Do general bundle validation and show errors

* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
  `missing_files`

6 files changed, 26 insertions, 30 deletions

diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
index 6491e6b..64fcdcd 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -1,5 +1,5 @@
 {%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%from "flash_messages.html" import flash_all_messages%}
 
 {%block title%}Upload R/qtl2 Bundle{%endblock%}
 
@@ -16,12 +16,12 @@
   <input type="hidden" name="population_id"
 	 value="{{population.InbredSetId}}" />
 
-  {{flash_messages("error-rqtl2")}}
+  {{flash_all_messages()}}
 
   <fieldset>
     <legend>file upload</legend>
     <label for="file:rqtl2-bundle">R/qtl2 bundle</label>
-    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle"
+    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle_file"
 	   accept="application/zip, .zip"
 	   required="required" />
     <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
index 9269a3c..01721e9 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -1,5 +1,5 @@
 {%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%from "flash_messages.html" import flash_all_messages%}
 
 {%block title%}Upload R/qtl2 Bundle{%endblock%}
 
@@ -20,6 +20,7 @@
 	      population_id=population.InbredSetId)}}"
       method="POST"
       enctype="multipart/form-data">
+  {{flash_all_messages()}}
   <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
   <input type="hidden" name="population_id"
 	 value="{{population.InbredSetId}}" />
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index eea49e1..2d032f8 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -18,6 +18,8 @@ from flask import (
     current_app as app)
 
 from r_qtl import r_qtl2
+from r_qtl import errors as rqe
+from r_qtl import r_qtl2_qc as rqc
 from r_qtl.errors import InvalidFormat
 
 from qc_app import jobs
@@ -157,11 +159,11 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
                                    species=species,
                                    population=population)
 
-        if not bool(request.files.get("rqtl2_bundle")):
+        if not bool(request.files.get("rqtl2_bundle_file")):
             raise __RequestError__("No R/qtl2 zip bundle provided.")
 
-        the_file = save_file(
-            request.files["rqtl2_bundle"], Path(app.config["UPLOAD_FOLDER"]))
+        the_file = save_file(request.files["rqtl2_bundle_file"],
+                             Path(app.config["UPLOAD_FOLDER"]))
         if not bool(the_file):
             raise __RequestError__("Please provide a valid R/qtl2 zip bundle.")
 
@@ -170,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
 
         try:
             with ZipFile(str(the_file), "r") as zfile:
-                r_qtl2.validate_bundle(zfile)
+                rqc.validate_bundle(zfile)
                 return render_template(
                     "rqtl2/upload-rqtl2-bundle-step-02.html",
                     species=species,
diff --git a/r_qtl/errors.py b/r_qtl/errors.py
index 20c5ced..417eb58 100644
--- a/r_qtl/errors.py
+++ b/r_qtl/errors.py
@@ -5,3 +5,9 @@ class RQTLError(Exception):
 
 class InvalidFormat(RQTLError):
     """Raised when the format of the file(s) is invalid."""
+
+class MissingFileError(InvalidFormat):
+    """
+    Raise when at least one file listed in the control file is missing from the
+    R/qtl2 bundle.
+    """
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index c2828d2..f8c08d9 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -288,28 +288,6 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
             key: chain(value, partial(replace_sex_info, cdata=cdata))
             for key, value in row.items() if key not in ci_fields}
 
-def validate_bundle(zfile: ZipFile):
-    """Ensure the R/qtl2 bundle is valid."""
-    cdata = control_data(zfile)
-    def __member_exists_p__(zfile, member):
-        if isinstance(member, str):
-            zfile.getinfo(member)
-        else:
-            for inner in member:
-                zfile.getinfo(inner)
-
-    try:
-        for member in (key for key in cdata.keys() if key in __FILE_TYPES__):
-            __member_exists_p__(zfile, cdata[member])
-
-        if "file" in cdata.get("sex", {}):
-            __member_exists_p__(zfile, cdata["sex"]["file"])
-
-        if "file" in cdata.get("cross_info", {}):
-            __member_exists_p__(zfile, cdata["cross_info"]["file"])
-    except KeyError as kerr:
-        raise InvalidFormat(*kerr.args) from kerr
-
 def genotype_data(zfile: ZipFile):
     """Convenience function to genotype data from R/qtl2 bundle."""
     cdata = control_data(zfile)
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index f666f40..261d300 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -3,6 +3,7 @@ from zipfile import ZipFile
 from functools import reduce
 from typing import Union, Sequence
 
+from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl.r_qtl2 import __FILE_TYPES__
 
@@ -45,3 +46,11 @@ def missing_files(zfile: ZipFile) -> tuple[str]:
 
     return tuple(filter(__missing_p__,
                         bundle_files_list(zfile, rqtl2.control_data(zfile))))
+
+def validate_bundle(zfile: ZipFile):
+    """Ensure the R/qtl2 bundle is valid."""
+    missing = missing_files(zfile)
+    if len(missing) > 0:
+        raise rqe.MissingFileError(
+                        "The following files do not exist in the bundle: " +
+                        ", ".join(missing))