Remove null bytes from StudyInstanceUID and SeriesInstanceUID

src/helpers.rs

@@ -1,6 +1,8 @@
 use crate::errors::DicomTagReadError;
 use dicom::core::Tag;
 use dicom::object::DefaultDicomObject;
+use regex::Regex;
+use std::sync::OnceLock;
 
 /// Get the `&str` to a DICOM object.
 ///
@@ -13,3 +15,21 @@ pub(crate) fn tt(dcm: &DefaultDicomObject, tag: Tag) -> Result<&str, DicomTagRea
             .map_err(|error| DicomTagReadError::NotString { error, tag })
     })
 }
+
+pub(crate) fn tts(dcm: &DefaultDicomObject, tag: Tag) -> Result<String, DicomTagReadError> {
+    tt(dcm, tag).map(|s| s.replace('\0', ""))
+}
+
+/// Replace disallowed characters with "_".
+/// https://github.com/FNNDSC/pypx/blob/7619c15f4d2303d6d5ca7c255d81d06c7ab8682b/pypx/repack.py#L424
+///
+/// Also, it's necessary to handle NUL bytes...
+pub(crate) fn sanitize<S: AsRef<str>>(s: S) -> String {
+    let s_nonull = s.as_ref().replace('\0', "");
+    VALID_CHARS_RE
+        .get_or_init(|| Regex::new(r#"[^A-Za-z0-9\.\-]+"#).unwrap())
+        .replace_all(&s_nonull, "_")
+        .to_string()
+}
+
+static VALID_CHARS_RE: OnceLock<Regex> = OnceLock::new();

src/log_models.rs

@@ -64,7 +64,7 @@ impl<'a> StudyDataMeta<'a> {
             PatientID: e.PatientID,
             StudyDescription: e.StudyDescription,
             StudyDate: e.StudyDate,
-            StudyInstanceUID: e.StudyInstanceUID,
+            StudyInstanceUID: &e.StudyInstanceUID,
             PerformedStationAETitle: tt(&d, tags::PERFORMED_STATION_AE_TITLE).unwrap_or(""),
         };
         Ok(data)
@@ -195,8 +195,8 @@ impl<'a> SeriesDataMeta<'a> {
     ) -> Result<Self, DicomTagReadError> {
         let data = Self {
             PatientID: e.PatientID,
-            StudyInstanceUID: e.StudyInstanceUID,
-            SeriesInstanceUID: e.SeriesInstanceUID,
+            StudyInstanceUID: &e.StudyInstanceUID,
+            SeriesInstanceUID: &e.SeriesInstanceUID,
             SeriesDescription: e.SeriesDescription,
             SeriesNumber: e.SeriesNumber.clone(),
             SeriesDate: e.StudyDate,

src/log_write.rs

@@ -48,7 +48,7 @@ pub(crate) fn write_logs(
             unpack.dir.to_string(),
             &dcm,
         )?;
-        let data: HashMap<_, _> = [(elements.StudyInstanceUID, study_series_meta)].into();
+        let data: HashMap<_, _> = [(&elements.StudyInstanceUID, study_series_meta)].into();
         write_json(data, study_series_meta_fname)?;
     }
 

src/pack_path.rs

@@ -1,12 +1,9 @@
 //! Functions for deciding where to copy the received DICOM to.
 use crate::errors::DicomTagReadError;
-use crate::helpers::tt;
+use crate::helpers::{sanitize, tt, tts};
 use camino::{Utf8Path, Utf8PathBuf};
 use dicom::dictionary_std::tags;
 use dicom::object::DefaultDicomObject;
-use regex::Regex;
-
-use std::sync::OnceLock;
 
 /// Destination directory and file name for the DICOM file.
 pub(crate) struct PypxPath {
@@ -63,8 +60,8 @@ pub(crate) struct PypxPathElements<'a> {
     pub SeriesDescription: &'a str,
 
     // these are not part of the path name, but used in the log path names.
-    pub StudyInstanceUID: &'a str,
-    pub SeriesInstanceUID: &'a str,
+    pub StudyInstanceUID: String,
+    pub SeriesInstanceUID: String,
 }
 
 impl<'a> TryFrom<&'a DefaultDicomObject> for PypxPathElements<'a> {
@@ -84,23 +81,9 @@ impl<'a> TryFrom<&'a DefaultDicomObject> for PypxPathElements<'a> {
             StudyDate: tt(&dcm, tags::STUDY_DATE)?,
             SeriesNumber: tt(&dcm, tags::SERIES_NUMBER)?.parse()?,
             SeriesDescription: tt(&dcm, tags::SERIES_DESCRIPTION)?,
-            StudyInstanceUID: tt(&dcm, tags::STUDY_INSTANCE_UID)?,
-            SeriesInstanceUID: tt(&dcm, tags::SERIES_INSTANCE_UID)?,
+            StudyInstanceUID: tts(&dcm, tags::STUDY_INSTANCE_UID)?,
+            SeriesInstanceUID: tts(&dcm, tags::SERIES_INSTANCE_UID)?,
         };
         Ok(data)
     }
 }
-
-/// Replace disallowed characters with "_".
-/// https://github.com/FNNDSC/pypx/blob/7619c15f4d2303d6d5ca7c255d81d06c7ab8682b/pypx/repack.py#L424
-///
-/// Also, it's necessary to handle NUL bytes...
-fn sanitize<S: AsRef<str>>(s: S) -> String {
-    let s_nonull = s.as_ref().replace('\0', "");
-    VALID_CHARS_RE
-        .get_or_init(|| Regex::new(r#"[^A-Za-z0-9\.\-]+"#).unwrap())
-        .replace_all(&s_nonull, "_")
-        .to_string()
-}
-
-static VALID_CHARS_RE: OnceLock<Regex> = OnceLock::new();