Repository: dbt-labs/dbt-core
Pull request: Handle seeds with utf-8 BOM (#1177)
Fixes #1177 

Instead of passing agate a filepath, open the file at that path, look at the first byte, and seek back if it's not a BOM. Regardless, pass the file handle to agate instead.

That way when agate gets the file handle, if there is a BOM, it won't see it.

Problem statement:
Strip BOM from Excel-generated UTF-8 CSV files
## Issue

UTF-8 CSV files generated by Excel have a byte order mark (BOM) which is included in the column title when using `dbt seed`.

### Issue description

Save Excel file as UTF-8 CSV on Microsoft Excel for Mac. Run `dbt seed` on the resulting file.

### Results

The first column name includes the unprintable BOM character which makes queries very difficult to write. I would expect the BOM to be stripped from the column name.

I was able to work around this by changing the file encoding in Emacs and re-saving the file.

### System information
The output of `dbt --version`:
```
installed version: 0.12.1
   latest version: 0.12.1

Up to date!
```

The operating system you're running on: MacOS Mojave 10.14.1

The python version you're using (probably the output of `python --version`): 3.7.1

### Steps to reproduce

1. Using Excel, save file as UTF-8 CSV.
2. Run `dbt seed`
3. `select <column> from <table>`, column cannot be found because of the BOM.

Hints from issue discussion:
I (fortunately) don't have an excel-generated csv lying around to test this on, but had written down some notes about this before.

I *think* the following enables you to read excel-generated csv files as expected, for what it's worth:

```
>>> import codecs
>>> import csv
>>> with codecs.open('excel_output.csv', encoding='utf-8-sig') as f:
...     reader = csv.reader(f)
...     rows = [row for row in reader]
```

Commit message: Always specify encodings to open()

Fixes some neat windows behavior where the default code page can be cp1252
Add BOM unit test

Patch to review:
diff --git a/core/dbt/clients/agate_helper.py b/core/dbt/clients/agate_helper.py
index e08c500f485..0d0d212c6c1 100644
--- a/core/dbt/clients/agate_helper.py
+++ b/core/dbt/clients/agate_helper.py
@@ -1,3 +1,4 @@
+import dbt.compat
 
 import agate
 
@@ -41,4 +42,7 @@ def as_matrix(table):
 
 
 def from_csv(abspath):
-    return agate.Table.from_csv(abspath, column_types=DEFAULT_TYPE_TESTER)
+    with dbt.compat.open_file(abspath) as fp:
+        if fp.read(1) != u'\ufeff':
+            fp.seek(0)
+        return agate.Table.from_csv(fp, column_types=DEFAULT_TYPE_TESTER)
diff --git a/core/dbt/compat.py b/core/dbt/compat.py
index 50f9c217914..b2533c6d8b9 100644
--- a/core/dbt/compat.py
+++ b/core/dbt/compat.py
@@ -82,11 +82,20 @@ def to_native_string(s):
 
 def write_file(path, s):
     if WHICH_PYTHON == 2:
-        with codecs.open(path, 'w', encoding='utf-8') as f:
-            return f.write(to_string(s))
+        open = codecs.open
     else:
-        with open(path, 'w') as f:
-            return f.write(to_string(s))
+        open = builtins.open
+    with open(path, 'w', encoding='utf-8') as f:
+        return f.write(to_string(s))
+
+
+def open_file(path):
+    """Open the path for reading. It must be utf-8 encoded."""
+    if WHICH_PYTHON == 2:
+        open = codecs.open
+    else:
+        open = builtins.open
+    return open(path, encoding='utf-8')
 
 
 if WHICH_PYTHON == 2:
diff --git a/test/integration/005_simple_seed_test/data-bom/seed_bom.csv b/test/integration/005_simple_seed_test/data-bom/seed_bom.csv
new file mode 100644
index 00000000000..1d37f5f2874
--- /dev/null
+++ b/test/integration/005_simple_seed_test/data-bom/seed_bom.csv
@@ -0,0 +1,501 @@
+﻿id,first_name,email,ip_address,birthday
+1,Larry,lking0@miitbeian.gov.cn,69.135.206.194,2008-09-12 19:08:31
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+3,Anna,amontgomery2@miitbeian.gov.cn,168.104.64.114,2011-10-16 04:07:57
+4,Sandra,sgeorge3@livejournal.com,229.235.252.98,1973-07-19 10:52:43
+5,Fred,fwoods4@google.cn,78.229.170.124,2012-09-30 16:38:29
+6,Stephen,shanson5@livejournal.com,182.227.157.105,1995-11-07 21:40:50
+7,William,wmartinez6@upenn.edu,135.139.249.50,1982-09-05 03:11:59
+8,Jessica,jlong7@hao123.com,203.62.178.210,1991-10-16 11:03:15
+9,Douglas,dwhite8@tamu.edu,178.187.247.1,1979-10-01 09:49:48
+10,Lisa,lcoleman9@nydailynews.com,168.234.128.249,2011-05-26 07:45:49
+11,Ralph,rfieldsa@home.pl,55.152.163.149,1972-11-18 19:06:11
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+13,Clarence,cduncanc@sfgate.com,81.171.31.133,2011-11-17 07:02:36
+14,Daniel,dfranklind@omniture.com,8.204.211.37,1980-09-13 00:09:04
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+16,Billy,bwardf@wikia.com,214.108.78.85,2003-10-19 02:14:47
+17,Annie,agarzag@ocn.ne.jp,190.108.42.70,1988-10-28 15:12:35
+18,Shirley,scolemanh@fastcompany.com,109.251.164.84,1988-08-24 10:50:57
+19,Roger,rfrazieri@scribd.com,38.145.218.108,1985-12-31 15:17:15
+20,Lillian,lstanleyj@goodreads.com,47.57.236.17,1970-06-08 02:09:05
+21,Aaron,arodriguezk@nps.gov,205.245.118.221,1985-10-11 23:07:49
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+24,Henry,hgarcian@newsvine.com,1.191.216.252,2008-08-28 08:30:44
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+117,Henry,hhughes38@webeden.co.uk,152.60.114.174,1973-01-27 09:00:42
+118,Teresa,thenry39@hao123.com,32.187.239.106,2015-11-06 01:48:44
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+129,Steve,sadams3k@economist.com,112.248.91.98,2004-03-21 09:07:43
+130,Katherine,krobertson3l@ow.ly,37.220.107.28,1977-03-18 19:28:50
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+170,Anne,along4p@squidoo.com,36.154.58.107,2012-08-19 23:35:31
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+173,Andrew,ahudson4s@nytimes.com,84.32.252.144,1998-09-15 14:20:04
+174,Keith,kgordon4t@cam.ac.uk,189.237.211.102,2009-01-22 05:34:38
+175,Patrick,pwheeler4u@mysql.com,47.22.117.226,1984-09-05 22:33:15
+176,Jesse,jfoster4v@mapquest.com,229.95.131.46,1990-01-20 12:19:15
+177,Arthur,afisher4w@jugem.jp,107.255.244.98,1983-10-13 11:08:46
+178,Nicole,nryan4x@wsj.com,243.211.33.221,1974-05-30 23:19:14
+179,Bruce,bjohnson4y@sfgate.com,17.41.200.101,1992-09-23 02:02:19
+180,Terry,tcox4z@reference.com,20.189.120.106,1982-02-13 12:43:14
+181,Ashley,astanley50@kickstarter.com,86.3.56.98,1976-05-09 01:27:16
+182,Michael,mrivera51@about.me,72.118.249.0,1971-11-11 17:28:37
+183,Steven,sgonzalez52@mozilla.org,169.112.247.47,2002-08-24 14:59:25
+184,Kathleen,kfuller53@bloglovin.com,80.93.59.30,2002-03-11 13:41:29
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+409,Irene,isanchezbc@cdbaby.com,109.255.50.119,1983-09-28 21:11:27
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+411,Michelle,mdiazbe@businessweek.com,236.249.6.226,1993-05-22 08:07:07
+412,Tammy,tbennettbf@wisc.edu,145.253.239.152,1978-12-31 20:24:51
+413,Christine,cgreenebg@flickr.com,97.25.140.118,1978-07-17 12:55:30
+414,Patricia,pgarzabh@tuttocitta.it,139.246.192.211,1984-02-27 13:40:08
+415,Kimberly,kromerobi@aol.com,73.56.88.247,1976-09-16 14:22:04
+416,George,gjohnstonbj@fda.gov,240.36.245.185,1979-07-24 14:36:02
+417,Eugene,efullerbk@sciencedaily.com,42.38.105.140,2012-09-12 01:56:41
+418,Andrea,astevensbl@goo.gl,31.152.207.204,1979-05-24 11:06:21
+419,Shirley,sreidbm@scientificamerican.com,103.60.31.241,1984-02-23 04:07:41
+420,Terry,tmorenobn@blinklist.com,92.161.34.42,1994-06-25 14:01:35
+421,Christopher,cmorenobo@go.com,158.86.176.82,1973-09-05 09:18:47
+422,Dennis,dhansonbp@ning.com,40.160.81.75,1982-01-20 10:19:41
+423,Beverly,brussellbq@de.vu,138.32.56.204,1997-11-06 07:20:19
+424,Howard,hparkerbr@163.com,103.171.134.171,2015-06-24 15:37:10
+425,Helen,hmccoybs@fema.gov,61.200.4.71,1995-06-20 08:59:10
+426,Ann,ahudsonbt@cafepress.com,239.187.71.125,1977-04-11 07:59:28
+427,Tina,twestbu@nhs.uk,80.213.117.74,1992-08-19 05:54:44
+428,Terry,tnguyenbv@noaa.gov,21.93.118.95,1991-09-19 23:22:55
+429,Ashley,aburtonbw@wix.com,233.176.205.109,2009-11-10 05:01:20
+430,Eric,emyersbx@1und1.de,168.91.212.67,1987-08-10 07:16:20
+431,Barbara,blittleby@lycos.com,242.14.189.239,2008-08-02 12:13:04
+432,Sean,sevansbz@instagram.com,14.39.177.13,2007-04-16 17:28:49
+433,Shirley,sburtonc0@newsvine.com,34.107.138.76,1980-12-10 02:19:29
+434,Patricia,pfreemanc1@so-net.ne.jp,219.213.142.117,1987-03-01 02:25:45
+435,Paula,pfosterc2@vkontakte.ru,227.14.138.141,1972-09-22 12:59:34
+436,Nicole,nstewartc3@1688.com,8.164.23.115,1998-10-27 00:10:17
+437,Earl,ekimc4@ovh.net,100.26.244.177,2013-01-22 10:05:46
+438,Beverly,breedc5@reuters.com,174.12.226.27,1974-09-22 07:29:36
+439,Lawrence,lbutlerc6@a8.net,105.164.42.164,1992-06-05 00:43:40
+440,Charles,cmoorec7@ucoz.com,252.197.131.69,1990-04-09 02:34:05
+441,Alice,alawsonc8@live.com,183.73.220.232,1989-02-28 09:11:04
+442,Dorothy,dcarpenterc9@arstechnica.com,241.47.200.14,2005-05-02 19:57:21
+443,Carolyn,cfowlerca@go.com,213.109.55.202,1978-09-10 20:18:20
+444,Anthony,alongcb@free.fr,169.221.158.204,1984-09-13 01:59:23
+445,Annie,amoorecc@e-recht24.de,50.34.148.61,2009-03-26 03:41:07
+446,Carlos,candrewscd@ihg.com,236.69.59.212,1972-03-29 22:42:48
+447,Beverly,bramosce@google.ca,164.250.184.49,1982-11-10 04:34:01
+448,Teresa,tlongcf@umich.edu,174.88.53.223,1987-05-17 12:48:00
+449,Roy,rboydcg@uol.com.br,91.58.243.215,1974-06-16 17:59:54
+450,Ashley,afieldsch@tamu.edu,130.138.11.126,1983-09-15 05:52:36
+451,Judith,jhawkinsci@cmu.edu,200.187.103.245,2003-10-22 12:24:03
+452,Rebecca,rwestcj@ocn.ne.jp,72.85.3.103,1980-11-13 11:01:26
+453,Raymond,rporterck@infoseek.co.jp,146.33.216.151,1982-05-17 23:58:03
+454,Janet,jmarshallcl@odnoklassniki.ru,52.46.193.166,1998-10-04 00:02:21
+455,Shirley,speterscm@salon.com,248.126.31.15,1987-01-30 06:04:59
+456,Annie,abowmancn@economist.com,222.213.248.59,2006-03-14 23:52:59
+457,Jean,jlarsonco@blogspot.com,71.41.25.195,2007-09-08 23:49:45
+458,Phillip,pmoralescp@stanford.edu,74.119.87.28,2011-03-14 20:25:40
+459,Norma,nrobinsoncq@economist.com,28.225.21.54,1989-10-21 01:22:43
+460,Kimberly,kclarkcr@dion.ne.jp,149.171.132.153,2008-06-27 02:27:30
+461,Ruby,rmorriscs@ucla.edu,177.85.163.249,2016-01-28 16:43:44
+462,Jonathan,jcastilloct@tripod.com,78.4.28.77,2000-05-24 17:33:06
+463,Edward,ebryantcu@jigsy.com,140.31.98.193,1992-12-17 08:32:47
+464,Chris,chamiltoncv@eepurl.com,195.171.234.206,1970-12-05 03:42:19
+465,Michael,mweavercw@reference.com,7.233.133.213,1987-03-29 02:30:54
+466,Howard,hlawrencecx@businessweek.com,113.225.124.224,1990-07-30 07:20:57
+467,Philip,phowardcy@comsenz.com,159.170.247.249,2010-10-15 10:18:37
+468,Mary,mmarshallcz@xing.com,125.132.189.70,2007-07-19 13:48:47
+469,Scott,salvarezd0@theguardian.com,78.49.103.230,1987-10-31 06:10:44
+470,Wayne,wcarrolld1@blog.com,238.1.120.204,1980-11-19 03:26:10
+471,Jennifer,jwoodsd2@multiply.com,92.20.224.49,2010-05-06 22:17:04
+472,Raymond,rwelchd3@toplist.cz,176.158.35.240,2007-12-12 19:02:51
+473,Steven,sdixond4@wisc.edu,167.55.237.52,1984-05-05 11:44:37
+474,Ralph,rjamesd5@ameblo.jp,241.190.50.133,2000-07-06 08:44:37
+475,Jason,jrobinsond6@hexun.com,138.119.139.56,2006-02-03 05:27:45
+476,Doris,dwoodd7@fema.gov,180.220.156.190,1978-05-11 20:14:20
+477,Elizabeth,eberryd8@youtu.be,74.188.53.229,2006-11-18 08:29:06
+478,Irene,igilbertd9@privacy.gov.au,194.152.218.1,1985-09-17 02:46:52
+479,Jessica,jdeanda@ameblo.jp,178.103.93.118,1974-06-07 19:04:05
+480,Rachel,ralvarezdb@phoca.cz,17.22.223.174,1999-03-08 02:43:25
+481,Kenneth,kthompsondc@shinystat.com,229.119.91.234,2007-05-15 13:17:32
+482,Harold,hmurraydd@parallels.com,133.26.188.80,1993-11-15 03:42:07
+483,Paula,phowellde@samsung.com,34.215.28.216,1993-11-29 15:55:00
+484,Ruth,rpiercedf@tripadvisor.com,111.30.130.123,1986-08-17 10:19:38
+485,Phyllis,paustindg@vk.com,50.84.34.178,1994-04-13 03:05:24
+486,Laura,lfosterdh@usnews.com,37.8.101.33,2001-06-30 08:58:59
+487,Eric,etaylordi@com.com,103.183.253.45,2006-09-15 20:18:46
+488,Doris,driveradj@prweb.com,247.16.2.199,1989-05-08 09:27:09
+489,Ryan,rhughesdk@elegantthemes.com,103.234.153.232,1989-08-01 18:36:06
+490,Steve,smoralesdl@jigsy.com,3.76.84.207,2011-03-13 17:01:05
+491,Louis,lsullivandm@who.int,78.135.44.208,1975-11-26 16:01:23
+492,Catherine,ctuckerdn@seattletimes.com,93.137.106.21,1990-03-13 16:14:56
+493,Ann,adixondo@gmpg.org,191.136.222.111,2002-06-05 14:22:18
+494,Johnny,jhartdp@amazon.com,103.252.198.39,1988-07-30 23:54:49
+495,Susan,srichardsdq@skype.com,126.247.192.11,2005-01-09 12:08:14
+496,Brenda,bparkerdr@skype.com,63.232.216.86,1974-05-18 05:58:29
+497,Tammy,tmurphyds@constantcontact.com,56.56.37.112,2014-08-05 18:22:25
+498,Larry,lhayesdt@wordpress.com,162.146.13.46,1997-02-26 14:01:53
+499,,ethomasdu@hhs.gov,6.241.88.250,2007-09-14 13:03:34
+500,Paula,pshawdv@networksolutions.com,123.27.47.249,2003-10-30 21:19:20
diff --git a/test/integration/005_simple_seed_test/test_simple_seed.py b/test/integration/005_simple_seed_test/test_simple_seed.py
index 94f6fa86dc2..2d834e675e7 100644
--- a/test/integration/005_simple_seed_test/test_simple_seed.py
+++ b/test/integration/005_simple_seed_test/test_simple_seed.py
@@ -1,6 +1,11 @@
+import os
+
 from test.integration.base import DBTIntegrationTest, use_profile
 
 from dbt.exceptions import CompilationException
+from dbt.compat import open_file
+
+
 
 class TestSimpleSeed(DBTIntegrationTest):
 
@@ -162,5 +167,33 @@ def test_postgres_dbt_run_skips_seeds(self):
             self.run_dbt(['seed'])
 
 
+class TestSimpleSeedWithBOM(DBTIntegrationTest):
+
+    def setUp(self):
+        DBTIntegrationTest.setUp(self)
+        self.run_sql_file("test/integration/005_simple_seed_test/seed.sql")
 
+    @property
+    def schema(self):
+        return "simple_seed_005"
 
+    @property
+    def models(self):
+        return "test/integration/005_simple_seed_test/models"
+
+    @property
+    def project_config(self):
+        return {
+            "data-paths": ['test/integration/005_simple_seed_test/data-bom']
+        }
+
+    @use_profile('postgres')
+    def test_simple_seed(self):
+        # first make sure nobody "fixed" the file by accident
+        seed_path = os.path.join(self.config.data_paths[0], 'seed_bom.csv')
+        # 'test/integration/005_simple_seed_test/data-bom/seed_bom.csv'
+        with open_file(seed_path) as fp:
+            self.assertEqual(fp.read(1), u'\ufeff')
+        results = self.run_dbt(["seed"])
+        self.assertEqual(len(results),  1)
+        self.assertTablesEqual("seed_bom", "seed_expected")
diff --git a/test/unit/test_agate_helper.py b/test/unit/test_agate_helper.py
index ba8c4785cec..e39afcba009 100644
--- a/test/unit/test_agate_helper.py
+++ b/test/unit/test_agate_helper.py
@@ -13,6 +13,8 @@
 1,n,test,3.2,20180806T11:33:29.320Z,True,NULL
 2,y,asdf,900,20180806T11:35:29.320Z,False,a string"""
 
+SAMPLE_CSV_BOM_DATA = u'\ufeff' + SAMPLE_CSV_DATA
+
 
 EXPECTED = [
     [1, 'n', 'test', Decimal('3.2'),
@@ -41,6 +43,15 @@ def test_from_csv(self):
         for idx, row in enumerate(tbl):
             self.assertEqual(list(row), EXPECTED[idx])
 
+    def test_bom_from_csv(self):
+        path = os.path.join(self.tempdir, 'input.csv')
+        with open(path, 'wb') as fp:
+            fp.write(SAMPLE_CSV_BOM_DATA.encode('utf-8'))
+        tbl = agate_helper.from_csv(path)
+        self.assertEqual(len(tbl), len(EXPECTED))
+        for idx, row in enumerate(tbl):
+            self.assertEqual(list(row), EXPECTED[idx])
+
     def test_from_data(self):
         column_names = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
         data = [


Code review comments:
diff_hunk: @@ -41,4 +42,7 @@ def as_matrix(table):
 
 
 def from_csv(abspath):
-    return agate.Table.from_csv(abspath, column_types=DEFAULT_TYPE_TESTER)
+    with dbt.compat.open_file(abspath) as fp:
+        if fp.read(1) != u'\ufeff':
path: core/dbt/clients/agate_helper.py
text: @user1:
did you try using `codecs.BOM_UTF8` instead of the hardcoded value here?

https://docs.python.org/2/library/codecs.html#codecs.BOM_UTF8
https://docs.python.org/3/library/codecs.html#codecs.BOM_UTF8

@author:
I'm explicitly opening the value as unicode (that's what `open_file` does), so examining the unicode code point rather than the byte sequence is correct.

@user1:
Not suggesting that your comparison is wrong, just that you could replace the magic value `u'\ufeff'` with `codecs.BOM_UTF8.decode('utf-8')`