From 61f9832dd7fb73ac4f8f94d030d5875f21467938 Mon Sep 17 00:00:00 2001
From: Jennings Zhang <jenni_zh@protonmail.com>
Date: Sat, 15 Jul 2023 04:27:28 -0400
Subject: [PATCH] px-recount

---
 .gitignore             |    2 +
 px-recount/.gitignore  |    1 +
 px-recount/Cargo.lock  | 1173 ++++++++++++++++++++++++++++++++++++++++
 px-recount/Cargo.toml  |   13 +
 px-recount/README.md   |    3 +
 px-recount/src/main.rs |  207 +++++++
 6 files changed, 1399 insertions(+)
 create mode 100644 px-recount/.gitignore
 create mode 100644 px-recount/Cargo.lock
 create mode 100644 px-recount/Cargo.toml
 create mode 100644 px-recount/README.md
 create mode 100644 px-recount/src/main.rs

diff --git a/.gitignore b/.gitignore
index 0d327a6..b4840f9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
+.idea
+
 # Compiled python modules.
 *.pyc
 
diff --git a/px-recount/.gitignore b/px-recount/.gitignore
new file mode 100644
index 0000000..c41cc9e
--- /dev/null
+++ b/px-recount/.gitignore
@@ -0,0 +1 @@
+/target
\ No newline at end of file
diff --git a/px-recount/Cargo.lock b/px-recount/Cargo.lock
new file mode 100644
index 0000000..904b73e
--- /dev/null
+++ b/px-recount/Cargo.lock
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diff --git a/px-recount/Cargo.toml b/px-recount/Cargo.toml
new file mode 100644
index 0000000..6fd4b36
--- /dev/null
+++ b/px-recount/Cargo.toml
@@ -0,0 +1,13 @@
+[package]
+name = "px-recount"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+anyhow = "1.0.71"
+dicom = "0.5.4"
+redis = "0.23.0"
+redis-derive = "0.1.7"
+time = { version = "0.3.23", features = ["formatting"] }
diff --git a/px-recount/README.md b/px-recount/README.md
new file mode 100644
index 0000000..06b0ad2
--- /dev/null
+++ b/px-recount/README.md
@@ -0,0 +1,3 @@
+
+Before PACS retrieve, `px-find` will write `NumberOfSeriesRelatedInstances` to
+`/home/dicom/log/NumberOfSeriesRelatedInstances/<SeriesInstanceUID>.txt`
diff --git a/px-recount/src/main.rs b/px-recount/src/main.rs
new file mode 100644
index 0000000..ee82ed4
--- /dev/null
+++ b/px-recount/src/main.rs
@@ -0,0 +1,207 @@
+use anyhow::Context;
+use std::path::Path;
+use std::process::{Command, ExitStatus};
+
+extern crate redis;
+use redis::Commands;
+use redis_derive::{FromRedisValue, ToRedisArgs};
+
+const HELP: &str = "px-recount: conditionally runs px-repack
+
+px-recount has the same command-line options as px-repack.
+Its intended usage is as a DICOM instance handler called by storescp:
+
+    storescp --fork -od /tmp/data -pm -sp -xcr 'px-recount --xcrdir \"#p\" --xcrfile \"#f\" --verbosity 0 --logdir /home/dicom/log --datadir /home/dicom/data --cleanup' 11113
+
+px-recount runs px-repack if the received DICOM file given by --xcrdir
+and --xcrfile is the last of its series. The number of files of a
+series received so far are counted by px-repack and saved to a Redis
+database.
+
+
+ENVIRONMENT VARIABLES
+
+    PYPX_REDIS_URL    Redis connection URL (example: redis://redis-server.svc.local:6379)
+
+
+NOTES
+
+- It is expected that px-find writes NumberOfSeriesRelatedInstances for
+  the series before px-recount runs. This is typically achieved by running
+  px-find --reallyEfficient --then receive ...
+- Generally, px-recount is fail-safe. It will call px-repack in the event
+  of any redis-related exceptions.
+
+";
+
+fn main() -> anyhow::Result<()> {
+    let args: Vec<String> = std::env::args().collect();
+    if args.iter().any(|a| a == "-h" || a.ends_with("-help")) {
+        println!("{}", HELP);
+        return anyhow::Ok(());
+    }
+    let (xcrdir, xcrfile) =
+        get_xcr_args(&args).context("arguments --xcrdir and --xcrfile must be given.")?;
+
+    let xcrdir = Path::new(xcrdir);
+    let xcrfile = xcrdir.join(xcrfile);
+
+    match increment_counter(&xcrfile) {
+        Ok(is_last) => {
+            // last DICOM file of its series, call px-repack on entire directory
+            if is_last {
+                repack_all(&args)?;
+            }
+            // else: series is not done being received, do nothing
+        }
+        Err(e) => {
+            // something went wrong -- print error and call px-repack on just this one file
+            eprintln!("{:?}", e);
+            repack_one(&args)?;
+            // TODO here we could do a "rescue" operation:
+            // Since the series is broken anyways, we could call repack_all(args)
+            // (will need to use a lock to prevent data race)
+        }
+    }
+    anyhow::Ok(())
+}
+
+/// Call px-repack with the same arguments.
+fn repack_one(args: &[String]) -> std::io::Result<ExitStatus> {
+    Command::new("px-repack").args(&args[1..]).spawn()?.wait()
+}
+
+/// Call px-repack with the same arguments, but replacing the
+/// arguments `--xcrfile MR_XXXXXX` with `--parseAllFilesWithSubStr ,`
+fn repack_all(args: &[String]) -> std::io::Result<ExitStatus> {
+    let mut prev = "";
+    let mut cmd = Command::new("px-repack");
+    for arg in &args[1..] {
+        if arg == "--xcrfile" {
+            cmd.arg("--parseAllFilesWithSubStr");
+        } else if prev == "--xcrfile" {
+            cmd.arg(",");
+        } else {
+            cmd.arg(arg);
+        }
+        prev = arg;
+    }
+    cmd.spawn()?.wait()
+}
+
+/// manual command-line argument parsing for ultra efficiency!
+fn get_xcr_args(args: &[String]) -> Option<(&String, &String)> {
+    let mut xcrdir = None;
+    let mut xcrfile = None;
+    let mut iter = args.iter();
+    let mut prev = iter.next()?;
+
+    for cur in iter {
+        if prev == "--xcrdir" {
+            xcrdir = Some(cur)
+        } else if prev == "--xcrfile" {
+            xcrfile = Some(cur)
+        }
+        prev = cur
+    }
+    xcrdir.zip(xcrfile)
+}
+
+/// Check Redis to see how many files of this series we've previously pulled.
+/// If the given file is the last of its series, delete its hset from Redis
+/// then return true. Otherwise, increment the counter in Redis and return false.
+fn increment_counter(dcm: &Path) -> anyhow::Result<bool> {
+    let series_key =
+        series_key_of(dcm).with_context(|| format!("Could not read DICOM tags of {:?}", &dcm))?;
+
+    let mut client = redis::Client::open(get_redis_url()?)?;
+
+    let is_last = redis::transaction(&mut client, &[&series_key], |con, pipe| {
+        let data: ReData = con.hgetall(&series_key)?;
+        let new_count = data.fileCounter + 1;
+        let status = if new_count == data.NumberOfSeriesRelatedInstances {
+            pipe.del(&series_key).ignore();
+            FileStatus::Last
+        } else {
+            pipe.hset(&series_key, "fileCounter", new_count)
+                .ignore()
+                .hset(&series_key, "lastUpdate", now_iso8901())
+                .ignore();
+            if new_count > data.NumberOfSeriesRelatedInstances {
+                let error = format!(
+                    "Received too many files for series. \
+                    !!!SOMETHING IS VERY WRONG!!! \
+                    key={} {:?}",
+                    &series_key, &data
+                );
+                FileStatus::Exception(error)
+            } else {
+                FileStatus::NotLast
+            }
+        };
+        pipe.query(con).map(|_: Option<()>| Some(status))
+    })?;
+    is_last.into_result()
+}
+
+/// Get the redis key name for a DICOM file.
+///
+/// Equivalent implementation of:
+/// https://github.com/FNNDSC/pypx/blob/f98282d1e7cdaa1e56ff4e05cb560e8d1c5aefef/pypx/find.py#L574-L575
+fn series_key_of(dicom_file: &Path) -> anyhow::Result<String> {
+    let dcm = dicom::object::open_file(dicom_file)?;
+    let study = dcm
+        .element(dicom::dictionary_std::tags::STUDY_INSTANCE_UID)?
+        .to_str()?;
+    let series = dcm
+        .element(dicom::dictionary_std::tags::SERIES_INSTANCE_UID)?
+        .to_str()?;
+    let key = format!("series:{study}/{series}");
+    Ok(key)
+}
+
+/// Gets the value of the environment variable `PYPX_REDIS_URL`.
+/// If not present, returns "redis://127.0.0.1/" by default.
+fn get_redis_url() -> anyhow::Result<String> {
+    match std::env::var("PYPX_REDIS_URL") {
+        Ok(url) => anyhow::Ok(url),
+        Err(e) => match e {
+            std::env::VarError::NotPresent => anyhow::Ok("redis://127.0.0.1/".to_string()),
+            std::env::VarError::NotUnicode(_) => Err(anyhow::Error::msg(
+                "Value of PYPX_REDIS_URL is not unicode.",
+            )),
+        },
+    }
+}
+
+/// Returns a ISO8601 timestamp.
+fn now_iso8901() -> String {
+    time::OffsetDateTime::now_utc()
+        .format(&time::format_description::well_known::Iso8601::DEFAULT)
+        .unwrap()
+}
+
+#[allow(non_snake_case)]
+#[derive(Debug, FromRedisValue, ToRedisArgs, PartialEq)]
+struct ReData {
+    fileCounter: u32,
+    NumberOfSeriesRelatedInstances: u32,
+    lastUpdate: String,
+}
+
+#[derive(Debug, PartialEq)]
+enum FileStatus {
+    Last,
+    NotLast,
+    Exception(String),
+}
+
+impl FileStatus {
+    fn into_result(self) -> anyhow::Result<bool> {
+        match self {
+            FileStatus::Last => anyhow::Ok(true),
+            FileStatus::NotLast => anyhow::Ok(false),
+            FileStatus::Exception(e) => Err(anyhow::Error::msg(e)),
+        }
+    }
+}