Fix (and test) the comparison of R's .rdb files after refactoring of temporary directory handling.

This was a regression introduced in 1ee33f4e -- what was happening was
that the two files to be compared were copied to a temporary directory,
overwriting each other. This commit ensures they do not collide.

Signed-off-by: Chris Lamb <lamby@debian.org>

diffoscope/comparators/rdata.py

@@ -74,7 +74,7 @@ def check_rds_extension(f):
     return f.name.endswith(".rds") or f.name.endswith(".rdx")
 
 
-def get_module_path_for_rdb(rdb, temp_dir):
+def get_module_path_for_rdb(rdb, temp_dir, module_name):
     """
     R's lazyLoad method does not take a filename directly to an .rdb file (eg.
     `/path/to/foo.rdb`) but rather the path without any extension (eg.
@@ -107,7 +107,7 @@ def get_module_path_for_rdb(rdb, temp_dir):
         # Corresponding .rdx does not exist
         return None
 
-    prefix = os.path.join(temp_dir, "temp")
+    prefix = os.path.join(temp_dir, module_name)
 
     logger.debug("Copying %s and %s to %s", rdx.path, rdb.path, temp_dir)
     shutil.copy(rdb.path, f"{prefix}.rdb")
@@ -163,8 +163,8 @@ class RdbFile(File):
 
     def compare_details(self, other, source=None):
         with get_temporary_directory(suffix="rdb") as tmpdir:
-            a = get_module_path_for_rdb(self, tmpdir)
-            b = get_module_path_for_rdb(other, tmpdir)
+            a = get_module_path_for_rdb(self, tmpdir, "a")
+            b = get_module_path_for_rdb(other, tmpdir, "b")
 
             if a is None or b is None:
                 return []

tests/comparators/test_rdata.py

@@ -20,36 +20,56 @@
 import pytest
 
 from diffoscope.comparators.gzip import GzipFile
+from diffoscope.comparators.rdata import RdbFile
 
 from ..utils.data import load_fixture, get_data, assert_diff
 from ..utils.tools import skip_unless_tools_exist
 
 
-file1 = load_fixture("test1.rdx")
-file2 = load_fixture("test2.rdx")
+rdb1 = load_fixture("test1.rdb")
+rdb2 = load_fixture("test2.rdb")
+rdx1 = load_fixture("test1.rdx")
+rdx2 = load_fixture("test2.rdx")
 
 
-def test_identification(file1):
-    assert isinstance(file1, GzipFile)
+def test_identification(rdb1, rdx1):
+    assert isinstance(rdb1, RdbFile)
+    assert isinstance(rdx1, GzipFile)
 
 
-def test_no_differences(file1):
-    difference = file1.compare(file1)
-    assert difference is None
+def test_no_differences(rdb1, rdx1):
+    assert rdx1.compare(rdx1) is None
+    assert rdx1.compare(rdx1) is None
 
 
 @pytest.fixture
-def differences(file1, file2):
-    return file1.compare(file2).details
+def differences_rdb(rdb1, rdb2):
+    return rdb1.compare(rdb2).details
+
+
+@pytest.fixture
+def differences_rdx(rdx1, rdx2):
+    return rdx1.compare(rdx2).details
+
+
+@skip_unless_tools_exist("Rscript")
+def test_num_items_rdb(differences_rdb):
+    assert len(differences_rdb) == 1
+
+
+@skip_unless_tools_exist("Rscript")
+def test_item_rdb(differences_rdb):
+    assert differences_rdb[0].source1.startswith("Rscript")
+    assert_diff(differences_rdb[0], "rdb_expected_diff")
 
 
 @skip_unless_tools_exist("Rscript")
-def test_num_items(differences):
-    assert len(differences) == 1
+def test_num_items_rdx(differences_rdx):
+    assert len(differences_rdx) == 1
 
 
 @skip_unless_tools_exist("Rscript")
-def test_item_rds(differences):
-    assert differences[0].source1 == "test1.rdx-content"
-    assert differences[0].source2 == "test2.rdx-content"
-    assert_diff(differences[0].details[0], "rds_expected_diff")
+def test_item_rdx(differences_rdx):
+    assert differences_rdx[0].source1 == "test1.rdx-content"
+    assert differences_rdx[0].source2 == "test2.rdx-content"
+    assert_diff(differences_rdx[0].details[0], "rds_expected_diff")

tests/data/rds_expected_diff

-@@ -1,40 +1,40 @@
+@@ -1,715 +1,367 @@
  $variables
- $variables$`%*t%`
--[1]  0 98
-+[1]  0 96
+-$variables$`%c%.matrix`
+-[1]   0 561
++$variables$.__C__Biodetection
++[1]   0 286
  
- $variables$`%t*%`
--[1]  98 101
-+[1] 96 99
+-$variables$.__NAMESPACE__.
+-[1] 7547   62
+-
+-$variables$.__S3MethodsTable__.
+-[1] 7749   62
+-
+-$variables$.onAttach
+-[1] 7811  820
+-
+-$variables$.onLoad
+-[1] 8631  299
+-
+-$variables$.packageName
+-[1] 8930   57
+-
+-$variables$add.isolates
+-[1] 8987  671
+-
+-$variables$as.edgelist.sna
+-[1] 9658 8752
+-
+-$variables$as.sociomatrix.sna
+-[1] 18410  6439
+-
+-$variables$bbnam
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+-
+-$variables$bbnam.actor
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+-
+-$variables$bbnam.bf
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+-$variables$bbnam.fixed
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+-
+-$variables$bbnam.jntlik
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+-
+-$variables$bbnam.jntlik.slice
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+-
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+-
+-$variables$bicomponent.dist
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+-
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+-
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+-
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+-
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+-
+-$variables$connectedness
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+-
+-$variables$consensus
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+-
+-$variables$cug.test
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+-
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+-
+-$variables$cutpoints
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+-
+-$variables$degree
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+-
+-$variables$diag.remove
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+-
+-$variables$dyad.census
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+-
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+-
+-$variables$ego.extract
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+-
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+-
+-$variables$eval.edgeperturbation
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+-
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+-
+-$variables$event2dichot
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+-
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+-
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+-
+-$variables$gclust.boxstats
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+-
+-$variables$gclust.centralgraph
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+-
+-$variables$gcor
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+-
+-$variables$gcov
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+-
+-$variables$gden
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+-
+-$variables$gdist.plotdiff
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+-
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+-
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+-
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+-
+-$variables$gliop
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+-
+-$variables$gplot
+-[1] 179888  22817
++$variables$.__C__CD
++[1] 286 283
  
- $variables$`%t*t%`
--[1] 199 104
-+[1] 195 103
+-$variables$gplot.arrow
+-[1] 202705   9429
++$variables$.__C__CountsBio
++[1] 569 288
  
- $variables$.__NAMESPACE__.
--[1] 877  45
-+[1] 854  43
+-$variables$gplot.layout.adj
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++$variables$.__C__GCbias
++[1] 857 286
  
- $variables$.__S3MethodsTable__.
--[1] 1043   45
-+[1] 1016   43
+-$variables$gplot.layout.circle
+-[1] 212733    735
++$variables$.__C__Output
++[1] 1143 2240
  
- $variables$.packageName
--[1] 1088   44
-+[1] 1059   42
+-$variables$gplot.layout.circrand
+-[1] 213468    459
++$variables$.__C__PCA
++[1] 3383  284
  
- $variables$tensor
--[1] 1132  775
-+[1] 1101  774
+-$variables$gplot.layout.eigen
+-[1] 213927   1512
++$variables$.__C__Saturation
++[1] 3667  285
  
+-$variables$gplot.layout.fruchtermanreingold
+-[1] 215439   2906
++$variables$.__C__lengthbias
++[1] 3952  288
  
- $references
- $references$`env::1`
--[1] 572 305
-+[1] 564 290
+-$variables$gplot.layout.geodist
+-[1] 218345    597
++$variables$.__C__myInfo
++[1] 4240 1158
  
- $references$`env::2`
--[1] 303 121
-+[1] 298 119
+-$variables$gplot.layout.hall
+-[1] 218942    866
+-
+-$variables$gplot.layout.kamadakawai
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
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+-
+-$variables$lnam
+-[1] 348482  18248
++$variables$.__NAMESPACE__.
++[1] 12405    62
  
- $references$`env::3`
--[1] 424 148
-+[1] 417 147
+-$variables$loadcent
+-[1] 366730   2278
++$variables$.__S3MethodsTable__.
++[1] 12607    62
  
- $references$`env::4`
--[1] 922 121
-+[1] 897 119
+-$variables$logMean
+-[1] 369008    555
++$variables$`.__T__dat2save:NOISeq`
++[1] 18038    62
+ 
+-$variables$logSub
+-[1] 369563    685
++$variables$`.__T__explo.plot:NOISeq`
++[1] 21700    62
+ 
+-$variables$logSum
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++$variables$`.__T__show:methods`
++[1] 185265     63
+ 
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++$variables$.calcFactorQuantile
++[1] 185328    643
+ 
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++$variables$.calcFactorWeighted
++[1] 185971   2087
+ 
+-$variables$make.stochastic
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++$variables$.calcNormFactors
++[1] 188058   1215
+ 
+-$variables$maxflow
+-[1] 378947   2646
++$variables$.packageName
++[1] 189273     60
+ 
+-$variables$mutuality
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++$variables$ARSyNcomponents
++[1] 189333   1768
+ 
+-$variables$nacf
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++$variables$ARSyNmodel
++[1] 191101   2635
+ 
+-$variables$neighborhood
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++$variables$ARSyNseq
++[1] 193736   2972
+ 
+-$variables$netcancor
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+ 
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++$variables$ASCA.2f
++[1] 198928   2743
+ 
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++$variables$ASCA.3f
++[1] 201671   3688
+ 
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++$variables$ASCAfun.res
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+ 
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++$variables$ASCAfun.triple
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+ 
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++$variables$ASCAfun1
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+ 
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+ 
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+ 
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+ 
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+ 
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+ 
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++$variables$Output
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+ 
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+ 
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++$variables$data2report
++[1] 335709   1640
+ 
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++[1] 337349   2298
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+ 
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+ 
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+ 
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+ 
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++$variables$miscolores
++[1] 357312    168
+ 
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++$variables$myDfunction
++[1] 357480    608
+ 
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++$variables$mypretty
++[1] 358088   1244
+ 
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++[1] 359332    421
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++[1] 359753    456
+ 
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++[1] 360209   4099
+ 
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++[1] 364308   6161
+ 
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++$variables$plot.y2
++[1] 370469   2410
+ 
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+-[1] 500706   8639
++$variables$probdeg
++[1] 372879   1399
+ 
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++$variables$ranking
++[1] 374278   1038
+ 
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+-[1] 510649   2096
++$variables$readData
++[1] 375316   2539
+ 
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++$variables$rpkm
++[1] 377855   1016
+ 
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++$variables$saturation.dat
++[1] 378871   6983
+ 
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+-[1] 515680   5254
++$variables$saturation.plot
++[1] 385854   6714
+ 
+-$variables$rewire.ud
+-[1] 520934   1289
++$variables$share.info
++[1] 392568   5438
+ 
+-$variables$rewire.ws
+-[1] 522223   1345
++$variables$sim.samples
++[1] 398006   1485
+ 
+-$variables$rgbn
+-[1] 523568   3630
++$variables$sinceros
++[1] 399491    761
+ 
+-$variables$rgnm
+-[1] 527198   2754
++$variables$tmm
++[1] 400252   1494
+ 
+-$variables$rgnmix
+-[1] 529952   3644
++$variables$uqua
++[1] 401746   1700
+ 
+-$variables$rgraph
+-[1] 533596   3332
+ 
+-$variables$rguman
+-[1] 536928   2836
++$references
++$references$`env::1`
++[1] 5706 6699
+ 
+-$variables$rgws
+-[1] 539764   1749
++$references$`env::10`
++[1] 20320   270
+ 
+-$variables$rmperm
+-[1] 541513   1394
++$references$`env::11`
++[1] 18100  1110
+ 
+-$variables$rperm
+-[1] 542907    710
++$references$`env::12`
++[1] 19210  1110
+ 
+-$variables$sdmat
+-[1] 543617   1626
++$references$`env::13`
++[1] 181233   4032
+ 
+-$variables$se.lnam
+-[1] 545243    906
++$references$`env::14`
++[1] 180761    472
+ 
+-$variables$sedist
+-[1] 546149   4970
++$references$`env::15`
++[1] 139943  20409
+ 
+-$variables$simmelian
+-[1] 551119   1029
++$references$`env::16`
++[1] 21762   183
+ 
+-$variables$sociomatrixplot
+-[1] 552148   3263
++$references$`env::17`
++[1] 21945  1535
+ 
+-$variables$sr2css
+-[1] 555411    826
++$references$`env::18`
++[1] 137619   2324
+ 
+-$variables$stackcount
+-[1] 556237    356
++$references$`env::19`
++[1] 123123    152
+ 
+-$variables$stresscent
+-[1] 556593   2275
++$references$`env::2`
++[1] 5398  140
+ 
+-$variables$structdist
+-[1] 558868   5365
++$references$`env::20`
++[1] 117923   5200
+ 
+-$variables$structure.statistics
+-[1] 564233   1325
++$references$`env::21`
++[1] 117182    741
+ 
+-$variables$summary.bayes.factor
+-[1] 565558   1076
++$references$`env::22`
++[1] 32250   152
+ 
+-$variables$summary.bbnam
+-[1] 566634    379
++$references$`env::23`
++[1] 23480  8770
+ 
+-$variables$summary.bbnam.actor
+-[1] 567013    385
++$references$`env::24`
++[1] 112363   4819
+ 
+-$variables$summary.bbnam.fixed
+-[1] 567398    386
++$references$`env::25`
++[1] 39689 49420
+ 
+-$variables$summary.bbnam.pooled
+-[1] 567784    386
++$references$`env::26`
++[1] 36359   347
+ 
+-$variables$summary.blockmodel
+-[1] 568170    334
++$references$`env::27`
++[1] 33177  3182
+ 
+-$variables$summary.bn
+-[1] 568504    376
++$references$`env::28`
++[1] 32402   775
+ 
+-$variables$summary.brokerage
+-[1] 568880    304
++$references$`env::29`
++[1] 36706   875
+ 
+-$variables$summary.cugtest
+-[1] 569184    381
++$references$`env::3`
++[1] 5538  168
+ 
+-$variables$summary.lnam
+-[1] 569565    349
++$references$`env::30`
++[1] 37581  1787
+ 
+-$variables$summary.netcancor
+-[1] 569914    383
++$references$`env::31`
++[1] 39368   321
+ 
+-$variables$summary.netlm
+-[1] 570297    379
++$references$`env::32`
++[1] 89109 23254
+ 
+-$variables$summary.netlogit
+-[1] 570676    382
++$references$`env::33`
++[1] 129040   2484
+ 
+-$variables$summary.qaptest
+-[1] 571058    381
++$references$`env::34`
++[1] 128873    167
+ 
+-$variables$symmetrize
+-[1] 571439   4336
++$references$`env::35`
++[1] 123275   5598
+ 
+-$variables$triad.census
+-[1] 575775   1992
++$references$`env::36`
++[1] 137467    152
+ 
+-$variables$triad.classify
+-[1] 577767   1663
++$references$`env::37`
++[1] 132265   5202
+ 
+-$variables$upper.tri.remove
+-[1] 579430   1036
++$references$`env::38`
++[1] 131524    741
+ 
+-$variables$write.dl
+-[1] 580466   2744
++$references$`env::39`
++[1] 160352  20409
+ 
+-$variables$write.nos
+-[1] 583210   1860
++$references$`env::4`
++[1] 12467   140
+ 
++$references$`env::5`
++[1] 16338  1700
+ 
+-$references
+-$references$`env::1`
+-[1]  866 6681
++$references$`env::6`
++[1] 16069   269
+ 
+-$references$`env::2`
+-[1] 561 140
++$references$`env::7`
++[1] 12669  1700
+ 
+-$references$`env::3`
+-[1] 701 165
++$references$`env::8`
++[1] 14369  1700
+ 
+-$references$`env::4`
+-[1] 7609  140
++$references$`env::9`
++[1] 20590  1110
  
  
  $compressed

tests/test_source.py

@@ -130,6 +130,7 @@ ALLOWED_TEST_FILES = {
     "test1.png",
     "test1.ppu",
     "test1.ps",
+    "test1.rdb",
     "test1.rdx",
     "test1.rlib",
     "test1.rpm",
@@ -191,6 +192,7 @@ ALLOWED_TEST_FILES = {
     "test2.png",
     "test2.ppu",
     "test2.ps",
+    "test2.rdb",
     "test2.rdx",
     "test2.rlib",
     "test2.rpm",

tests/utils/data.py

@@ -24,6 +24,7 @@ import re
 import pytest
 
 from diffoscope.comparators.binary import FilesystemFile
+from diffoscope.comparators.directory import FilesystemDirectory
 from diffoscope.comparators.utils.specialize import specialize
 
 re_normalize_zeros = re.compile(
@@ -31,8 +32,17 @@ re_normalize_zeros = re.compile(
 )
 
 
+def init_file(filename):
+    # Ensure that any (specialized) FilesystemFile in tests have a
+    # corresponding Container for any comparator that needs to know which
+    # directory the file came from (eg. rdata)
+    container = FilesystemDirectory(os.path.dirname(filename)).as_container
+
+    return specialize(FilesystemFile(filename, container))
+
+
 def init_fixture(filename):
-    return pytest.fixture(lambda: specialize(FilesystemFile(filename)))
+    return pytest.fixture(lambda: init_file(filename))
 
 
 def data(filename):