Call parsing function. Fix a few issues.

* qc_app/entry.py: Pass filetype onward to parsing endpoint
* qc_app/parse.py: Call the function(s) necessary to parse a file
* quality_control/errors.py: Fix argument passing to super class

3 files changed, 61 insertions, 14 deletions

diff --git a/qc_app/entry.py b/qc_app/entry.py
index e7ed294..31d64ca 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -11,8 +11,6 @@ from flask import (
     render_template,
     current_app as app)
 
-from quality_control.parsing import FileType
-
 entrybp = Blueprint("entry", __name__)
 
 @entrybp.route("/", methods=["GET", "POST"])
@@ -40,12 +38,11 @@ def upload_file():
     if errors:
         return render_template("index.html")
 
-    filetype = (
-        FileType.AVERAGE if request.form["filetype"] == "average"
-        else FileType.STANDARD_ERROR)
     filename = secure_filename(text_file.filename)
     if not os.path.exists(app.config["UPLOAD_FOLDER"]):
         os.mkdir(app.config["UPLOAD_FOLDER"])
     text_file.save(os.path.join(app.config["UPLOAD_FOLDER"], filename))
 
-    return redirect(url_for("parse.parse_file", filename=filename))
+    return redirect(url_for(
+        "parse.parse", filename=filename,
+        filetype=request.form["filetype"]))
diff --git a/qc_app/parse.py b/qc_app/parse.py
index 1d9e3c8..aa88260 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -1,14 +1,64 @@
 """File parsing module"""
-from flask import Blueprint
+import os
+
+from flask import request, url_for, redirect, Blueprint, current_app as app
+
+from quality_control.errors import ParseError
+from quality_control.parsing import (
+    FileType,
+    parse_file,
+    strain_names,
+    parse_strains)
 
 parsebp = Blueprint("parse", __name__)
 
-@parsebp.route("/parse/<filename>", methods=["GET"])
-def parse_file(filename):
+@parsebp.route("/parse", methods=["GET"])
+def parse():
     """Trigger file parsing"""
-    return f"STUB: Parse of '{filename}' ongoing!!!"
+    # TODO: figure out how to redirect with post
+    # TODO: figure out how to stat file and get: total number of lines
+    # TODO: Maybe implement external process to parse the files
+    errors = False
+    filename = request.args.get("filename")
+    filetype = request.args.get("filetype")
+    if filename is None:
+        flash("No file provided", "alert-error")
+        errors = True
+
+    if filetype is None:
+        flash("No filetype provided", "alert-error")
+        errors = True
+
+    filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
+    if not os.path.exists(filepath):
+        flash("Selected file does not exist (any longer)", "alert-danger")
+        errors = True
+
+    if errors:
+        return redirect(url_for("entry.index"))
+
+    filetype = (
+        FileType.AVERAGE if filetype == "average" else FileType.STANDARD_ERROR)
+    try:
+        parsed = parse_file(
+            filepath, filetype, strain_names(parse_strains("strains.csv")))
+        for line in parsed:
+            pass
+        os.remove(filepath)
+        return redirect(url_for(
+            "parse.success", filename=filename, filetype=filetype))
+    except ParseError as pe:
+        pe_dict = pe.args[0]
+        return redirect(url_for(
+            "parse.fail", filename = filename, filetype = filetype,
+            position = pe_dict["position"]))
 
 @parsebp.route("/success", methods=["GET"])
 def success():
     """Indicates success if parsing the file is successful"""
     return "STUB: Parse success!!!"
+
+@parsebp.route("/fail", methods=["GET"])
+def fail():
+    """Indicates success if parsing the file is successful"""
+    return "STUB: Parse Failure!!!"
diff --git a/quality_control/errors.py b/quality_control/errors.py
index 0802159..29a38f9 100644
--- a/quality_control/errors.py
+++ b/quality_control/errors.py
@@ -4,21 +4,21 @@ class InvalidCellValue(Exception):
     """Raised when a function encounters an invalid value"""
 
     def __init__(self, *args):
-        super().__init__(self, *args)
+        super().__init__(*args)
 
 class InvalidHeaderValue(Exception):
     """Raised when a header contains values not in the reference file."""
 
     def __init__(self, *args):
-        super().__init__(self, *args)
+        super().__init__(*args)
 
 class DuplicateHeader(Exception):
     """Raised when a header contains 2 similar headers."""
 
     def __init__(self, *args):
-        super().__init__(self, *args)
+        super().__init__(*args)
 
 class ParseError(Exception):
     """Raised if any of the above exceptions are raised"""
     def __init__(self, *args):
-        super().__init__(self, *args)
+        super().__init__(*args)