Merge pull request #441 from seoklab/fmt/fuzz

test(fmt): add fuzz test and fix various bugs
seoklab · Dec 24, 2024 · 0dd9030 · 0dd9030
2 parents e009867 + 5a049f9
commit 0dd9030
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Showing 106 changed files with 1,912 additions and 46 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,14 +20,14 @@ repos:
       - id: check-symlinks
       - id: destroyed-symlinks
       - id: end-of-file-fixer
-        exclude: ^test/test_data/
+        exclude: ^(test/test_data/|fuzz/corpus-min/)
       - id: fix-byte-order-marker
-        exclude: ^test/test_data/
+        exclude: ^(test/test_data/|fuzz/corpus-min/)
       - id: trailing-whitespace
-        exclude: ^test/test_data/
+        exclude: ^(test/test_data/|fuzz/corpus-min/)
         args: ["--markdown-linebreak-ext=md"]
       - id: mixed-line-ending
-        exclude: ^test/test_data/
+        exclude: ^(test/test_data/|fuzz/corpus-min/)
         args: ["--fix=lf"]
   - repo: https://github.com/seoklab/shared-hooks
     rev: v0.1.4

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -95,9 +95,8 @@ if(NURI_BUILD_FUZZING)
     message(FATAL_ERROR "Fuzzing build is only supported with Clang")
   endif()
 
-  message("Fuzzing build: enabling sanitizers")
+  message("Fuzzing build: enabling sanitizers and sanitizer coverage")
   set(NURI_ENABLE_SANITIZERS ON)
-  add_compile_options(-fsanitize=fuzzer)
 endif()
 
 set_sanitizer_envs()
@@ -127,6 +126,11 @@ endif()
 find_or_fetch_abseil()
 add_subdirectory(third-party EXCLUDE_FROM_ALL)
 
+if(NURI_BUILD_FUZZING)
+  add_compile_options(-fsanitize=fuzzer)
+  string(APPEND CMAKE_CXX_FLAGS " -fprofile-instr-generate -fcoverage-mapping")
+endif()
+
 add_compile_options(
   -pedantic
   -Wall

diff --git a/fuzz/corpus-min/cif/1a8o.cif b/fuzz/corpus-min/cif/1a8o.cif
@@ -0,0 +1 @@
+../../../test/test_data/1a8o.cif
diff --git a/fuzz/corpus-min/cif/components_stdres.cif b/fuzz/corpus-min/cif/components_stdres.cif
@@ -0,0 +1 @@
+../../../test/test_data/components_stdres.cif
diff --git a/fuzz/corpus-min/cif/line_cont.cif b/fuzz/corpus-min/cif/line_cont.cif
@@ -0,0 +1,27 @@
+data_contin
+_test1
+;C:\\foldername\\filename
+;
+_test2
+;\\
+C:\\foldername\\filename
+;
+_test3
+
+;\\
+C:\\foldername\\file\\
+name
+;
+_test4
+;
+C:\\foldername\\file\\
+name
+;
+_test5
+;\\
+C:\\foldername\\file\\\\
+
+name\\
+
+
+;
diff --git a/fuzz/corpus-min/cif/line_cont_new.cif b/fuzz/corpus-min/cif/line_cont_new.cif
@@ -0,0 +1,27 @@
+data_contin
+_test1
+;C:\foldername\filename
+;
+_test2
+;\
+C:\foldername\filename
+;
+_test3
+
+;\
+C:\foldername\file\
+name
+;
+_test4
+;
+C:\foldername\file\
+name
+;
+_test5
+;\
+C:\foldername\file\\
+
+name\
+
+
+;
diff --git a/fuzz/corpus-min/cif/simple_loop.cif b/fuzz/corpus-min/cif/simple_loop.cif
@@ -0,0 +1,10 @@
+data_loop
+loop_
+_pdbx_audit_revision_item.ordinal
+_pdbx_audit_revision_item.revision_ordinal
+_pdbx_audit_revision_item.data_content_type
+_pdbx_audit_revision_item.item
+1  5 'Structure model' '_atom_site.B_iso_or_equiv'
+2  5 'Structure model' '_atom_site.Cartn_x'
+3  5 'Structure model' '_atom_site.Cartn_y'
+4  5 'Structure model' '_atom_site.Cartn_z'
diff --git a/fuzz/corpus-min/cif/star_fig1.cif b/fuzz/corpus-min/cif/star_fig1.cif
@@ -0,0 +1,26 @@
+global_
+  _compound.trial     4
+  _compound.source    FDA
+data_synthesis
+  _sample.length      5.84
+  _sample.shape       'needle'
+  _solvent.base       Methanol
+  _sample.orientation '[1,0,2]'
+global_
+  _experiment.source  'ConvBeamEI'
+  _experiment.date    2011-06-09
+data_experiment
+  _images.collected   1289
+  _images.refined     894
+save_fragment_1
+  _molecular.weight   234
+  _bond_length.max    2.7
+save_
+save_fragment_2
+  _molecular.weight   23
+  _bond_length.max    1.1
+  _fragment.parent    fragment_1
+save_
+data_publication
+  _author.details     'A.B. Smith'
+  _author.laboratory  'LLNL'
diff --git a/fuzz/corpus-min/mol2/basic.mol2 b/fuzz/corpus-min/mol2/basic.mol2
@@ -0,0 +1,9 @@
+@<TRIPOS>MOLECULE
+methane
+1 0 0 0 0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1            -0.0127     1.0858     0.0080 C.3
diff --git a/fuzz/corpus-min/mol2/cba.mol2 b/fuzz/corpus-min/mol2/cba.mol2
@@ -0,0 +1,16 @@
+@<TRIPOS>MOLECULE
+carboxylic acid
+   4    3    0    0    0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1            -0.0127     1.0858     0.0080 C.3
+   2 C2            -0.7181     1.5718     1.2479 C.2
+   3 O3            -0.8566     2.8886     1.4687 O.3
+   4 O4            -1.1590     0.7762     2.0432 O.2
+@<TRIPOS>BOND
+   1    1    2 1
+   2    2    3 1
+   3    2    4 2
diff --git a/fuzz/corpus-min/mol2/cba2.mol2 b/fuzz/corpus-min/mol2/cba2.mol2
@@ -0,0 +1,15 @@
+@<TRIPOS>MOLECULE
+carboxylic acid
+ 4 3 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.0331
+      2 C           0.0000    0.0000    0.0000 C.2     1  UNL1        0.3016
+      3 O           0.0000    0.0000    0.0000 O.3     1  UNL1       -0.4808
+      4 O           0.0000    0.0000    0.0000 O.2     1  UNL1       -0.2513
+@<TRIPOS>BOND
+     1     1     2    1
+     2     2     3    1
+     3     2     4    2
diff --git a/fuzz/corpus-min/mol2/cba3.mol2 b/fuzz/corpus-min/mol2/cba3.mol2
@@ -0,0 +1,16 @@
+@<TRIPOS>MOLECULE
+carboxylate
+   4    3    0    0    0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1            -0.0127     1.0858     0.0080 C.3
+   2 C2            -0.7181     1.5718     1.2479 C.2
+   3 O3            -0.0841     1.7780     2.2687 O.co2
+   4 O4            -1.9227     1.7588     1.2302 O.co2
+@<TRIPOS>BOND
+   1    1    2 1
+   2    2    3 ar
+   3    2    4 ar
diff --git a/fuzz/corpus-min/mol2/cba4.mol2 b/fuzz/corpus-min/mol2/cba4.mol2
@@ -0,0 +1,15 @@
+@<TRIPOS>MOLECULE
+carboxylate
+ 4 3 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.1258
+      2 C           0.0000    0.0000    0.0000 C.2     1  UNL1        0.3654
+      3 O           0.0000    0.0000    0.0000 O.co2   1  UNL1       -0.2456
+      4 O           0.0000    0.0000    0.0000 O.co2   1  UNL1       -0.2456
+@<TRIPOS>BOND
+     1     1     2    1
+     2     2     3   ar
+     3     2     4   ar
diff --git a/fuzz/corpus-min/mol2/charged.mol2 b/fuzz/corpus-min/mol2/charged.mol2
@@ -0,0 +1,17 @@
+@<TRIPOS>MOLECULE
+quaternary ammonium salt
+ 5 4 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.1712
+      2 N           0.0000    0.0000    0.0000 N.4     1  UNL1        0.3151
+      3 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.1712
+      4 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.1712
+      5 C           0.0000    0.0000    0.0000 C.3     1  UNL1        0.1712
+@<TRIPOS>BOND
+     1     1     2    1
+     2     2     3    1
+     3     2     4    1
+     4     2     5    1
diff --git a/fuzz/corpus-min/mol2/charged2.mol2 b/fuzz/corpus-min/mol2/charged2.mol2
@@ -0,0 +1,18 @@
+@<TRIPOS>MOLECULE
+quaternary ammonium salt
+   5    4    0    0    0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1             0.0021    -0.0041     0.0020 C.3
+   2 N2            -0.0178     1.4648     0.0101 N.4
+   3 C3             1.3603     1.9732    -0.0003 C.3
+   4 C4            -0.7283     1.9514    -1.1800 C.3
+   5 C5            -0.7054     1.9385     1.2187 C.3
+@<TRIPOS>BOND
+   1    1    2 1
+   2    2    3 1
+   3    2    4 1
+   4    2    5 1
diff --git a/fuzz/corpus-min/mol2/cpm.mol2 b/fuzz/corpus-min/mol2/cpm.mol2
@@ -0,0 +1,24 @@
+@<TRIPOS>MOLECULE
+Cyclopentadienyl anion
+ 5 5 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.2250
+      2 C           0.0000    0.0000    0.0000 C.2     1  UNL1       -0.4635
+      3 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.2250
+      4 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.0433
+      5 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.0433
+@<TRIPOS>UNITY_ATOM_ATTR
+2 1
+charge -1
+@<TRIPOS>BOND
+     1     1     2   ar
+     2     2     3   ar
+     3     3     4   ar
+     4     4     5   ar
+     5     1     5   ar
+#	Name: NoName
+
+#	Program:	corina 4.4.0 0026  12.08.2021
diff --git a/fuzz/corpus-min/mol2/cpm2.mol2 b/fuzz/corpus-min/mol2/cpm2.mol2
@@ -0,0 +1,24 @@
+@<TRIPOS>MOLECULE
+Cyclopentadienyl anion
+   5    5    0    0    0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1             1.0980     1.9060     0.0018 C.2
+   2 C2            -0.0126     1.0758     0.0080 C.2
+   3 C4            -1.1453     1.8755     0.0170 C.2
+   4 C5            -0.7347     3.1999     0.0254 C.2
+   5 C6             0.6517     3.2188     0.0126 C.2
+@<TRIPOS>BOND
+   1    1    5 2
+   2    1    2 1
+   3    2    3 1
+   4    3    4 2
+   5    4    5 1
+@<TRIPOS>UNITY_ATOM_ATTR
+2 1
+charge -1
+
+#	End of record
diff --git a/fuzz/corpus-min/mol2/cpm3.mol2 b/fuzz/corpus-min/mol2/cpm3.mol2
@@ -0,0 +1,21 @@
+@<TRIPOS>MOLECULE
+Cyclopentadienyl anion
+ 5 5 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.2250
+      2 C           0.0000    0.0000    0.0000 C.2     1  UNL1       -0.4635
+      3 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.2250
+      4 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.0433
+      5 C           0.0000    0.0000    0.0000 C.ar    1  UNL1       -0.0433
+@<TRIPOS>BOND
+     1     1     2   ar
+     2     2     3   ar
+     3     3     4   ar
+     4     4     5   ar
+     5     1     5   ar
+#	Name: NoName
+
+#	Program:	corina 4.4.0 0026  12.08.2021
diff --git a/fuzz/corpus-min/mol2/cpm4.mol2 b/fuzz/corpus-min/mol2/cpm4.mol2
@@ -0,0 +1,20 @@
+@<TRIPOS>MOLECULE
+Cyclopentadienyl anion
+   5    5    0    0    0
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+   1 C1             1.0980     1.9060     0.0018 C.ar
+   2 C2            -0.0126     1.0758     0.0080 C.ar
+   3 C4            -1.1453     1.8755     0.0170 C.ar
+   4 C5            -0.7347     3.1999     0.0254 C.ar
+   5 C6             0.6517     3.2188     0.0126 C.ar
+@<TRIPOS>BOND
+   1    1    5 2
+   2    1    2 1
+   3    2    3 1
+   4    3    4 2
+   5    4    5 1
+#	End of record
diff --git a/fuzz/corpus-min/mol2/extraprop.mol2 b/fuzz/corpus-min/mol2/extraprop.mol2
@@ -0,0 +1,12 @@
+@<TRIPOS>MOLECULE
+****
+ 1 0 0 0 0
+SMALL
+GASTEIGER
+****
+
+@<TRIPOS>ATOM
+      1 N           0.0000    0.0000    0.0000 N.4     1  UNL1        1.0000
+@<TRIPOS>UNITY_ATOM_ATTR
+1 1
+test prop
diff --git a/fuzz/corpus-min/mol2/guanidine.mol2 b/fuzz/corpus-min/mol2/guanidine.mol2
@@ -0,0 +1,24 @@
+@<TRIPOS>MOLECULE
+guadinium-like
+ 7 6 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 N           0.0000    0.0000    0.0000 N.pl3   1  UNL1        0.1360
+      2 C           0.0000    0.0000    0.0000 C.cat   1  UNL1        0.5446
+      3 N           0.0000    0.0000    0.0000 N.pl3   1  UNL1        0.0168
+      4 C           0.0000    0.0000    0.0000 C.cat   1  UNL1        0.5446
+      5 N           0.0000    0.0000    0.0000 N.pl3   1  UNL1        0.1360
+      6 N           0.0000    0.0000    0.0000 N.pl3   1  UNL1        0.1360
+      7 N           0.0000    0.0000    0.0000 N.pl3   1  UNL1        0.1360
+@<TRIPOS>BOND
+     1     1     2    1
+     2     2     3    1
+     3     3     4    1
+     4     4     5    1
+     5     4     6    2
+     6     2     7    2
+#	Name: NoName
+
+#	Program:	corina 4.4.0 0026  12.08.2021