|
||||||
|
#
|
||||||
|
# In Bash we could simply go:
|
||||||
|
#
|
||||||
|
# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
|
||||||
|
# set -- "${ARGS[@]}" "$@"
|
||||||
|
#
|
||||||
|
# but POSIX shell has neither arrays nor command substitution, so instead we
|
||||||
|
# post-process each arg (as a line of input to sed) to backslash-escape any
|
||||||
|
# character that might be a shell metacharacter, then use eval to reverse
|
||||||
|
# that process (while maintaining the separation between arguments), and wrap
|
||||||
|
# the whole thing up as a single "set" statement.
|
||||||
|
#
|
||||||
|
# This will of course break if any of these variables contains a newline or
|
||||||
|
# an unmatched quote.
|
||||||
|
#
|
||||||
|
|
||||||
|
eval "set -- $(
|
||||||
|
printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
|
||||||
|
xargs -n1 |
|
||||||
|
sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
|
||||||
|
tr '\n' ' '
|
||||||
|
)" '"$@"'
|
||||||
|
|
||||||
|
exec "$JAVACMD" "$@"
|
||||||
94
gradlew.bat
vendored
Normal file
94
gradlew.bat
vendored
Normal file
@ -0,0 +1,94 @@
|
|||||||
|
@rem
|
||||||
|
@rem Copyright 2015 the original author or authors.
|
||||||
|
@rem
|
||||||
|
@rem Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
@rem you may not use this file except in compliance with the License.
|
||||||
|
@rem You may obtain a copy of the License at
|
||||||
|
@rem
|
||||||
|
@rem https://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
@rem
|
||||||
|
@rem Unless required by applicable law or agreed to in writing, software
|
||||||
|
@rem distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
@rem See the License for the specific language governing permissions and
|
||||||
|
@rem limitations under the License.
|
||||||
|
@rem
|
||||||
|
@rem SPDX-License-Identifier: Apache-2.0
|
||||||
|
@rem
|
||||||
|
|
||||||
|
@if "%DEBUG%"=="" @echo off
|
||||||
|
@rem ##########################################################################
|
||||||
|
@rem
|
||||||
|
@rem Gradle startup script for Windows
|
||||||
|
@rem
|
||||||
|
@rem ##########################################################################
|
||||||
|
|
||||||
|
@rem Set local scope for the variables with windows NT shell
|
||||||
|
if "%OS%"=="Windows_NT" setlocal
|
||||||
|
|
||||||
|
set DIRNAME=%~dp0
|
||||||
|
if "%DIRNAME%"=="" set DIRNAME=.
|
||||||
|
@rem This is normally unused
|
||||||
|
set APP_BASE_NAME=%~n0
|
||||||
|
set APP_HOME=%DIRNAME%
|
||||||
|
|
||||||
|
@rem Resolve any "." and ".." in APP_HOME to make it shorter.
|
||||||
|
for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
|
||||||
|
|
||||||
|
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
|
||||||
|
|
||||||
|
@rem Find java.exe
|
||||||
|
if defined JAVA_HOME goto findJavaFromJavaHome
|
||||||
|
|
||||||
|
set JAVA_EXE=java.exe
|
||||||
|
%JAVA_EXE% -version >NUL 2>&1
|
||||||
|
if %ERRORLEVEL% equ 0 goto execute
|
||||||
|
|
||||||
|
echo. 1>&2
|
||||||
|
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
|
||||||
|
echo. 1>&2
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
|
||||||
|
echo location of your Java installation. 1>&2
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:findJavaFromJavaHome
|
||||||
|
set JAVA_HOME=%JAVA_HOME:"=%
|
||||||
|
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
|
||||||
|
|
||||||
|
if exist "%JAVA_EXE%" goto execute
|
||||||
|
|
||||||
|
echo. 1>&2
|
||||||
|
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
|
||||||
|
echo. 1>&2
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
|
||||||
|
echo location of your Java installation. 1>&2
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:execute
|
||||||
|
@rem Setup the command line
|
||||||
|
|
||||||
|
set CLASSPATH=
|
||||||
|
|
||||||
|
|
||||||
|
@rem Execute Gradle
|
||||||
|
"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %*
|
||||||
|
|
||||||
|
:end
|
||||||
|
@rem End local scope for the variables with windows NT shell
|
||||||
|
if %ERRORLEVEL% equ 0 goto mainEnd
|
||||||
|
|
||||||
|
:fail
|
||||||
|
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
|
||||||
|
rem the _cmd.exe /c_ return code!
|
||||||
|
set EXIT_CODE=%ERRORLEVEL%
|
||||||
|
if %EXIT_CODE% equ 0 set EXIT_CODE=1
|
||||||
|
if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
|
||||||
|
exit /b %EXIT_CODE%
|
||||||
|
|
||||||
|
:mainEnd
|
||||||
|
if "%OS%"=="Windows_NT" endlocal
|
||||||
|
|
||||||
|
:omega
|
||||||
23
package.json
Normal file
23
package.json
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
{
|
||||||
|
"name": "grz-metadata-processor",
|
||||||
|
"version": "0.1.0",
|
||||||
|
"description": "",
|
||||||
|
"dependencies": {
|
||||||
|
"htmx.org": "~2.0.4",
|
||||||
|
"tailwindcss": "~4.1.8"
|
||||||
|
},
|
||||||
|
"devDependencies": {
|
||||||
|
"@rspack/core": "~1.3.15",
|
||||||
|
"@rspack/cli": "~1.3.15",
|
||||||
|
"@tailwindcss/postcss": "~4.1.8",
|
||||||
|
"@tailwindcss/cli": "~4.1.8",
|
||||||
|
"autoprefixer": "~10.4.21",
|
||||||
|
"postcss": "~8.5.4",
|
||||||
|
"postcss-loader": "~8.1.1"
|
||||||
|
},
|
||||||
|
"scripts": {
|
||||||
|
"dev": "rspack build --watch --config ./src/main/web/rspack.config.js",
|
||||||
|
"build": "rspack build --config ./src/main/web/rspack.config.js"
|
||||||
|
},
|
||||||
|
"private": true
|
||||||
|
}
|
||||||
1
settings.gradle.kts
Normal file
1
settings.gradle.kts
Normal file
@ -0,0 +1 @@
|
|||||||
|
rootProject.name = "grz-metadata-processor"
|
||||||
@ -0,0 +1,11 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor
|
||||||
|
|
||||||
|
import org.springframework.boot.autoconfigure.SpringBootApplication
|
||||||
|
import org.springframework.boot.runApplication
|
||||||
|
|
||||||
|
@SpringBootApplication
|
||||||
|
class GrzMetadataProcessorApplication
|
||||||
|
|
||||||
|
fun main(args: Array<String>) {
|
||||||
|
runApplication<GrzMetadataProcessorApplication>(*args)
|
||||||
|
}
|
||||||
@ -0,0 +1,52 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.data
|
||||||
|
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
|
||||||
|
@Table("tbl_case")
|
||||||
|
data class Case(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
var localCaseId: String = "",
|
||||||
|
var coverageType: CoverageType = CoverageType.UNK,
|
||||||
|
var submitterId: String = "",
|
||||||
|
var genomicDataCenterId: String = "",
|
||||||
|
var clinicalDataCenterId: String = "",
|
||||||
|
var diseaseType: DiseaseType? = null,
|
||||||
|
var genomicStudyType: GenomicStudyType? = null,
|
||||||
|
var genomicStudySubtype: GenomicStudySubtype? = null,
|
||||||
|
var labName: String = "",
|
||||||
|
)
|
||||||
|
|
||||||
|
enum class CoverageType {
|
||||||
|
GKV,
|
||||||
|
PKV,
|
||||||
|
BG,
|
||||||
|
SEL,
|
||||||
|
SOZ,
|
||||||
|
GPV,
|
||||||
|
PPV,
|
||||||
|
BEI,
|
||||||
|
SKT,
|
||||||
|
UNK
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class DiseaseType(value: String) {
|
||||||
|
ONCOLOGICAL("oncological"),
|
||||||
|
RARE("rare"),
|
||||||
|
HEREDITARY("hereditary"),
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class GenomicStudyType(value: String) {
|
||||||
|
SINGLE("single"),
|
||||||
|
DUO("duo"),
|
||||||
|
TRIO("trio"),
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class GenomicStudySubtype(value: String) {
|
||||||
|
TUMOR_ONLY("tumor-only"),
|
||||||
|
TUMOR_GERMLINE("tumor+germline"),
|
||||||
|
GERMLINE_ONLY("germline-only"),
|
||||||
|
}
|
||||||
|
|
||||||
|
interface CaseRepository : CrudRepository<Case, Long>
|
||||||
@ -0,0 +1,35 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.data
|
||||||
|
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
|
||||||
|
@Table("tbl_donor")
|
||||||
|
data class Donor(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
val caseId: Long?,
|
||||||
|
val donorPseudonym: String = "",
|
||||||
|
val gender: Gender? = null,
|
||||||
|
val relation: Relation? = null,
|
||||||
|
)
|
||||||
|
|
||||||
|
enum class Gender(val value: String) {
|
||||||
|
MALE("male"),
|
||||||
|
FEMALE("female"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class Relation(val value: String) {
|
||||||
|
MOTHER("mother"),
|
||||||
|
FATHER("father"),
|
||||||
|
BROTHER("brother"),
|
||||||
|
SISTER("sister"),
|
||||||
|
CHILD("child"),
|
||||||
|
INDEX("index"),
|
||||||
|
OTHER("other")
|
||||||
|
}
|
||||||
|
|
||||||
|
interface DonorRepository : CrudRepository<Donor, Long> {
|
||||||
|
fun findByCaseId(caseId: Long): MutableList<Donor>
|
||||||
|
}
|
||||||
@ -0,0 +1,63 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.data
|
||||||
|
|
||||||
|
import org.apache.tomcat.util.buf.HexUtils
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
import java.nio.file.Path
|
||||||
|
import java.security.DigestInputStream
|
||||||
|
import java.security.MessageDigest
|
||||||
|
import java.util.*
|
||||||
|
import kotlin.io.path.fileSize
|
||||||
|
import kotlin.io.path.inputStream
|
||||||
|
|
||||||
|
@Table("tbl_file")
|
||||||
|
data class File(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
val labDataId: Long?,
|
||||||
|
val filePath: String? = null,
|
||||||
|
val fileType: FileType? = null,
|
||||||
|
var fileChecksum: String? = null,
|
||||||
|
var fileSizeInBytes: Long? = null,
|
||||||
|
) {
|
||||||
|
init {
|
||||||
|
if (fileChecksum.isNullOrBlank()) {
|
||||||
|
fileChecksum = calcFileChecksum()
|
||||||
|
}
|
||||||
|
|
||||||
|
if (fileSizeInBytes?.or(0)!! < 1) {
|
||||||
|
fileSizeInBytes = calcFileSize()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
fun calcFileChecksum(): String {
|
||||||
|
if (filePath == null) {
|
||||||
|
return ""
|
||||||
|
}
|
||||||
|
val path = Path.of(filePath)
|
||||||
|
val messageDigest = MessageDigest.getInstance("SHA-256")
|
||||||
|
|
||||||
|
val digestInputStream = DigestInputStream(path.inputStream(), messageDigest)
|
||||||
|
digestInputStream.readAllBytes()
|
||||||
|
return HexUtils.toHexString(messageDigest.digest())
|
||||||
|
}
|
||||||
|
|
||||||
|
fun calcFileSize(): Long {
|
||||||
|
if (filePath == null) {
|
||||||
|
return 0
|
||||||
|
}
|
||||||
|
return Path.of(filePath).fileSize()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class FileType(val value: String) {
|
||||||
|
BAM("bam"),
|
||||||
|
VCF("vcf"),
|
||||||
|
BED("bed"),
|
||||||
|
FASTQ("fastq")
|
||||||
|
}
|
||||||
|
|
||||||
|
interface FileRepository : CrudRepository<File, Long> {
|
||||||
|
fun findByLabDataId(labDataId: Long): MutableList<File>
|
||||||
|
fun findByLabDataIdIsNull(): List<File>
|
||||||
|
}
|
||||||
@ -0,0 +1,109 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.data
|
||||||
|
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
|
||||||
|
@Table("tbl_lab_data")
|
||||||
|
data class LabData(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
val donorId: Long?,
|
||||||
|
val einsendenummer: String = "",
|
||||||
|
val labDataName: String = "",
|
||||||
|
val sampleDate: String = "",
|
||||||
|
val sampleConservation: SampleConservation? = null,
|
||||||
|
val sequenceType: SequenceType? = null,
|
||||||
|
val sequenceSubtype: SequenceSubtype? = null,
|
||||||
|
val fragmentationMethod: FragmentationMethod? = null,
|
||||||
|
val libraryType: LibraryType? = null,
|
||||||
|
val libraryPrepKit: String = "",
|
||||||
|
val libraryPrepKitManufacturer: String = "",
|
||||||
|
val sequencerModel: String = "",
|
||||||
|
val sequencerManufacturer: String = "",
|
||||||
|
val kitName: String = "",
|
||||||
|
val kitManufacturer: String = "",
|
||||||
|
val enrichmentKit: String = "",
|
||||||
|
val enrichmentKitManufacturer: EnrichmentKitManufacturer? = null,
|
||||||
|
val sequencingLayout: SequencingLayout? = null,
|
||||||
|
val tumorCellCount: Int = 0,
|
||||||
|
val tumorCellCountMethod: TumorCellCountMethod? = null,
|
||||||
|
val bioinformaticsPipelineName: String = "",
|
||||||
|
val bioinformaticsPipelineVersion: String = "",
|
||||||
|
val referenceGenome: ReferenceGenome? = null,
|
||||||
|
)
|
||||||
|
|
||||||
|
enum class SampleConservation(val value: String) {
|
||||||
|
FRESH_TISSUE("fresh-tissue"),
|
||||||
|
CRYO_FROZEN("cryo-frozen"),
|
||||||
|
FFPE("ffpe"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class SequenceType(val value: String) {
|
||||||
|
DNA("dna"),
|
||||||
|
RNA("rna")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class SequenceSubtype(val value: String) {
|
||||||
|
GERMLINE("germline"),
|
||||||
|
SOMATIC("somatic"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class FragmentationMethod(val value: String) {
|
||||||
|
SONICATION("sonication"),
|
||||||
|
ENZYMATIC("enzymatic"),
|
||||||
|
NONE("none"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class LibraryType(val value: String) {
|
||||||
|
PANEL("panel"),
|
||||||
|
PANEL_LR("panel_lr"),
|
||||||
|
WES("wes"),
|
||||||
|
WES_LR("wes_lr"),
|
||||||
|
WGS("wgs"),
|
||||||
|
WGS_LR("wgs_lr"),
|
||||||
|
WXS("wxs"),
|
||||||
|
WXS_LR("wxs_lr"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class EnrichmentKitManufacturer(val value: String) {
|
||||||
|
ILLUMINA("Illumina"),
|
||||||
|
AGILENT("Agilent"),
|
||||||
|
TWIST("Twist"),
|
||||||
|
NEB("NEB"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown"),
|
||||||
|
NONE("none")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class SequencingLayout(val value: String) {
|
||||||
|
SINGLE_END("single-end"),
|
||||||
|
PAIRED_END("paired-end"),
|
||||||
|
REVERSE("reverse"),
|
||||||
|
OTHER("other"),
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class TumorCellCountMethod(val value: String) {
|
||||||
|
PATHOLOGY("pathology"),
|
||||||
|
BIOINFORMATICS("bioinformatics"),
|
||||||
|
OTHER("other"),
|
||||||
|
UNKNOWN("unknown")
|
||||||
|
}
|
||||||
|
|
||||||
|
enum class ReferenceGenome(val value: String) {
|
||||||
|
GRCH37("GRCh37"),
|
||||||
|
GRCH38("GRCh38"),
|
||||||
|
}
|
||||||
|
|
||||||
|
interface LabDataRepository : CrudRepository<LabData, Long> {
|
||||||
|
fun findByDonorId(donorId: Long): MutableList<LabData>
|
||||||
|
fun countLabDataByDonorIdIsNull(): Long
|
||||||
|
fun findByEinsendenummer(einsendenummer: String): LabData
|
||||||
|
}
|
||||||
@ -0,0 +1,3 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.exceptions
|
||||||
|
|
||||||
|
class NotFoundException: RuntimeException()
|
||||||
@ -0,0 +1,65 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.Case
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.CaseRepository
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.exceptions.NotFoundException
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import org.springframework.http.ResponseEntity
|
||||||
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
|
import org.springframework.web.bind.annotation.*
|
||||||
|
|
||||||
|
@Controller
|
||||||
|
@RequestMapping(path = ["/cases"])
|
||||||
|
class CaseController(
|
||||||
|
private val repository: CaseRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@GetMapping
|
||||||
|
fun getAllCase(model: Model): String {
|
||||||
|
model.addAttribute("cases", repository.findAll())
|
||||||
|
return "cases"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(path = ["{caseId}"])
|
||||||
|
fun getCase(@PathVariable caseId: Long, model: Model): String {
|
||||||
|
repository.findById(caseId).ifPresentOrElse({
|
||||||
|
model.addAttribute("case", it)
|
||||||
|
}, {
|
||||||
|
throw NotFoundException()
|
||||||
|
})
|
||||||
|
return "case"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PostMapping
|
||||||
|
fun postCase(model: Model): ResponseEntity<Unit> {
|
||||||
|
val createdCase = repository.save(Case())
|
||||||
|
model.addAttribute("cases", repository.findAll())
|
||||||
|
return ResponseEntity
|
||||||
|
.noContent()
|
||||||
|
.headers { headers ->
|
||||||
|
headers.add("HX-Redirect", "/cases/${createdCase.id}")
|
||||||
|
}
|
||||||
|
.build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["{caseId}"], consumes = [MediaType.APPLICATION_FORM_URLENCODED_VALUE])
|
||||||
|
fun putCase(@PathVariable caseId: Long, case: Case, model: Model): String {
|
||||||
|
val savedCase = repository.save(case)
|
||||||
|
model.addAttribute("case", savedCase)
|
||||||
|
return "case"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["{caseId}"])
|
||||||
|
fun deleteCase(@PathVariable caseId: Long, model: Model): ResponseEntity<Unit> {
|
||||||
|
repository.deleteById(caseId)
|
||||||
|
model.addAttribute("cases", repository.findAll())
|
||||||
|
return ResponseEntity
|
||||||
|
.noContent()
|
||||||
|
.headers { headers ->
|
||||||
|
headers.add("HX-Redirect", "/")
|
||||||
|
}
|
||||||
|
.build()
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
@ -0,0 +1,15 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.exceptions.NotFoundException
|
||||||
|
import org.springframework.web.bind.annotation.ControllerAdvice
|
||||||
|
import org.springframework.web.bind.annotation.ExceptionHandler
|
||||||
|
|
||||||
|
@ControllerAdvice
|
||||||
|
class ControllerAdvices {
|
||||||
|
|
||||||
|
@ExceptionHandler(NotFoundException::class)
|
||||||
|
fun handleNotFoundException(e: NotFoundException): String {
|
||||||
|
return "error/notfound"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
@ -0,0 +1,45 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.Donor
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.DonorRepository
|
||||||
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
|
import org.springframework.web.bind.annotation.*
|
||||||
|
|
||||||
|
@Controller
|
||||||
|
@RequestMapping("/cases/{caseId}/donors")
|
||||||
|
class DonorController(
|
||||||
|
private val repository: DonorRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@GetMapping
|
||||||
|
fun getAllDonors(@PathVariable caseId: Long, model: Model): String {
|
||||||
|
model.addAttribute("caseId", caseId)
|
||||||
|
model.addAttribute("donors", repository.findByCaseId(caseId))
|
||||||
|
return "donors"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PostMapping
|
||||||
|
fun postDonor(@PathVariable caseId: Long, model: Model): String {
|
||||||
|
repository.save(Donor(caseId = caseId))
|
||||||
|
model.addAttribute("caseId", caseId)
|
||||||
|
model.addAttribute("donors", repository.findByCaseId(caseId))
|
||||||
|
return "donors"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["{donorId}"])
|
||||||
|
fun postDonor(@PathVariable caseId: Long, @PathVariable donorId: Long, donor: Donor, model: Model): String {
|
||||||
|
repository.save(donor)
|
||||||
|
model.addAttribute("caseId", caseId)
|
||||||
|
model.addAttribute("donors", repository.findByCaseId(caseId))
|
||||||
|
return "donors"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["{donorId}"])
|
||||||
|
fun deleteDonor(@PathVariable caseId: Long, @PathVariable donorId: Long, model: Model): String {
|
||||||
|
repository.deleteById(donorId)
|
||||||
|
model.addAttribute("donors", repository.findByCaseId(caseId))
|
||||||
|
return "donors"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
@ -0,0 +1,69 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.File
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.FileRepository
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataRepository
|
||||||
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
|
import org.springframework.web.bind.annotation.*
|
||||||
|
|
||||||
|
@Controller
|
||||||
|
@RequestMapping
|
||||||
|
class FileController(
|
||||||
|
private val fileRepository: FileRepository,
|
||||||
|
private val labDataRepository: LabDataRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@GetMapping(path = ["/labdatas/{labDataId}/files"])
|
||||||
|
fun getAllFiles(@PathVariable labDataId: Long, model: Model): String {
|
||||||
|
model.addAttribute("labDataId", labDataId)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataId(labDataId))
|
||||||
|
return "files"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(path = ["/files/unused"])
|
||||||
|
fun getAllUnusedFiles(model: Model): String {
|
||||||
|
model.addAttribute("labDatas", labDataRepository.findAll().filterNot { it.einsendenummer.isBlank() })
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataIdIsNull())
|
||||||
|
return "unusedfiles"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PostMapping(path = ["/labdatas/{labDataId}/files"])
|
||||||
|
fun postFile(@PathVariable labDataId: Long, model: Model): String {
|
||||||
|
fileRepository.save(File(labDataId = labDataId))
|
||||||
|
model.addAttribute("labDataId", labDataId)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataId(labDataId))
|
||||||
|
return "files"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["/labdatas/{labDataId}/files/{fileId}"])
|
||||||
|
fun putFile(@PathVariable labDataId: Long, @PathVariable fileId: Long, file: File, model: Model): String {
|
||||||
|
fileRepository.save(file)
|
||||||
|
model.addAttribute("labDataId", labDataId)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataId(labDataId))
|
||||||
|
return "files"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["/files/unused/{fileId}"])
|
||||||
|
fun putUnusedFile(@PathVariable fileId: Long, file: File, model: Model): String {
|
||||||
|
fileRepository.save(file)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataIdIsNull())
|
||||||
|
return "unusedfiles"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["/labdatas/{labDataId}/files/{fileId}"])
|
||||||
|
fun deleteFile(@PathVariable fileId: Long, @PathVariable labDataId: Long, model: Model): String {
|
||||||
|
fileRepository.deleteById(fileId)
|
||||||
|
model.addAttribute("fileId", fileId)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataId(labDataId))
|
||||||
|
return "files"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["/files/unused/{fileId}"])
|
||||||
|
fun deleteUnusedFile(@PathVariable fileId: Long, model: Model): String {
|
||||||
|
fileRepository.deleteById(fileId)
|
||||||
|
model.addAttribute("files", fileRepository.findByLabDataIdIsNull())
|
||||||
|
return "unusedfiles"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
@ -0,0 +1,42 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabData
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataRepository
|
||||||
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
|
import org.springframework.web.bind.annotation.*
|
||||||
|
|
||||||
|
@Controller
|
||||||
|
@RequestMapping("/donors/{donorId}/labdatas")
|
||||||
|
class LabDataController(
|
||||||
|
private val repository: LabDataRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@GetMapping
|
||||||
|
fun getAllLabData(@PathVariable donorId: Long, model: Model): String {
|
||||||
|
model.addAttribute("labdatas", repository.findByDonorId(donorId))
|
||||||
|
return "labdatas"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PostMapping
|
||||||
|
fun postLabData(@PathVariable donorId: Long, model: Model): String {
|
||||||
|
repository.save(LabData(donorId = donorId))
|
||||||
|
model.addAttribute("labdatas", repository.findByDonorId(donorId))
|
||||||
|
return "labdatas"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["{labdataId}"])
|
||||||
|
fun putLabData(@PathVariable donorId: Long, labData: LabData, model: Model): String {
|
||||||
|
repository.save(labData)
|
||||||
|
model.addAttribute("labdatas", repository.findByDonorId(donorId))
|
||||||
|
return "labdatas"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["{labdataId}"])
|
||||||
|
fun deleteLabData(@PathVariable donorId: Long, @PathVariable labdataId: Long, model: Model): String {
|
||||||
|
repository.deleteById(labdataId)
|
||||||
|
model.addAttribute("labdatas", repository.findByDonorId(donorId))
|
||||||
|
return "labdatas"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
@ -0,0 +1,25 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor.web
|
||||||
|
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.CaseRepository
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.FileRepository
|
||||||
|
import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataRepository
|
||||||
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
|
import org.springframework.web.bind.annotation.GetMapping
|
||||||
|
|
||||||
|
@Controller
|
||||||
|
class MenuController(
|
||||||
|
private val caseRepository: CaseRepository,
|
||||||
|
private val labDataRepository: LabDataRepository,
|
||||||
|
private val fileRepository: FileRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@GetMapping("/cases/menu")
|
||||||
|
fun getCaseMenus(model: Model): String {
|
||||||
|
model.addAttribute("cases", caseRepository.findAll().count())
|
||||||
|
model.addAttribute("unusedLabData", labDataRepository.countLabDataByDonorIdIsNull())
|
||||||
|
model.addAttribute("unusedFiles", fileRepository.findByLabDataIdIsNull().size)
|
||||||
|
return "casemenu"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
4
src/main/resources/application-dev.yml
Normal file
4
src/main/resources/application-dev.yml
Normal file
@ -0,0 +1,4 @@
|
|||||||
|
spring:
|
||||||
|
docker:
|
||||||
|
compose:
|
||||||
|
file: compose-dev.yml
|
||||||
5
src/main/resources/application.yml
Normal file
5
src/main/resources/application.yml
Normal file
@ -0,0 +1,5 @@
|
|||||||
|
spring:
|
||||||
|
application:
|
||||||
|
name: grz-metadata-processor
|
||||||
|
flyway:
|
||||||
|
locations: "classpath:db/migrations/{vendor}"
|
||||||
61
src/main/resources/db/migrations/mariadb/V0_1_0__Init.sql
Normal file
61
src/main/resources/db/migrations/mariadb/V0_1_0__Init.sql
Normal file
@ -0,0 +1,61 @@
|
|||||||
|
CREATE TABLE IF NOT EXISTS tbl_case
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
local_case_id varchar(255) not null,
|
||||||
|
coverage_type varchar(255) not null,
|
||||||
|
submitter_id varchar(16) not null,
|
||||||
|
genomic_data_center_id varchar(16) not null,
|
||||||
|
clinical_data_center_id varchar(16) not null,
|
||||||
|
disease_type varchar(24),
|
||||||
|
genomic_study_type varchar(24),
|
||||||
|
genomic_study_subtype varchar(24),
|
||||||
|
lab_name varchar(255) not null
|
||||||
|
);
|
||||||
|
|
||||||
|
CREATE TABLE IF NOT EXISTS tbl_donor
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
case_id int,
|
||||||
|
donor_pseudonym varchar(255) not null,
|
||||||
|
gender varchar(16),
|
||||||
|
relation varchar(16)
|
||||||
|
|
||||||
|
);
|
||||||
|
|
||||||
|
CREATE TABLE IF NOT EXISTS tbl_lab_data
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
donor_id int,
|
||||||
|
einsendenummer varchar(255) unique,
|
||||||
|
lab_data_name varchar(255) not null,
|
||||||
|
sample_date varchar(16) not null,
|
||||||
|
sample_conservation varchar(255),
|
||||||
|
sequence_type varchar(255),
|
||||||
|
sequence_subtype varchar(255),
|
||||||
|
fragmentation_method varchar(255),
|
||||||
|
library_type varchar(255),
|
||||||
|
library_prep_kit varchar(255) not null,
|
||||||
|
library_prep_kit_manufacturer varchar(255) not null,
|
||||||
|
sequencer_model varchar(255) not null,
|
||||||
|
sequencer_manufacturer varchar(255) not null,
|
||||||
|
kit_name varchar(255) not null,
|
||||||
|
kit_manufacturer varchar(255) not null,
|
||||||
|
enrichment_kit varchar(255) not null,
|
||||||
|
enrichment_kit_manufacturer varchar(255),
|
||||||
|
sequencing_layout varchar(255),
|
||||||
|
tumor_cell_count int,
|
||||||
|
tumor_cell_count_method varchar(255),
|
||||||
|
bioinformatics_pipeline_name varchar(255) not null,
|
||||||
|
bioinformatics_pipeline_version varchar(255) not null,
|
||||||
|
reference_genome varchar(8)
|
||||||
|
);
|
||||||
|
|
||||||
|
CREATE TABLE IF NOT EXISTS tbl_file
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
lab_data_id int,
|
||||||
|
file_path varchar(255) unique,
|
||||||
|
file_type varchar(8),
|
||||||
|
file_checksum varchar(64) unique,
|
||||||
|
file_size_in_bytes int
|
||||||
|
);
|
||||||
118
src/main/resources/templates/case.html
Normal file
118
src/main/resources/templates/case.html
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
<link th:href="@{/main.css}" rel="stylesheet" />
|
||||||
|
<base href="@{/}">
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<aside th:hx-get="@{/cases/menu}" hx-trigger="load"></aside>
|
||||||
|
|
||||||
|
<main>
|
||||||
|
<div>
|
||||||
|
<h1>Fall <tt th:text="${case.localCaseId}"></tt></h1>
|
||||||
|
|
||||||
|
<form class="case">
|
||||||
|
<input type="hidden" name="id" th:value="${case.id}" />
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Lokale Fall-ID
|
||||||
|
<input type="text" name="localCaseId" th:value="${case.localCaseId}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Versicherungsart
|
||||||
|
<select name="coverageType" th:field="${case.coverageType}">
|
||||||
|
<option th:value="'GKV'">GKV</option>
|
||||||
|
<option th:value="'PKV'">PKV</option>
|
||||||
|
<option th:value="'BG'">BG</option>
|
||||||
|
<option th:value="'SEL'">SEL</option>
|
||||||
|
<option th:value="'SOZ'">SOZ</option>
|
||||||
|
<option th:value="'GPV'">GPV</option>
|
||||||
|
<option th:value="'PPV'">PPV</option>
|
||||||
|
<option th:value="'BEI'">BEI</option>
|
||||||
|
<option th:value="'SKT'">SKT</option>
|
||||||
|
<option th:value="'UNK'">UNK</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Submitter-ID
|
||||||
|
<input type="text" name="submitterId" th:value="${case.submitterId}" pattern="[0-9]{9}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
GRZ-ID
|
||||||
|
<input type="text" name="genomicDataCenterId" th:value="${case.genomicDataCenterId}" pattern="^(GRZ)[A-Z0-9]{3}[0-9]{3}$" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
KDK-ID
|
||||||
|
<input type="text" name="clinicalDataCenterId" th:value="${case.clinicalDataCenterId}" pattern="^(GRZ)[A-Z0-9]{3}[0-9]{3}$" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Erkrankungsart
|
||||||
|
<select name="diseaseType" th:field="${case.diseaseType}">
|
||||||
|
<option th:value="ONCOLOGICAL">oncological</option>
|
||||||
|
<option th:value="RARE">rare</option>
|
||||||
|
<option th:value="HEREDITARY">hereditary</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Genomische Studienart
|
||||||
|
<select name="genomicStudyType" th:field="${case.genomicStudyType}">
|
||||||
|
<option th:value="SINGLE">single</option>
|
||||||
|
<option th:value="DUO">duo</option>
|
||||||
|
<option th:value="TRIO">trio</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Genomische Unterstudienart
|
||||||
|
<select name="genomicStudySubtype" th:field="${case.genomicStudySubtype}">
|
||||||
|
<option th:value="TUMOR_ONLY">tumor-only</option>
|
||||||
|
<option th:value="TUMOR_GERMLINE">tumor+germline</option>
|
||||||
|
<option th:value="GERMLINE_ONLY">germline-only</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Laborname
|
||||||
|
<input name="labName" th:value="${case.labName}" type="text" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<button class="save" th:hx-put="@{/cases/{caseId}(caseId=${case.id})}" hx-target="body">Änderungen übernehmen</button>
|
||||||
|
<button class="new" th:hx-post="@{/cases}">Neu</button>
|
||||||
|
<button class="delete" th:hx-delete="@{/cases/{caseId}(caseId=${case.id})}">Löschen</button>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:hx-get="@{/cases/{caseId}/donors(caseId=${case.id})}" hx-trigger="load"></div>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</main>
|
||||||
|
|
||||||
|
<script th:src="@{/main.js}"></script>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
25
src/main/resources/templates/casemenu.html
Normal file
25
src/main/resources/templates/casemenu.html
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
<div class="title">GRZ-Metadaten</div>
|
||||||
|
|
||||||
|
<nav>
|
||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<a th:href="@{/}">
|
||||||
|
<span>Fallübersicht</span>
|
||||||
|
<span class="counter">[[ ${cases} ]]</span>
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a th:href="@{/}">
|
||||||
|
<span>Ungenutzte Proben</span>
|
||||||
|
<span th:if="${unusedLabData > 0}" class="counter">[[ ${unusedLabData} ]]</span>
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a th:href="@{/files/unused}">
|
||||||
|
<span>Ungenutzte Dateien</span>
|
||||||
|
<span th:if="${unusedFiles}" class="counter">[[ ${unusedFiles} ]]</span>
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</nav>
|
||||||
|
|
||||||
23
src/main/resources/templates/cases.html
Normal file
23
src/main/resources/templates/cases.html
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<div>
|
||||||
|
<h1>
|
||||||
|
[[ ${cases.size()} ]] Fälle
|
||||||
|
</h1>
|
||||||
|
<form class="case">
|
||||||
|
<ul class="case-list">
|
||||||
|
<li th:each="case : ${cases}">
|
||||||
|
<a th:href="@{/cases/{caseId}(caseId=${case.id})}">#[[ ${case.id} ]] - Fallnummer: [[ ${case.localCaseId} ]]</a>
|
||||||
|
<button class="delete left" th:hx-delete="@{/cases/{caseId}(caseId=${case.id})}" hx-target="#cases">Eintrag löschen</button>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<button class="new" th:hx-post="@{/cases}">Neuen Fall anlegen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
72
src/main/resources/templates/donors.html
Normal file
72
src/main/resources/templates/donors.html
Normal file
@ -0,0 +1,72 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<div th:id="'cases_' + ${caseId} + '_donors'">
|
||||||
|
|
||||||
|
<div th:if="${donors.isEmpty()}">
|
||||||
|
<h2>Probenspender</h2>
|
||||||
|
<form class="donor" th:hx-post="@{/cases/{caseId}/donors(caseId=${caseId})}" th:hx-target="'#cases_' + ${caseId} + '_donors'">
|
||||||
|
<div>Keine Probenspender gefunden</div>
|
||||||
|
<button>Neuen Probenspender hinzufügen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<!-- Probenspender -->
|
||||||
|
<div th:each="donor : ${donors}">
|
||||||
|
<h2>Probenspender</h2>
|
||||||
|
|
||||||
|
<form class="donor" th:id="'cases_' + ${caseId} + '_donors'">
|
||||||
|
<input type="hidden" name="id" th:value="${donor.id}">
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Spender-Pseudonym
|
||||||
|
<input type="text" name="donorPseudonym" th:value="${donor.donorPseudonym}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Gender
|
||||||
|
<select name="gender">
|
||||||
|
<option th:selected="${donor.gender != null and donor.gender.value == 'male'}" value="MALE">male</option>
|
||||||
|
<option th:selected="${donor.gender != null and donor.gender.value == 'female'}" value="FEMALE">female</option>
|
||||||
|
<option th:selected="${donor.gender != null and donor.gender.value == 'other'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${donor.gender != null and donor.gender.value == 'unknown'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Verwandschaft
|
||||||
|
<select name="relation">
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'mother'}" value="MOTHER">mother</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'father'}" value="FATHER">father</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'brother'}" value="BROTHER">brother</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'sister'}" value="SISTER">sister</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'child'}" value="CHILD">child</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'index'}" value="INDEX">index</option>
|
||||||
|
<option th:selected="${donor.relation != null and donor.relation.value == 'other'}" value="OTHER">other</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<button class="save" th:hx-put="@{/cases/{caseId}/donors/{donorId}(caseId=${caseId},donorId=${donor.id})}" th:hx-target="'#cases_' + ${caseId} + '_donors'">Änderungen übernehmen</button>
|
||||||
|
<button class="new" th:hx-post="@{/cases/{caseId}/donors(caseId=${caseId})}" th:hx-target="'#cases_' + ${caseId} + '_donors'">Neu</button>
|
||||||
|
<button class="delete" th:hx-delete="@{/cases/{caseId}/donors/{donorId}(caseId=${caseId},donorId=${donor.id})}" th:hx-target="'#cases_' + ${caseId} + '_donors'">Löschen</button>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:hx-get="@{/donors/{donorId}/labdatas(donorId=${donor.id})}" hx-trigger="load"></div>
|
||||||
|
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
10
src/main/resources/templates/error/notfound.html
Normal file
10
src/main/resources/templates/error/notfound.html
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Fehler</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<a th:href="@{/}">Zurück</a>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
70
src/main/resources/templates/files.html
Normal file
70
src/main/resources/templates/files.html
Normal file
@ -0,0 +1,70 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
|
||||||
|
<div th:id="'labdatas_' + ${labDataId} + '_files'">
|
||||||
|
<div th:if="${files.isEmpty()}">
|
||||||
|
<h4>Datei</h4>
|
||||||
|
<form class="file" th:hx-post="@{/labdatas/{labDataId}/files(labDataId=${labDataId})}" th:hx-target="'#labdatas_' + ${labDataId} + '_files'">
|
||||||
|
<div>Keine Datei gefunden</div>
|
||||||
|
<button>Neuen Datei hinzufügen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:each="file : ${files}">
|
||||||
|
<!-- File -->
|
||||||
|
<h4>Datei</h4>
|
||||||
|
<form class="file">
|
||||||
|
<input type="hidden" name="id" th:value="${file.id}" />
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Datei
|
||||||
|
<input type="text" name="filePath" th:value="${file.filePath}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Dateityp
|
||||||
|
<select name="fileType">
|
||||||
|
<option th:selected="${file.fileType != null and file.fileType.value == 'bam'}">BAM</option>
|
||||||
|
<option th:selected="${file.fileType != null and file.fileType.value == 'vcf'}">Vcf</option>
|
||||||
|
<option th:selected="${file.fileType != null and file.fileType.value == 'bed'}">BED</option>
|
||||||
|
<option th:selected="${file.fileType != null and file.fileType.value == 'fastq'}">FASTQ</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Prüfsumme - SHA256
|
||||||
|
<input type="text" pattern="[A-Fa-f0-9]{64}" name="fileChecksum" th:value="${file.fileChecksum} " />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Dateigröße in Bytes
|
||||||
|
<input type="number" min="0" name="fileSizeInBytes" th:value="${file.fileSizeInBytes} " />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<button class="save" th:hx-put="@{/labdatas/{labDataId}/files/{fileId}(labDataId=${labDataId},fileId=${file.id})}" th:hx-target="'#labdatas_' + ${labDataId} + '_files'">Änderungen übernehmen</button>
|
||||||
|
<button class="new" th:hx-post="@{/labdatas/{labDataId}/files(labDataId=${labDataId})}" th:hx-target="'#labdatas_' + ${labDataId} + '_files'">Neu</button>
|
||||||
|
<button class="delete" th:hx-delete="@{/labdatas/{labDataId}/files/{fileId}(labDataId=${labDataId},fileId=${file.id})}" th:hx-target="'#labdatas_' + ${labDataId} + '_files'">Löschen</button>
|
||||||
|
</div>
|
||||||
|
</form>
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<script th:src="@{/main.js}"></script>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
18
src/main/resources/templates/index.html
Normal file
18
src/main/resources/templates/index.html
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
<link th:href="@{/main.css}" rel="stylesheet" />
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
|
||||||
|
<aside th:hx-get="@{/cases/menu}" hx-trigger="load"></aside>
|
||||||
|
|
||||||
|
<main>
|
||||||
|
<div id="cases" th:hx-get="@{/cases}" hx-trigger="load"></div>
|
||||||
|
</main>
|
||||||
|
|
||||||
|
<script th:src="@{/main.js}"></script>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
232
src/main/resources/templates/labdatas.html
Normal file
232
src/main/resources/templates/labdatas.html
Normal file
@ -0,0 +1,232 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
|
||||||
|
<div th:id="'donors_' + ${donorId} + '_labdatas'">
|
||||||
|
<div th:if="${labdatas.isEmpty()}">
|
||||||
|
<h3>Probe</h3>
|
||||||
|
<form class="lab-data" th:hx-post="@{/donors/{donorId}/labdatas(donorId=${donorId})}" th:hx-target="'#donors_' + ${donorId} + '_labdatas'">
|
||||||
|
<div>Keine Probe gefunden</div>
|
||||||
|
<button>Neuen Probe hinzufügen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:each="labdata : ${labdatas}">
|
||||||
|
<h3>Probe/Sequenzierung</h3>
|
||||||
|
|
||||||
|
<form class="lab-data">
|
||||||
|
<input type="hidden" name="id" th:value="${labdata.id}" />
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label class="optional">
|
||||||
|
Einsendenummer (Optionale Angabe)
|
||||||
|
<input type="text" name="einsendenummer" th:value="${labdata.einsendenummer}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
LabData Name
|
||||||
|
<input type="text" name="labDataName" th:value="${labdata.labDataName}"/>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Datum der Probe
|
||||||
|
<input type="date" name="sampleDate" th:value="${labdata.sampleDate}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Konservierung der Probe
|
||||||
|
<select name="sampleConservation">
|
||||||
|
<option th:selected="${labdata.sampleConservation != null and labdata.sampleConservation.value == 'FRESH_TISSUE'}" value="FRESH_TISSUE">fresh-tissue</option>
|
||||||
|
<option th:selected="${labdata.sampleConservation != null and labdata.sampleConservation.value == 'CRYO_FROZEN'}" value="CRYO_FROZEN">cryo-frozen</option>
|
||||||
|
<option th:selected="${labdata.sampleConservation != null and labdata.sampleConservation.value == 'FFPE'}" value="FFPE">ffpe</option>
|
||||||
|
<option th:selected="${labdata.sampleConservation != null and labdata.sampleConservation.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.sampleConservation != null and labdata.sampleConservation.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Sequenzierungsart
|
||||||
|
<select name="sequenceType">
|
||||||
|
<option th:selected="${labdata.sequenceType != null and labdata.sequenceType.value == 'DNA'}" value="DNA">dna</option>
|
||||||
|
<option th:selected="${labdata.sequenceType != null and labdata.sequenceType.value == 'RNA'}" value="RNA">rna</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Sequenzierungsunterart
|
||||||
|
<select name="sequenceSubtype">
|
||||||
|
<option th:selected="${labdata.sequenceSubtype != null and labdata.sequenceSubtype.value == 'GERMLINE'}" value="GERMLINE">germline</option>
|
||||||
|
<option th:selected="${labdata.sequenceSubtype != null and labdata.sequenceSubtype.value == 'SOMATIC'}" value="SOMATIC">somatic</option>
|
||||||
|
<option th:selected="${labdata.sequenceSubtype != null and labdata.sequenceSubtype.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.sequenceSubtype != null and labdata.sequenceSubtype.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Fragmentierungsart
|
||||||
|
<select name="fragmentationMethod">
|
||||||
|
<option th:selected="${labdata.fragmentationMethod != null and labdata.fragmentationMethod.value == 'SONICATION'}" value="SONICATION">sonication</option>
|
||||||
|
<option th:selected="${labdata.fragmentationMethod != null and labdata.fragmentationMethod.value == 'ENZYMATIC'}" value="ENZYMATIC">enzymatic</option>
|
||||||
|
<option th:selected="${labdata.fragmentationMethod != null and labdata.fragmentationMethod.value == 'NONE'}" value="NONE">none</option>
|
||||||
|
<option th:selected="${labdata.fragmentationMethod != null and labdata.fragmentationMethod.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.fragmentationMethod != null and labdata.fragmentationMethod.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Library Type
|
||||||
|
<select name="libraryType">
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'PANEL'}" value="PANEL">panel</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'PANEL_LR'}" value="PANEL_LR">panel_lr</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WES'}" value="WES">wes</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WES_LR'}" value="WES_LR">wes_lr</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WGS'}" value="WGS">wgs</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WGS_LR'}" value="WGS_LR">wgs_lr</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WXS'}" value="WXS">wxs</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'WXS_LR'}" value="WXS_LR">wxs_lr</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Preparation Kit - Name
|
||||||
|
<input type="text" name="libraryPrepKit" th:value="${labdata.libraryPrepKit}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Hersteller
|
||||||
|
<input type="text" name="libraryPrepKitManufacturer" th:value="${labdata.libraryPrepKitManufacturer}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Sequencer - Modell
|
||||||
|
<input type="text" name="sequencerModel" th:value="${labdata.sequencerModel}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Hersteller
|
||||||
|
<input type="text" name="sequencerManufacturer" th:value="${labdata.sequencerManufacturer}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Kit - Name/Version
|
||||||
|
<input type="text" name="kitName" th:value="${labdata.kitName}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Hersteller
|
||||||
|
<input type="text" name="kitManufacturer" th:value="${labdata.kitManufacturer}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Enrichment Kit - Name und Version
|
||||||
|
<input type="text" name="enrichmentKit" th:value="${labdata.enrichmentKit}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Hersteller
|
||||||
|
<select name="enrichmentKitManufacturer">
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'ILLUMINA'}" value="ILLUMINA">Illumina</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'AGILENT'}" value="AGILENT">Agilent</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'TIST'}" value="TIST">Twist</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'NEB'}" value="NEB">NEB</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'NONE'}" value="NONE">none</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Sequencing Layout
|
||||||
|
<select name="sequencingLayout">
|
||||||
|
<option th:selected="${labdata.sequencingLayout != null and labdata.sequencingLayout.value == 'SINGLE_END'}" value="SINGLE_END">single-end</option>
|
||||||
|
<option th:selected="${labdata.sequencingLayout != null and labdata.sequencingLayout.value == 'PAIRED_END'}" value="PAIRED_END">paired-end</option>
|
||||||
|
<option th:selected="${labdata.sequencingLayout != null and labdata.sequencingLayout.value == 'REVERSE'}" value="REVERSE">reverse</option>
|
||||||
|
<option th:selected="${labdata.sequencingLayout != null and labdata.sequencingLayout.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Tumorzellgehalt in %
|
||||||
|
<input type="number" name="tumorCellCount" th:value="${labdata.tumorCellCount}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Methode
|
||||||
|
<select name="tumorCellCountMethod">
|
||||||
|
<option th:selected="${labdata.tumorCellCountMethod != null and labdata.tumorCellCountMethod.value == 'PATHOLOGY'}" value="PATHOLOGY">pathology</option>
|
||||||
|
<option th:selected="${labdata.tumorCellCountMethod != null and labdata.tumorCellCountMethod.value == 'BIOINFORMATICS'}" value="BIOINFORMATICS">bioinformatics</option>
|
||||||
|
<option th:selected="${labdata.tumorCellCountMethod != null and labdata.tumorCellCountMethod.value == 'OTHER'}" value="OTHER">other</option>
|
||||||
|
<option th:selected="${labdata.tumorCellCountMethod != null and labdata.tumorCellCountMethod.value == 'UNKNOWN'}" value="UNKNOWN">unknown</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Bioinformatik-Pipeline
|
||||||
|
<input type="text" name="bioinformaticsPipelineName" th:value="${labdata.bioinformaticsPipelineName}" />
|
||||||
|
</label>
|
||||||
|
|
||||||
|
<label>
|
||||||
|
Version
|
||||||
|
<input type="text" name="bioinformaticsPipelineVersion" th:value="${labdata.bioinformaticsPipelineVersion}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Referenz-Genom
|
||||||
|
<select name="referenceGenome">
|
||||||
|
<option th:selected="${labdata.referenceGenome != null and labdata.referenceGenome.value == 'GRCH37'}" value="GRCH37">GRCh37</option>
|
||||||
|
<option th:selected="${labdata.referenceGenome != null and labdata.referenceGenome.value == 'GRCH38'}" value="GRCH38">GRCh38</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<button class="save" th:hx-put="@{/donors/{donorId}/labdatas/{labdataId}(donorId=${donorId},labdataId=${labdata.id})}" th:hx-target="'#donors_' + ${donorId} + '_labdatas'">Änderungen übernehmen</button>
|
||||||
|
<button class="new" th:hx-post="@{/donors/{donorId}/labdatas(donorId=${donorId})}" th:hx-target="'#donors_' + ${donorId} + '_labdatas'">Neu</button>
|
||||||
|
<button class="delete" th:hx-delete="@{/donors/{donorId}/labdatas/{labdataId}(donorId=${donorId},labdataId=${labdata.id})}" th:hx-target="'#donors_' + ${donorId} + '_labdatas'">Löschen</button>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:hx-get="@{/labdatas/{labdataId}/files(labdataId=${labdata.id})}" hx-trigger="load"></div>
|
||||||
|
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
83
src/main/resources/templates/unusedfiles.html
Normal file
83
src/main/resources/templates/unusedfiles.html
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
|
||||||
|
<head>
|
||||||
|
<meta charset="UTF-8">
|
||||||
|
<title>Title</title>
|
||||||
|
<link th:href="@{/main.css}" rel="stylesheet" />
|
||||||
|
<base href="@{/}">
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<div>
|
||||||
|
<aside th:hx-get="@{/cases/menu}" hx-trigger="load"></aside>
|
||||||
|
|
||||||
|
<main>
|
||||||
|
<div id="unused_files">
|
||||||
|
|
||||||
|
<div th:if="${files.isEmpty()}">
|
||||||
|
<h4>Datei</h4>
|
||||||
|
<form class="file">
|
||||||
|
<div>Keine ungenutzte Datei gefunden</div>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div th:each="file : ${files}">
|
||||||
|
<!-- File -->
|
||||||
|
<h4>Datei</h4>
|
||||||
|
<form class="file">
|
||||||
|
<input type="hidden" name="id" th:value="${file.id}" />
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Datei
|
||||||
|
<input type="text" name="filePath" th:value="${file.filePath}" />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label class="optional">
|
||||||
|
Zugehörige Probe (Einsendenummer)
|
||||||
|
<select name="labDataId">
|
||||||
|
<option>Keine Zuordnung</option>
|
||||||
|
<option th:each="labData : ${labDatas}" th:selected="${file.labDataId == labData.id}" th:value="${labData.id}" th:text="${labData.einsendenummer}"></option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Dateityp
|
||||||
|
<select name="fileType">
|
||||||
|
<option th:selected="${file.fileType.value == 'bam'}">BAM</option>
|
||||||
|
<option th:selected="${file.fileType.value == 'vcf'}">Vcf</option>
|
||||||
|
<option th:selected="${file.fileType.value == 'bed'}">BED</option>
|
||||||
|
<option th:selected="${file.fileType.value == 'fastq'}">FASTQ</option>
|
||||||
|
</select>
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Prüfsumme - SHA256
|
||||||
|
<input type="text" pattern="[A-Fa-f0-9]{64}" name="fileChecksum" th:value="${file.fileChecksum} " />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<label>
|
||||||
|
Dateigröße in Bytes
|
||||||
|
<input type="number" min="0" name="fileSizeInBytes" th:value="${file.fileSizeInBytes} " />
|
||||||
|
</label>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<button class="save" th:hx-put="@{/files/unused/{fileId}(fileId=${file.id})}" hx-target="body">Änderungen übernehmen</button>
|
||||||
|
</div>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</main>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<script th:src="@{/main.js}"></script>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
30
src/main/web/rspack.config.js
Normal file
30
src/main/web/rspack.config.js
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
export default {
|
||||||
|
entry: {
|
||||||
|
main: './src/main/web/script.js',
|
||||||
|
},
|
||||||
|
output: {
|
||||||
|
path: './src/main/resources/static',
|
||||||
|
chunkFilename: '[id].js'
|
||||||
|
},
|
||||||
|
module: {
|
||||||
|
rules: [
|
||||||
|
{
|
||||||
|
test: /\.css$/,
|
||||||
|
use: [{
|
||||||
|
loader: "postcss-loader",
|
||||||
|
options: {
|
||||||
|
postcssOptions: {
|
||||||
|
plugins: {
|
||||||
|
"@tailwindcss/postcss": {},
|
||||||
|
},
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}],
|
||||||
|
type: "css"
|
||||||
|
},
|
||||||
|
]
|
||||||
|
},
|
||||||
|
experiments: {
|
||||||
|
css: true,
|
||||||
|
}
|
||||||
|
}
|
||||||
3
src/main/web/script.js
Normal file
3
src/main/web/script.js
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
import 'htmx.org';
|
||||||
|
|
||||||
|
import * as styles from './style.css';
|
||||||
190
src/main/web/style.css
Normal file
190
src/main/web/style.css
Normal file
@ -0,0 +1,190 @@
|
|||||||
|
@import "tailwindcss";
|
||||||
|
|
||||||
|
body {
|
||||||
|
@apply bg-white dark:bg-gray-950 flex flex-col h-screen;
|
||||||
|
}
|
||||||
|
|
||||||
|
aside {
|
||||||
|
@apply fixed top-0 left-0 z-40 w-80 p-5 h-screen bg-gray-100 text-gray-600
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > .title {
|
||||||
|
@apply m-2 text-2xl font-bold
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav {
|
||||||
|
@apply mt-2
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav ul {
|
||||||
|
@apply m-2
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a:before {
|
||||||
|
content: '🗎';
|
||||||
|
margin-right: 4px;
|
||||||
|
opacity: 0.8;
|
||||||
|
width: 1.2em;
|
||||||
|
text-align: center;
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a:hover:before {
|
||||||
|
opacity: 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a:hover {
|
||||||
|
@apply text-gray-900 bg-gray-300
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a {
|
||||||
|
@apply flex p-1 rounded-sm
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a > span {
|
||||||
|
@apply nth-[1]:flex-1
|
||||||
|
}
|
||||||
|
|
||||||
|
aside > nav a .counter {
|
||||||
|
@apply inline-flex items-center justify-center min-w-3 h-3 p-3 font-bold text-xs text-white bg-gray-500 rounded-full
|
||||||
|
}
|
||||||
|
|
||||||
|
main {
|
||||||
|
@apply mx-auto pl-84 px-10 py-1 w-full;
|
||||||
|
}
|
||||||
|
|
||||||
|
h1, h2, h3, h4 {
|
||||||
|
@apply mt-5 text-white py-1 px-3 rounded-t-sm
|
||||||
|
}
|
||||||
|
|
||||||
|
h1 {
|
||||||
|
@apply text-3xl font-bold bg-blue-900
|
||||||
|
}
|
||||||
|
|
||||||
|
h2 {
|
||||||
|
@apply text-2xl font-bold bg-green-900
|
||||||
|
}
|
||||||
|
|
||||||
|
h3 {
|
||||||
|
@apply text-xl font-bold bg-yellow-900
|
||||||
|
}
|
||||||
|
|
||||||
|
h4 {
|
||||||
|
@apply font-bold bg-red-900
|
||||||
|
}
|
||||||
|
|
||||||
|
form {
|
||||||
|
@apply p-2 rounded-b-sm
|
||||||
|
}
|
||||||
|
|
||||||
|
label {
|
||||||
|
@apply mr-4 w-1/2 text-sm
|
||||||
|
}
|
||||||
|
|
||||||
|
input,
|
||||||
|
select {
|
||||||
|
@apply text-base w-full text-black
|
||||||
|
}
|
||||||
|
|
||||||
|
label.optional {
|
||||||
|
@apply italic
|
||||||
|
}
|
||||||
|
label.optional input,
|
||||||
|
label.optional select {
|
||||||
|
font-style: normal;
|
||||||
|
background: repeating-linear-gradient(135deg, var(--color-white), var(--color-white) 4px, transparent 4px, transparent 8px)
|
||||||
|
}
|
||||||
|
|
||||||
|
input[type=text],
|
||||||
|
input[type=date],
|
||||||
|
input[type=number],
|
||||||
|
select {
|
||||||
|
@apply block font-mono border-b-2 border-b-gray-300 bg-gray-50 focus:outline-none focus:border-gray-600 focus:bg-gray-200 h-8 p-1
|
||||||
|
}
|
||||||
|
|
||||||
|
input[type=submit],
|
||||||
|
input[type=reset],
|
||||||
|
button {
|
||||||
|
@apply cursor-pointer bg-gray-700 text-white rounded-sm px-6 py-2 mx-auto my-2 w-fit transition-colors
|
||||||
|
}
|
||||||
|
|
||||||
|
input[type=submit]:hover,
|
||||||
|
input[type=reset]:hover,
|
||||||
|
button:hover {
|
||||||
|
@apply bg-gray-900
|
||||||
|
}
|
||||||
|
|
||||||
|
div:has(> label) {
|
||||||
|
@apply my-2 flex
|
||||||
|
}
|
||||||
|
|
||||||
|
.case {
|
||||||
|
@apply border-l-4 border-l-blue-900 bg-blue-100
|
||||||
|
}
|
||||||
|
|
||||||
|
.case input[type=text],
|
||||||
|
.case input[type=date],
|
||||||
|
.case input[type=number],
|
||||||
|
.case select {
|
||||||
|
@apply focus:border-blue-600 focus:bg-blue-200
|
||||||
|
}
|
||||||
|
|
||||||
|
.donor {
|
||||||
|
@apply border-l-4 border-l-green-900 bg-green-100
|
||||||
|
}
|
||||||
|
|
||||||
|
.donor input[type=text],
|
||||||
|
.donor input[type=date],
|
||||||
|
.donor input[type=number],
|
||||||
|
.donor select {
|
||||||
|
@apply focus:border-green-600 focus:bg-green-200
|
||||||
|
}
|
||||||
|
|
||||||
|
.lab-data {
|
||||||
|
@apply border-l-4 border-l-yellow-900 bg-yellow-100
|
||||||
|
}
|
||||||
|
|
||||||
|
.lab-data input[type=text],
|
||||||
|
.lab-data input[type=date],
|
||||||
|
.lab-data input[type=number],
|
||||||
|
.lab-data select {
|
||||||
|
@apply focus:border-yellow-600 focus:bg-yellow-200
|
||||||
|
}
|
||||||
|
|
||||||
|
.file {
|
||||||
|
@apply border-l-4 border-l-red-900 bg-red-100
|
||||||
|
}
|
||||||
|
|
||||||
|
.file input[type=text],
|
||||||
|
.file input[type=date],
|
||||||
|
.file input[type=number],
|
||||||
|
.file select {
|
||||||
|
@apply focus:border-red-600 focus:bg-red-200
|
||||||
|
}
|
||||||
|
|
||||||
|
button {
|
||||||
|
@apply text-base font-normal
|
||||||
|
}
|
||||||
|
|
||||||
|
button.left {
|
||||||
|
@apply m-0 py-0 px-1 mx-1 float-right text-base font-normal
|
||||||
|
}
|
||||||
|
button.new:before {
|
||||||
|
content: '➕';
|
||||||
|
margin-right: .5em;
|
||||||
|
}
|
||||||
|
button.delete:before {
|
||||||
|
content: '🗑';
|
||||||
|
margin-right: .5em;
|
||||||
|
}
|
||||||
|
button.save:before {
|
||||||
|
content: '💾';
|
||||||
|
margin-right: .5em;
|
||||||
|
}
|
||||||
|
|
||||||
|
.case-list > li {
|
||||||
|
@apply my-2 p-1 odd:bg-blue-200
|
||||||
|
}
|
||||||
|
|
||||||
|
.case-list > li > a {
|
||||||
|
@apply w-full
|
||||||
|
}
|
||||||
@ -0,0 +1,13 @@
|
|||||||
|
package dev.pcvolkmer.onco.grzmetadataprocessor
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.springframework.boot.test.context.SpringBootTest
|
||||||
|
|
||||||
|
@SpringBootTest
|
||||||
|
class GrzMetadataProcessorApplicationTests {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun contextLoads() {
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Reference in New Issue
Block a user