Merge pull request #7 from Australian-Imaging-Service/develop

Bug fixes for TBP workflow
Australian-Imaging-Service · Apr 16, 2024 · 9d3a5f7 · 9d3a5f7
2 parents df0faff + b8401f0
commit 9d3a5f7
Show file tree

Hide file tree

Showing 3 changed files with 28 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -6,8 +6,14 @@ RUN apt-get update && apt-get install -y \
   wget \
   git \
   mrtrix3 \
+  curl \
+  zip \
   && rm -rf /var/lib/apt/lists/*
 
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" \
+  && unzip awscliv2.zip \
+  && ./aws/install
+
 # Add application code
 ADD . /app
 

diff --git a/xnat_ingest/cli/transfer.py b/xnat_ingest/cli/transfer.py
@@ -194,7 +194,7 @@ def transfer(
             ):
                 if session_dir.name.startswith("UNKNOWN"):
                     logger.error(
-                        "Session % in subject %s in project %s is not recognised and "
+                        "Session %s in subject %s in project %s is not recognised and "
                         "will not be transferred, please rename manually and transfer again",
                         session_dir.name,
                         subject_dir.name,

diff --git a/xnat_ingest/session.py b/xnat_ingest/session.py
@@ -281,19 +281,28 @@ def from_dicoms(
         for session_dicom_series in dicom_sessions.values():
 
             def get_id(field):
-                ids = set(s.metadata[field.keyword] for s in session_dicom_series)
-                if len(ids) > 1:
-                    raise DicomParseError(
-                        f"Multiple values for '{field}' tag found across scans in session: "
-                        f"{session_dicom_series}"
-                    )
-                id_ = next(iter(ids))
-                if isinstance(id_, list):
-                    raise DicomParseError(
-                        f"Multiple values for '{field}' tag found within scans in session: "
-                        f"{session_dicom_series}"
+                ids = set(s.metadata.get(field.keyword) for s in session_dicom_series)
+                ids.discard(None)
+                if ids:
+                    if len(ids) > 1:
+                        raise DicomParseError(
+                            f"Multiple values for '{field}' tag found across scans in session: "
+                            f"{session_dicom_series}"
+                        )
+                    id_ = next(iter(ids))
+                    if isinstance(id_, list):
+                        raise DicomParseError(
+                            f"Multiple values for '{field}' tag found within scans in session: "
+                            f"{session_dicom_series}"
+                        )
+                    id_ = cls.id_escape_re.sub("", id_)
+                else:
+                    logger.warning(
+                        "Did not find %s field in DICOM series %s",
+                        field.keyword,
+                        session_dicom_series,
                     )
-                id_ = cls.id_escape_re.sub("", id_)
+                    id_ = None
                 if not id_:
                     id_ = "UNKNOWN" + "".join(
                         random.choices(string.ascii_letters + string.digits, k=8)