From fa410aa2d6d4355115855f6047770d4384175b02 Mon Sep 17 00:00:00 2001
From: greg <ghv2@psu.edu>
Date: Mon, 21 Nov 2022 09:18:36 -0500
Subject: [PATCH] Review fixes

---
 lib/galaxy/datatypes/registry.py |  3 --
 lib/galaxy/datatypes/tabular.py  | 83 +++++++-------------------------
 2 files changed, 18 insertions(+), 68 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 4fa5b3d9e27..746761d9a74 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -711,7 +711,6 @@ class Registry:
                 "customtrack": interval.CustomTrack(),
                 "csfasta": sequence.csFasta(),
                 "fasta": sequence.Fasta(),
-                "psl": tabular.Psl(),
                 "eland": tabular.Eland(),
                 "fastq": sequence.Fastq(),
                 "fastqsanger": sequence.FastqSanger(),
@@ -760,7 +759,6 @@ class Registry:
                 "maf": "text/plain",
                 "memexml": "application/xml",
                 "pileup": "text/plain",
-                "psl": "text/plain",
                 "qualsolid": "text/plain",
                 "qualsolexa": "text/plain",
                 "qual454": "text/plain",
@@ -805,7 +803,6 @@ class Registry:
                 interval.Gff(),
                 interval.Gff3(),
                 tabular.Pileup(),
-                tabular.Psl(),
                 interval.Interval(),
                 tabular.Sam(),
                 tabular.Eland(),
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 473576da9fe..4c38d82dc51 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -1817,10 +1817,6 @@ class Psl(Tabular):
             "tStarts",
         ]
 
-    def display_peek(self, dataset):
-        """Returns formated html of peek"""
-        return self.make_html_table(dataset, column_names=self.column_names)
-
     def sniff_prefix(self, file_prefix: FilePrefix):
         """
         PSL lines represent alignments, and are typically generated
@@ -1862,6 +1858,11 @@ class Psl(Tabular):
         >>> Psl().sniff( fname )
         False
         """
+        def check_items(s):
+            s_items = s.split(",")
+            for item in s_items:
+                if int(item) < 0:
+                    raise Exception("Out of range")
         count = 0
         for line in file_prefix.line_iterator():
             line = line.strip()
@@ -1874,72 +1875,24 @@ class Psl(Tabular):
                 items = line.split("\t")
                 if len(items) != 21:
                     return False
-                # matches
-                if int(items[0]) < 0:
-                    raise Exception("Out of range")
-                # misMatches
-                if int(items[1]) < 0:
-                    raise Exception("Out of range")
-                # repMatches
-                if int(items[2]) < 0:
-                    raise Exception("Out of range")
-                # nCount
-                if int(items[3]) < 0:
-                    raise Exception("Out of range")
-                # qNumInsert
-                if int(items[4]) < 0:
-                    raise Exception("Out of range")
-                # qBaseInsert
-                if int(items[5]) < 0:
-                    raise Exception("Out of range")
-                # tNumInsert
-                if int(items[6]) < 0:
-                    raise Exception("Out of range")
-                # tBaseInsert
-                if int(items[7]) < 0:
-                    raise Exception("Out of range")
+                # tName is a string
+                items.pop(13)
+                # qName is a string
+                items.pop(9)
                 # strand
-                if items[8] not in ["-", "+", "+-", "-+"]:
+                if items.pop(8) not in ["-", "+", "+-", "-+"]:
                     raise Exception("Invalid strand")
-                # qSize
-                if int(items[10]) < 0:
-                    raise Exception("Out of range")
-                # qStart
-                if int(items[11]) < 0:
-                    raise Exception("Out of range")
-                # qEnd
-                if int(items[12]) < 0:
-                    raise Exception("Out of range")
-                # tSize
-                if int(items[14]) < 0:
-                    raise Exception("Out of range")
-                # tStart
-                if int(items[15]) < 0:
-                    raise Exception("Out of range")
-                # tEnd
-                if int(items[16]) < 0:
-                    raise Exception("Out of range")
-                # blockCount
-                if int(items[17]) < 0:
-                    raise Exception("Out of range")
                 # blockSizes
-                s = items[18].rstrip(",")
-                s_items = s.split(",")
-                for item in s_items:
-                    if int(item) < 0:
-                        raise Exception("Out of range")
+                s = items.pop(15).rstrip(",")
+                check_items(s)
                 # qStarts
-                s = items[19].rstrip(",")
-                s_items = s.split(",")
-                for item in s_items:
-                    if int(item) < 0:
-                        raise Exception("Out of range")
+                s = items.pop(15).rstrip(",")
+                check_items(s)
                 # tStarts
-                s = items[20].rstrip(",")
-                s_items = s.split(",")
-                for item in s_items:
-                    if int(item) < 0:
-                        raise Exception("Out of range")
+                s = items.pop(15).rstrip(",")
+                check_items(s)
+                if any(int(item) < 0 for item in items):
+                    raise Exception("Out of range")
                 count += 1
                 if count == 10:
                     break