From 0037e6c8bb2cdb24ed83612df231e73354f42ef3 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Fri, 23 Feb 2024 12:47:37 +0100 Subject: [PATCH] Initial commit --- .gitignore | 5 + Cargo.toml | 14 +++ LICENSE | 339 ++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 29 +++++ src/cli.rs | 49 ++++++++ src/common.rs | 90 ++++++++++++++ src/main.rs | 52 ++++++++ src/opal.rs | 54 ++++++++ 8 files changed, 632 insertions(+) create mode 100644 .gitignore create mode 100644 Cargo.toml create mode 100644 LICENSE create mode 100644 README.md create mode 100644 src/cli.rs create mode 100644 src/common.rs create mode 100644 src/main.rs create mode 100644 src/opal.rs diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e87dd5f --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.idea/ +target/ + +*.iml +*.lock \ No newline at end of file diff --git a/Cargo.toml b/Cargo.toml new file mode 100644 index 0000000..9f5a36a --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,14 @@ +[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"] } + diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d159169 --- /dev/null +++ b/LICENSE @@ -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. + + 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. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + + We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + + Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + + Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + + The precise terms and conditions for copying, distribution and +modification follow. + + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + 0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not +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 +Program (independent of having been made by running the Program). +Whether that is true depends on what the Program does. + + 1. You may copy and distribute 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 and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. You may modify your copy or copies of the Program or any portion +of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 +above, provided that you also meet all of these conditions: + + a) You must cause the modified files to carry prominent notices + stating that you changed the files and the date of any change. + + b) You must cause any work that you distribute or publish, that in + whole or in part contains or is derived from the Program or any + part thereof, to be licensed as a whole at no charge to all third + parties under the terms of this License. + + c) If the modified program normally reads commands interactively + when run, you must cause it, when started running for such + interactive use in the most ordinary way, to print or display an + announcement including an appropriate copyright notice and a + notice that there is no warranty (or else, saying that you provide + a warranty) and that users may redistribute the program under + these conditions, and telling the user how to view a copy of this + License. (Exception: if the Program itself is interactive but + does not normally print such an announcement, your work based on + the Program is not required to print an announcement.) + +These requirements apply to the modified work as a whole. If +identifiable sections of that work are not derived from the Program, +and can be reasonably considered independent and separate works in +themselves, then this License, and its terms, do not apply to those +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 +this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest +your rights to work written entirely by you; rather, the intent is to +exercise the right to control the distribution of derivative or +collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program +with the Program (or with a work based on the Program) on a volume of +a storage or distribution medium does not bring the other work under +the scope of this License. + + 3. You may copy and distribute the Program (or a work based on it, +under Section 2) in object code or executable form under the terms of +Sections 1 and 2 above provided that you also do one of the following: + + a) Accompany it with the complete corresponding machine-readable + source code, which must be distributed under the terms of Sections + 1 and 2 above on a medium customarily used for software interchange; or, + + 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 + cost of physically performing source distribution, a complete + machine-readable copy of the corresponding source code, to be + distributed under the terms of Sections 1 and 2 above on a medium + customarily used for software interchange; or, + + c) Accompany it with the information you received as to the offer + to distribute corresponding source code. (This alternative is + allowed only for noncommercial distribution and only if you + received the program in object code or executable form with such + an offer, in accord with Subsection b above.) + +The source code for a work means the preferred form of the work for +making modifications to it. For an executable work, complete source +code means all the source code for all modules it contains, plus any +associated interface definition files, plus the scripts used to +control compilation and installation of the executable. However, as a +special exception, the source code distributed need not include +anything that is normally distributed (in either source or binary +form) with the major components (compiler, kernel, and so on) of the +operating system on which the executable runs, unless that component +itself accompanies the executable. + +If distribution of executable or object code is made by offering +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 +compelled to copy the source along with the object code. + + 4. You may not copy, modify, sublicense, or distribute the Program +except as expressly provided under this License. Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + + 5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + 6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + + 7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +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 +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +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. + +If any portion of this section is held invalid or unenforceable under +any particular circumstance, the balance of the section is intended to +apply and the section as a whole is intended to apply in other +circumstances. + +It is not the purpose of this section to induce you to infringe any +patents or other property right claims or to contest validity of any +such claims; this section has the sole purpose of protecting the +integrity of the free software distribution system, which is +implemented by public license practices. Many people have made +generous contributions to the wide range of software distributed +through that system in reliance on consistent application of that +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. + +This section is intended to make thoroughly clear what is believed to +be a consequence of the rest of this License. + + 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. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +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 +this License, you may choose any version ever published by the Free Software +Foundation. + + 10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +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. + + NO WARRANTY + + 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, 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. + + 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 +REDISTRIBUTE 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. + + 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. + + + Copyright (C) + + 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. + + , 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. diff --git a/README.md b/README.md new file mode 100644 index 0000000..c0b9430 --- /dev/null +++ b/README.md @@ -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 .csv +``` + +Die Anwendung gibt nun eine Liste der ICD-10-Gruppen mit Anzahl der _Conditions_ aus. \ No newline at end of file diff --git a/src/cli.rs b/src/cli.rs new file mode 100644 index 0000000..8129b84 --- /dev/null +++ b/src/cli.rs @@ -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, + } + + +} \ No newline at end of file diff --git a/src/common.rs b/src/common.rs new file mode 100644 index 0000000..74dd1db --- /dev/null +++ b/src/common.rs @@ -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, ()> { + 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::>())) + .map(|record| Icd10GroupSize { + name: record.0, + size: record.1.iter().count() + }).collect::>(); + + Ok(items) + } + + fn map_icd_code(code: &str) -> String { + let icd10 = match code { + "D39.1" | "D09.0" | "D41.4" => code, + _ => code.split('.').collect::>().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() + } +} diff --git a/src/main.rs b/src/main.rs new file mode 100644 index 0000000..f1c6e99 --- /dev/null +++ b/src/main.rs @@ -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> { + 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(()) +} diff --git a/src/opal.rs b/src/opal.rs new file mode 100644 index 0000000..2e5a18b --- /dev/null +++ b/src/opal.rs @@ -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, ()> { + let mut reader = Reader::from_path(path).expect("open file"); + + let items = reader.deserialize::() + .filter(|record| record.is_ok()) + .map(|record| record.unwrap()) + .map(|record| Record { + condition_id: record.cond_id, + icd10_code: record.cond_coding_code + }) + .collect::>(); + + Check::collect(&items) + } + +} \ No newline at end of file