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5
.gitignore
vendored
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5
.gitignore
vendored
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|||||||
|
.idea/
|
||||||
|
target/
|
||||||
|
|
||||||
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*.iml
|
||||||
|
*.lock
|
||||||
14
Cargo.toml
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14
Cargo.toml
Normal file
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|
|||||||
|
[package]
|
||||||
|
name = "bzkf-rwdp-check"
|
||||||
|
version = "0.1.0"
|
||||||
|
edition = "2021"
|
||||||
|
|
||||||
|
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
||||||
|
|
||||||
|
[dependencies]
|
||||||
|
clap = { version = "4.4", features = ["std", "help", "usage", "derive", "error-context"], default-features = false }
|
||||||
|
console = "0.15"
|
||||||
|
csv = "1.3"
|
||||||
|
itertools = "0.12"
|
||||||
|
serde = { version = "1.0", features = ["derive"] }
|
||||||
|
|
||||||
339
LICENSE
Normal file
339
LICENSE
Normal file
@ -0,0 +1,339 @@
|
|||||||
|
GNU GENERAL PUBLIC LICENSE
|
||||||
|
Version 2, June 1991
|
||||||
|
|
||||||
|
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
|
||||||
|
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||||
|
Everyone is permitted to copy and distribute verbatim copies
|
||||||
|
of this license document, but changing it is not allowed.
|
||||||
|
|
||||||
|
Preamble
|
||||||
|
|
||||||
|
The licenses for most software are designed to take away your
|
||||||
|
freedom to share and change it. By contrast, the GNU General Public
|
||||||
|
License is intended to guarantee your freedom to share and change free
|
||||||
|
software--to make sure the software is free for all its users. This
|
||||||
|
General Public License applies to most of the Free Software
|
||||||
|
Foundation's software and to any other program whose authors commit to
|
||||||
|
using it. (Some other Free Software Foundation software is covered by
|
||||||
|
the GNU Lesser General Public License instead.) You can apply it to
|
||||||
|
your programs, too.
|
||||||
|
|
||||||
|
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
|
||||||
|
this service 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.
|
||||||
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|
||||||
|
To protect your rights, we need to make restrictions that forbid
|
||||||
|
anyone to deny you these rights or to ask you to surrender the rights.
|
||||||
|
These restrictions translate to certain responsibilities for you if you
|
||||||
|
distribute copies of the software, or if you modify it.
|
||||||
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|
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|
For example, if you distribute copies of such a program, whether
|
||||||
|
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|
||||||
|
you have. You must make sure that they, too, receive or can get the
|
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|
source code. And you must show them these terms so they know their
|
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|
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|
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We protect your rights with two steps: (1) copyright the software, and
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(2) offer you this license which gives you legal permission to copy,
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Also, for each author's protection and ours, we want to make certain
|
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|
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|
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|
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|
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|
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Finally, any free program is threatened constantly by software
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|
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|
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|
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|
The precise terms and conditions for copying, distribution and
|
||||||
|
modification follow.
|
||||||
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|
||||||
|
GNU GENERAL PUBLIC LICENSE
|
||||||
|
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||||
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|
||||||
|
0. This License applies to any program or other work which contains
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||||||
|
a notice placed by the copyright holder saying it may be distributed
|
||||||
|
under the terms of this General Public License. The "Program", below,
|
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either verbatim or with modifications and/or translated into another
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|
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the term "modification".) Each licensee is addressed as "you".
|
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|
||||||
|
Activities other than copying, distribution and modification are not
|
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covered by this License; they are outside its scope. The act of
|
||||||
|
running the Program is not restricted, and the output from the Program
|
||||||
|
is covered only if its contents constitute a work based on the
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Program (independent of having been made by running the Program).
|
||||||
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Whether that is true depends on what the Program does.
|
||||||
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|
||||||
|
1. You may copy and distribute verbatim copies of the Program's
|
||||||
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conspicuously and appropriately publish on each copy an appropriate
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|
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|
||||||
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and give any other recipients of the Program a copy of this License
|
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along with the Program.
|
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|
||||||
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You may charge a fee for the physical act of transferring a copy, and
|
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|
you may at your option offer warranty protection in exchange for a fee.
|
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|
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2. You may modify your copy or copies of the Program or any portion
|
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||||||
|
distribute such modifications or work under the terms of Section 1
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||||||
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above, provided that you also meet all of these conditions:
|
||||||
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|
||||||
|
a) You must cause the modified files to carry prominent notices
|
||||||
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b) You must cause any work that you distribute or publish, that in
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|
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|
||||||
|
c) If the modified program normally reads commands interactively
|
||||||
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when run, you must cause it, when started running for such
|
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interactive use in the most ordinary way, to print or display an
|
||||||
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announcement including an appropriate copyright notice and a
|
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a warranty) and that users may redistribute the program under
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|
||||||
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License. (Exception: if the Program itself is interactive but
|
||||||
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does not normally print such an announcement, your work based on
|
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the Program is not required to print an announcement.)
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|
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These requirements apply to the modified work as a whole. If
|
||||||
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identifiable sections of that work are not derived from the Program,
|
||||||
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||||||
|
sections when you distribute them as separate works. But when you
|
||||||
|
distribute the same sections as part of a whole which is a work based
|
||||||
|
on the Program, the distribution of the whole must be on the terms of
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||||||
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this License, whose permissions for other licensees extend to the
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entire whole, and thus to each and every part regardless of who wrote it.
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Thus, it is not the intent of this section to claim rights or contest
|
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||||||
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exercise the right to control the distribution of derivative or
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||||||
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In addition, mere aggregation of another work not based on the Program
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3. You may copy and distribute the Program (or a work based on it,
|
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under Section 2) in object code or executable form under the terms of
|
||||||
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Sections 1 and 2 above provided that you also do one of the following:
|
||||||
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|
||||||
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a) Accompany it with the complete corresponding machine-readable
|
||||||
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source code, which must be distributed under the terms of Sections
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||||||
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1 and 2 above on a medium customarily used for software interchange; or,
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||||||
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|
||||||
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b) Accompany it with a written offer, valid for at least three
|
||||||
|
years, to give any third party, for a charge no more than your
|
||||||
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cost of physically performing source distribution, a complete
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||||||
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machine-readable copy of the corresponding source code, to be
|
||||||
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distributed under the terms of Sections 1 and 2 above on a medium
|
||||||
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customarily used for software interchange; or,
|
||||||
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|
||||||
|
c) Accompany it with the information you received as to the offer
|
||||||
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to distribute corresponding source code. (This alternative is
|
||||||
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allowed only for noncommercial distribution and only if you
|
||||||
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received the program in object code or executable form with such
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an offer, in accord with Subsection b above.)
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||||||
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The source code for a work means the preferred form of the work for
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||||||
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making modifications to it. For an executable work, complete source
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||||||
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associated interface definition files, plus the scripts used to
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||||||
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control compilation and installation of the executable. However, as a
|
||||||
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special exception, the source code distributed need not include
|
||||||
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anything that is normally distributed (in either source or binary
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form) with the major components (compiler, kernel, and so on) of the
|
||||||
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operating system on which the executable runs, unless that component
|
||||||
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itself accompanies the executable.
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|
||||||
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If distribution of executable or object code is made by offering
|
||||||
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access to copy from a designated place, then offering equivalent
|
||||||
|
access to copy the source code from the same place counts as
|
||||||
|
distribution of the source code, even though third parties are not
|
||||||
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compelled to copy the source along with the object code.
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||||||
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|
||||||
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4. You may not copy, modify, sublicense, or distribute the Program
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||||||
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except as expressly provided under this License. Any attempt
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||||||
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otherwise to copy, modify, sublicense or distribute the Program is
|
||||||
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void, and will automatically terminate your rights under this License.
|
||||||
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However, parties who have received copies, or rights, from you under
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||||||
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this License will not have their licenses terminated so long as such
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parties remain in full compliance.
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||||||
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|
||||||
|
5. You are not required to accept this License, since you have not
|
||||||
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signed it. However, nothing else grants you permission to modify or
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||||||
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distribute the Program or its derivative works. These actions are
|
||||||
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prohibited by law if you do not accept this License. Therefore, by
|
||||||
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modifying or distributing the Program (or any work based on the
|
||||||
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Program), you indicate your acceptance of this License to do so, and
|
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all its terms and conditions for copying, distributing or modifying
|
||||||
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the Program or works based on it.
|
||||||
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|
||||||
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6. Each time you redistribute the Program (or any work based on the
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||||||
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Program), the recipient automatically receives a license from the
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original licensor to copy, distribute or modify the Program subject to
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these terms and conditions. You may not impose any further
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restrictions on the recipients' exercise of the rights granted herein.
|
||||||
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You are not responsible for enforcing compliance by third parties to
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this License.
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||||||
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|
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7. If, as a consequence of a court judgment or allegation of patent
|
||||||
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infringement or for any other reason (not limited to patent issues),
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||||||
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conditions are imposed on you (whether by court order, agreement or
|
||||||
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otherwise) that contradict the conditions of this License, they do not
|
||||||
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excuse you from the conditions of this License. If you cannot
|
||||||
|
distribute so as to satisfy simultaneously your obligations under this
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||||||
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License and any other pertinent obligations, then as a consequence you
|
||||||
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may not distribute the Program at all. For example, if a patent
|
||||||
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license would not permit royalty-free redistribution of the Program by
|
||||||
|
all those who receive copies directly or indirectly through you, then
|
||||||
|
the only way you could satisfy both it and this License would be to
|
||||||
|
refrain entirely from distribution of the Program.
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||||||
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|
||||||
|
If any portion of this section is held invalid or unenforceable under
|
||||||
|
any particular circumstance, the balance of the section is intended to
|
||||||
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apply and the section as a whole is intended to apply in other
|
||||||
|
circumstances.
|
||||||
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|
||||||
|
It is not the purpose of this section to induce you to infringe any
|
||||||
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patents or other property right claims or to contest validity of any
|
||||||
|
such claims; this section has the sole purpose of protecting the
|
||||||
|
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|
||||||
|
implemented by public license practices. Many people have made
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||||||
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|
||||||
|
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|
||||||
|
system; it is up to the author/donor to decide if he or she is willing
|
||||||
|
to distribute software through any other system and a licensee cannot
|
||||||
|
impose that choice.
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||||||
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|
||||||
|
This section is intended to make thoroughly clear what is believed to
|
||||||
|
be a consequence of the rest of this License.
|
||||||
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|
||||||
|
8. If the distribution and/or use of the Program is restricted in
|
||||||
|
certain countries either by patents or by copyrighted interfaces, the
|
||||||
|
original copyright holder who places the Program under this License
|
||||||
|
may add an explicit geographical distribution limitation excluding
|
||||||
|
those countries, so that distribution is permitted only in or among
|
||||||
|
countries not thus excluded. In such case, this License incorporates
|
||||||
|
the limitation as if written in the body of this License.
|
||||||
|
|
||||||
|
9. The Free Software Foundation may publish revised and/or new versions
|
||||||
|
of the 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.
|
||||||
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|
||||||
|
Each version is given a distinguishing version number. If the Program
|
||||||
|
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|
||||||
|
later version", you have the option of following the terms and conditions
|
||||||
|
either of that version or of any later version published by the Free
|
||||||
|
Software Foundation. If the Program does not specify a version number of
|
||||||
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this License, you may choose any version ever published by the Free Software
|
||||||
|
Foundation.
|
||||||
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|
||||||
|
10. If you wish to incorporate parts of the Program into other free
|
||||||
|
programs whose distribution conditions are different, write to the author
|
||||||
|
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|
||||||
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Software Foundation, write to the Free Software Foundation; we sometimes
|
||||||
|
make exceptions for this. Our decision will be guided by the two goals
|
||||||
|
of preserving the free status of all derivatives of our free software and
|
||||||
|
of promoting the sharing and reuse of software generally.
|
||||||
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|
||||||
|
NO WARRANTY
|
||||||
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|
||||||
|
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
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|
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
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OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
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|
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
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TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
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PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||||
|
REPAIR OR CORRECTION.
|
||||||
|
|
||||||
|
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
|
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||||
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INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
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TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
|
||||||
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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.
|
||||||
|
|
||||||
|
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
|
||||||
|
convey 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 General Public License as published by
|
||||||
|
the Free Software Foundation; either version 2 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 General Public License for more details.
|
||||||
|
|
||||||
|
You should have received a copy of the GNU General Public License along
|
||||||
|
with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
|
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||||
|
|
||||||
|
Also add information on how to contact you by electronic and paper mail.
|
||||||
|
|
||||||
|
If the program is interactive, make it output a short notice like this
|
||||||
|
when it starts in an interactive mode:
|
||||||
|
|
||||||
|
Gnomovision version 69, Copyright (C) year name of author
|
||||||
|
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
|
||||||
|
This is free software, and you are welcome to redistribute it
|
||||||
|
under certain conditions; type `show c' for details.
|
||||||
|
|
||||||
|
The hypothetical commands `show w' and `show c' should show the appropriate
|
||||||
|
parts of the General Public License. Of course, the commands you use may
|
||||||
|
be called something other than `show w' and `show c'; they could even be
|
||||||
|
mouse-clicks or menu items--whatever suits your program.
|
||||||
|
|
||||||
|
You should also get your employer (if you work as a programmer) or your
|
||||||
|
school, if any, to sign a "copyright disclaimer" for the program, if
|
||||||
|
necessary. Here is a sample; alter the names:
|
||||||
|
|
||||||
|
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
|
||||||
|
`Gnomovision' (which makes passes at compilers) written by James Hacker.
|
||||||
|
|
||||||
|
<signature of Ty Coon>, 1 April 1989
|
||||||
|
Ty Coon, President of Vice
|
||||||
|
|
||||||
|
This General Public License does not permit incorporating your program into
|
||||||
|
proprietary programs. If your program is a subroutine library, you may
|
||||||
|
consider it more useful to permit linking proprietary applications with the
|
||||||
|
library. If this is what you want to do, use the GNU Lesser General
|
||||||
|
Public License instead of this License.
|
||||||
29
README.md
Normal file
29
README.md
Normal file
@ -0,0 +1,29 @@
|
|||||||
|
# BZKF Real World Data Platform - Plausibilitätsprüfung
|
||||||
|
|
||||||
|
Anwendung zur Durchführung einer Plausibilitätsprüfung anhand der Daten für die BZKF Real World Data Platform.
|
||||||
|
|
||||||
|
## Aufbau der ETL-Strecke an den Standorten
|
||||||
|
|
||||||
|
Die Daten werden aus der Onkostar-Datenbank ausgelesen und in Apache-Kafka eingespeist.
|
||||||
|
Nach Durchlauf der ETL-Strecke wird das Ergebnis in einer CSV-Datei gespeichert.
|
||||||
|
Diese wird dann (aktuell) manuell in OPAL importiert.
|
||||||
|
|
||||||
|
```mermaid
|
||||||
|
flowchart LR
|
||||||
|
A[Database] --> B[Kafka-Connect]
|
||||||
|
B --> C[ADT to FHIR]
|
||||||
|
C --> D[fhir-pseudonymizer]
|
||||||
|
D --> E[obds-fhir-to-opal]
|
||||||
|
E -->|CSV-File| F[OPAL]
|
||||||
|
```
|
||||||
|
|
||||||
|
## Prüfung der Daten in der CSV-Datei
|
||||||
|
|
||||||
|
Vor Veröffentlichung der Daten der CSV-Datei in Opal kann die Anzahl der _Conditions_, gruppiert nach ICD-10 Gruppen,
|
||||||
|
mit dem Befehl `opal-file` aus der CSV-Datei gewonnen werden.
|
||||||
|
|
||||||
|
```
|
||||||
|
bzkf-rwdp-check opal-file --file <Opal-CSV-Datei>.csv
|
||||||
|
```
|
||||||
|
|
||||||
|
Die Anwendung gibt nun eine Liste der ICD-10-Gruppen mit Anzahl der _Conditions_ aus.
|
||||||
49
src/cli.rs
Normal file
49
src/cli.rs
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of bzkf-rwdp-check
|
||||||
|
*
|
||||||
|
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken and contributors.
|
||||||
|
*
|
||||||
|
* This program is free software; you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU General Public License as published by
|
||||||
|
* the Free Software Foundation; either version 2 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 General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU General Public License along
|
||||||
|
* with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
|
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||||
|
*/
|
||||||
|
|
||||||
|
use clap::{Parser, Subcommand};
|
||||||
|
|
||||||
|
#[derive(Parser)]
|
||||||
|
#[command(author, version, about)]
|
||||||
|
#[command(arg_required_else_help(true))]
|
||||||
|
pub struct Cli {
|
||||||
|
#[command(subcommand)]
|
||||||
|
pub cmd: SubCommand,
|
||||||
|
}
|
||||||
|
|
||||||
|
#[derive(Subcommand)]
|
||||||
|
pub enum SubCommand {
|
||||||
|
#[command(
|
||||||
|
about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL"
|
||||||
|
)]
|
||||||
|
OpalFile {
|
||||||
|
#[arg(short, long, help = "CSV-File für Opal")] file: String
|
||||||
|
},
|
||||||
|
#[command(
|
||||||
|
about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL"
|
||||||
|
)]
|
||||||
|
Database {
|
||||||
|
#[arg(long, help = "Datenbank-Host", default_value="localhost")] host: String,
|
||||||
|
#[arg(long, help = "Datenbank-Host", default_value="3306")] port: u16,
|
||||||
|
#[arg(long, help = "Benutzername")] user: String,
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
90
src/common.rs
Normal file
90
src/common.rs
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of bzkf-rwdp-check
|
||||||
|
*
|
||||||
|
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken and contributors.
|
||||||
|
*
|
||||||
|
* This program is free software; you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU General Public License as published by
|
||||||
|
* the Free Software Foundation; either version 2 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 General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU General Public License along
|
||||||
|
* with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
|
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||||
|
*/
|
||||||
|
|
||||||
|
use itertools::Itertools;
|
||||||
|
|
||||||
|
pub struct Icd10GroupSize {
|
||||||
|
pub name: String,
|
||||||
|
pub size: usize
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct Record {
|
||||||
|
pub condition_id: String,
|
||||||
|
pub icd10_code: String,
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct Check;
|
||||||
|
|
||||||
|
impl Check {
|
||||||
|
|
||||||
|
/// Collects all records by grouping by ICD10 group
|
||||||
|
pub fn collect(records: &[Record]) -> Result<Vec<Icd10GroupSize>, ()> {
|
||||||
|
let items = records.iter()
|
||||||
|
.map(|record| Record {
|
||||||
|
condition_id: record.condition_id.to_string(),
|
||||||
|
icd10_code: Self::map_icd_code(&record.icd10_code)
|
||||||
|
})
|
||||||
|
.sorted_by_key(|record| record.icd10_code.to_string())
|
||||||
|
.group_by(|record| record.icd10_code.to_string())
|
||||||
|
.into_iter()
|
||||||
|
.map(|(icd10, group)| (icd10, group.collect::<Vec<_>>()))
|
||||||
|
.map(|record| Icd10GroupSize {
|
||||||
|
name: record.0,
|
||||||
|
size: record.1.iter().count()
|
||||||
|
}).collect::<Vec<_>>();
|
||||||
|
|
||||||
|
Ok(items)
|
||||||
|
}
|
||||||
|
|
||||||
|
fn map_icd_code(code: &str) -> String {
|
||||||
|
let icd10 = match code {
|
||||||
|
"D39.1" | "D09.0" | "D41.4" => code,
|
||||||
|
_ => code.split('.').collect::<Vec<_>>().first().unwrap()
|
||||||
|
};
|
||||||
|
|
||||||
|
match icd10 {
|
||||||
|
"C00" | "C01" | "C02" | "C03" | "C04" | "C05" | "C06" | "C07" | "C08" | "C09" | "C10" | "C11" | "C12" | "C13" | "C14" => "C00-C14",
|
||||||
|
"C15" => "C15",
|
||||||
|
"C16" => "C16",
|
||||||
|
"C18" | "C19" | "C20" | "C21" => "C18-C21",
|
||||||
|
"C22" => "C22",
|
||||||
|
"C23" | "C24" => "C23-C24",
|
||||||
|
"C25" => "C25",
|
||||||
|
"C32" => "C32",
|
||||||
|
"C33" | "C34" => "C33-C34",
|
||||||
|
"C43" => "C43",
|
||||||
|
"C50" | "D05" => "C50, D05",
|
||||||
|
"C53" | "D06" => "C53, D06",
|
||||||
|
"C54" | "C55" => "C54-C55",
|
||||||
|
"C56" | "D39.1" => "C56, D39.1",
|
||||||
|
"C61" => "C61",
|
||||||
|
"C62" => "C62",
|
||||||
|
"C64" => "C64",
|
||||||
|
"C67" | "D09.0" | "D41.4" => "C67, D09.0, D41.4",
|
||||||
|
"C70" | "C71" | "C72" => "C70-C72",
|
||||||
|
"C73" => "C73",
|
||||||
|
"C81" => "C81",
|
||||||
|
"C82" | "C83" | "C84" | "C85" | "C86" | "C87" | "C88" | "C96" => "C82-C88, C96",
|
||||||
|
"C90" => "C90",
|
||||||
|
"C91" | "C92" | "C93" | "C94" | "C95" => "C91-C95",
|
||||||
|
_ => "Other"
|
||||||
|
}.to_string()
|
||||||
|
}
|
||||||
|
}
|
||||||
52
src/main.rs
Normal file
52
src/main.rs
Normal file
@ -0,0 +1,52 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of bzkf-rwdp-check
|
||||||
|
*
|
||||||
|
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken and contributors.
|
||||||
|
*
|
||||||
|
* This program is free software; you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU General Public License as published by
|
||||||
|
* the Free Software Foundation; either version 2 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 General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU General Public License along
|
||||||
|
* with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
|
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||||
|
*/
|
||||||
|
|
||||||
|
use std::error::Error;
|
||||||
|
use std::path::Path;
|
||||||
|
|
||||||
|
use clap::Parser;
|
||||||
|
use console::{style, Term};
|
||||||
|
|
||||||
|
use crate::cli::{Cli, SubCommand};
|
||||||
|
|
||||||
|
mod opal;
|
||||||
|
mod common;
|
||||||
|
mod cli;
|
||||||
|
|
||||||
|
fn main() -> Result<(), Box<dyn Error>> {
|
||||||
|
let term = Term::stdout();
|
||||||
|
|
||||||
|
match Cli::parse().cmd {
|
||||||
|
SubCommand::OpalFile { file } => {
|
||||||
|
let items = opal::OpalCsvFile::check(Path::new(&file))
|
||||||
|
.map_err(|_e| "Kann Datei nicht lesen")?;
|
||||||
|
|
||||||
|
let _ = term.write_line(&style("Anzahl der Conditions nach ICD-Gruppe").yellow().to_string());
|
||||||
|
items.iter().for_each(|item| {
|
||||||
|
let _ = term.write_line(&format!("{:<20}={:>6}", item.name, item.size));
|
||||||
|
});
|
||||||
|
},
|
||||||
|
SubCommand::Database { .. } => {
|
||||||
|
todo!("Not implemented yet")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
54
src/opal.rs
Normal file
54
src/opal.rs
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of bzkf-rwdp-check
|
||||||
|
*
|
||||||
|
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken and contributors.
|
||||||
|
*
|
||||||
|
* This program is free software; you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU General Public License as published by
|
||||||
|
* the Free Software Foundation; either version 2 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 General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU General Public License along
|
||||||
|
* with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
|
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||||
|
*/
|
||||||
|
|
||||||
|
use std::path::Path;
|
||||||
|
|
||||||
|
use csv::Reader;
|
||||||
|
use serde::Deserialize;
|
||||||
|
|
||||||
|
use crate::common::{Check, Icd10GroupSize, Record};
|
||||||
|
|
||||||
|
#[derive(Deserialize)]
|
||||||
|
pub struct OpalRecord {
|
||||||
|
#[serde(rename = "cond_id")]
|
||||||
|
cond_id: String,
|
||||||
|
#[serde(rename = "condcodingcode")]
|
||||||
|
cond_coding_code: String,
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct OpalCsvFile;
|
||||||
|
|
||||||
|
impl OpalCsvFile {
|
||||||
|
pub fn check(path: &Path) -> Result<Vec<Icd10GroupSize>, ()> {
|
||||||
|
let mut reader = Reader::from_path(path).expect("open file");
|
||||||
|
|
||||||
|
let items = reader.deserialize::<OpalRecord>()
|
||||||
|
.filter(|record| record.is_ok())
|
||||||
|
.map(|record| record.unwrap())
|
||||||
|
.map(|record| Record {
|
||||||
|
condition_id: record.cond_id,
|
||||||
|
icd10_code: record.cond_coding_code
|
||||||
|
})
|
||||||
|
.collect::<Vec<_>>();
|
||||||
|
|
||||||
|
Check::collect(&items)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
x
Reference in New Issue
Block a user