diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index 118d6ca913945d41fc79b34e09949b4ae7830920..b95f03012205f4ec02832d610833f39797d43a15 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -101,7 +101,7 @@ class File() :
return ret
#__tempFileWrapper
- def __parseCsvFile(self, handle) :
+ def __parseCsvFile(self, handle_) :
"""
Parse a CSV file.
The stream is not rewinded after use.
@@ -112,6 +112,14 @@ class File() :
@return: list of lists
@rtype: list
"""
+ # We wrap the file in a temporary file just to have universal newlines
+ # which is not always possible to have on incoming files (thinks web
+ # and rpc frontends). This transparently solves the problem of Unix
+ # versus Windows versus Mac style newlines.
+ handle = tempfile.TemporaryFile('rU+w')
+ for chunk in handle_:
+ handle.write(chunk)
+
handle.seek(0)
buf = handle.read(BUFFER_SIZE)
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index ebec512a302b57cfd417a8a22ededabd8cd5aea8..f8d0dee86b886b52ee1fc3a712cc58ccac942028 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -91,10 +91,7 @@ class Scheduler() :
@arg url: The url containing the results
@type url: string
"""
- # Mail is set to 'test@test.test" if the batch job was submitted from
- # a unit test.
- # Todo: Use `settings.TESTING` instead.
- if mailTo == 'test@test.test':
+ if settings.TESTING:
return
# Mail is set to 'job@webservice' if the batch job was submitted using
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index ca9982824df6d42421c4b8da1509bd118c7e1844..e82836638af058a695bf19145cf5e28bad8b9a13 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -10,7 +10,6 @@ from itertools import izip_longest
from Bio import SeqIO, Entrez
from Bio.Alphabet import ProteinAlphabet
-from sqlalchemy import and_, or_
from mutalyzer.config import settings
from mutalyzer.db import queries
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 362b6639c530073d47606f37f524bd37d93b5ea4..6a287117a800b9c041693f06a646013b7a82e3e5 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -16,6 +16,7 @@ from spyne.model.complex import Array
from spyne.model.fault import Fault
import os
import socket
+from cStringIO import StringIO
import tempfile
from operator import itemgetter, attrgetter
from sqlalchemy import and_, or_
@@ -96,24 +97,15 @@ class MutalyzerService(ServiceBase):
# Todo: Set maximum request size by specifying the max_content_length
# argument for spyne.server.wsgi.WsgiApplication in all webservice
# instantiations.
- max_size = settings.MAX_FILE_SIZE
-
- batch_file = tempfile.TemporaryFile()
- size = 0
- try:
- for chunk in data:
- size += len(chunk)
- if size > max_size:
- raise Fault('EMAXSIZE',
- 'Only files up to %s megabytes are accepted.' % (float(max_size) / 1048576))
- batch_file.write(chunk)
- batch_file.seek(0)
- job, columns = file_instance.parseBatchFile(batch_file)
- finally:
- try:
- batch_file.close()
- except IOError:
- pass
+ if sum(len(s) for s in data) > settings.MAX_FILE_SIZE:
+ raise Fault('EMAXSIZE',
+ 'Only files up to %d megabytes are accepted.'
+ % (settings.MAX_FILE_SIZE // 1048576))
+
+ batch_file = StringIO(data)
+
+ job, columns = file_instance.parseBatchFile(batch_file)
+ batch_file.close()
if job is None:
raise Fault('EPARSE', 'Could not parse input file, please check your file format.')
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 702584c03974c9e67d17dcdbb628c651fd966a69..936f0812b6abb077cb17dcb252a146cb3a5285f5 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -809,42 +809,6 @@ def format_usage(usage=None, keywords={}):
#format_usage
-def slow(f):
- """
- Decorator for slow tests. This makes them to pass immediately, without
- running them. But only if the environment variable MUTALYZER_QUICK_TEST
- is 1.
-
- @todo: I don't think this actually belongs here (a separate util module
- for the unit tests?).
- """
- @wraps(f)
- def slow_f(*args, **kwargs):
- if 'MUTALYZER_QUICK_TEST' in os.environ \
- and os.environ['MUTALYZER_QUICK_TEST'] == '1':
- return
- else:
- return f(*args, **kwargs)
- return slow_f
-#slow
-
-
-def skip(f):
- """
- Decorator to disable a unit test. This makes it pass immediately, without
- running them.
-
- @todo: Perhaps it's possible to indicate to nose that the test is skipped?
- @todo: I don't think this actually belongs here (a separate util module
- for the unit tests?).
- """
- @wraps(f)
- def disabled_f(*args, **kwargs):
- return
- return disabled_f
-#skip
-
-
def singleton(cls):
"""
Decorator to define a class with a singleton instance.
diff --git a/mutalyzer/website/templates/reference-loader.html b/mutalyzer/website/templates/reference-loader.html
index 44045ce4cad817d497078dae9ee904f14cb18139..6631298c2a77867d0f6f38755bccf379c5ece44c 100644
--- a/mutalyzer/website/templates/reference-loader.html
+++ b/mutalyzer/website/templates/reference-loader.html
@@ -179,7 +179,7 @@ sequence (maximum size is {{ max_file_size }} megabytes):
reference: <b>{{ ud }}</b>
</p>
<p>
- <a href="{{ url_for('.reference', filename=ud + '.gb') }}">Download this reference sequence.</a>
+ <a href="{{ url_for('.reference', filename=ud + '.gb') }}" id="reference_download">Download this reference sequence.</a>
</p>
{% endif %}
diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py
index 63ae9031796b211e9a0dcc347b89fefc9450ffbf..9d85548dba88c350145e943dede74eefb10892e5 100644
--- a/mutalyzer/website/views.py
+++ b/mutalyzer/website/views.py
@@ -292,7 +292,7 @@ def name_checker():
'cdsStop_c' : output.getIndexedOutput('cdsStop_c', 0),
'restrictionSites' : output.getOutput('restrictionSites'),
'legends' : output.getOutput('legends'),
- 'reference_filename' : reference_filename,
+ 'reference_filename' : reference_filename, # Todo: Download link is not shown...
'browserLink' : browser_link,
'extractedDescription': extracted,
'extractedProtein' : extractedProt,
diff --git a/requirements.txt b/requirements.txt
index 5e5f2130dd594cc048f4bb6dab356c45e726705c..9ff2792de21b7f19262e2bee566d1d82cf8c16fe 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,8 +10,6 @@ spyne==2.10.9
suds==0.4
wsgiref==0.1.2
xlrd==0.9.2
-WebOb==1.1.1
-WebTest==1.4.2
cssselect==0.9.1
Jinja2==2.7.1
-e git+https://github.com/mammadori/magic-python.git#egg=Magic_file_extensions
@@ -19,3 +17,4 @@ Flask==0.10.1
SQLAlchemy==0.9.1
redis==2.8.0
mockredispy==2.8.0.2
+mock==1.0.1
diff --git a/tests/data/AA010203.1.gb.bz2 b/tests/data/AA010203.1.gb.bz2
new file mode 100644
index 0000000000000000000000000000000000000000..fceb1e828997fbfb732029db9961f3184d2b4ab3
Binary files /dev/null and b/tests/data/AA010203.1.gb.bz2 differ
diff --git a/tests/data/AB026906.1.gb b/tests/data/AB026906.1.gb
deleted file mode 100644
index 634426657cd37708d92af19c826eefbf41cbb88d..0000000000000000000000000000000000000000
--- a/tests/data/AB026906.1.gb
+++ /dev/null
@@ -1,369 +0,0 @@
-LOCUS AB026906 18678 bp DNA linear PRI 08-DEC-1999
-DEFINITION Homo sapiens SDHD gene for small subunit of cytochrome b of
- succinate dehydrogenase, complete cds.
-ACCESSION AB026906
-VERSION AB026906.1 GI:5295993
-KEYWORDS small subunit of cytochrome b of succinate dehydrogenase.
-SOURCE Homo sapiens (human)
- ORGANISM Homo sapiens
- Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
- Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
- Catarrhini; Hominidae; Homo.
-REFERENCE 1
- AUTHORS Hirawake,H., Taniwaki,M., Tamura,A., Kojima,S. and Kita,K.
- TITLE Cytochrome b in human complex II (succinate-ubiquinone
- oxidoreductase): cDNA cloning of the components in liver
- mitochondria and chromosome assignment of the genes for the large
- (SDHC) and small (SDHD) subunits to 1q21 and 11q23
- JOURNAL Cytogenet. Cell Genet. 79 (1-2), 132-138 (1997)
- PUBMED 9533030
-REFERENCE 2
- AUTHORS Hirawake,H., Taniwaki,M., Tamura,A., Amino,H., Tomitsuka,E. and
- Kita,K.
- TITLE Characterization of the human SDHD gene encoding the small subunit
- of cytochrome b (cybS) in mitochondrial succinate-ubiquinone
- oxidoreductase
- JOURNAL Biochim. Biophys. Acta 1412 (3), 295-300 (1999)
- PUBMED 10482792
-REFERENCE 3 (bases 1 to 18678)
- AUTHORS Kita,K.
- TITLE Direct Submission
- JOURNAL Submitted (01-MAY-1999) Kiyoshi Kita, The University of Tokyo,
- Department of Biomedical Science, Graduate School of Medicine;
- 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- (E-mail:kitak@m.u-tokyo.ac.jp, Tel:81-3-5841-3526,
- Fax:81-3-5841-3444)
-FEATURES Location/Qualifiers
- source 1..18678
- /organism="Homo sapiens"
- /mol_type="genomic DNA"
- /db_xref="taxon:9606"
- /chromosome="11"
- /map="11q23"
- gene join(5809..5860,6758..6874,7768..7912,13710..13875)
- /gene="SDHD"
- CDS join(5809..5860,6758..6874,7768..7912,13710..13875)
- /gene="SDHD"
- /codon_start=1
- /product="small subunit of cytochrome b of succinate
- dehydrogenase"
- /protein_id="BAA81889.1"
- /db_xref="GI:5295994"
- /translation="MAVLWRLSAVCGALGGRALLLRTPVVRPAHISAFLQDRPIPEWC
- GVQHIHLSPSHHSGSKAASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLH
- GHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKL"
-ORIGIN
- 1 gatcacgagg tcaagagatt gagaccatcc tagccaacat ggtgaaaccc cagctctact
- 61 aaaaatacaa aaattagccg ggcgtggtgg catgcgcctg tagtcccagc tactcgggag
- 121 gctgaggcag gagaatcact tgaacccagg aggtggaggt tgcagttgag ccgagattgc
- 181 accactgcac tccagcctgg caactgagtg agactctgtc tcaagaaaaa aagaaaaaaa
- 241 taataataag gctgggcgcg gtggctcatg cttgtaatcc cagcactttg ggaggccaaa
- 301 gcgggcagat ccatgaggtc aggagtttga gaccagcctg gccaacataa tgaaacccca
- 361 tctctactaa aaatacaaaa attagccagg catggtagca tgtgcctgta gtcccagcta
- 421 ctcgggaggc taaggcagga gaatcacttg aaatcgggag gcggaggttg cagtgagctg
- 481 agatcacgcc actgcactcc agcctgggca agagtgagac tccatctcaa aaaaaaaaaa
- 541 aaaaaattgt ccccatgtag acagcatgat attatgaagt gtttttggaa aagtgcttca
- 601 tagctaaaga gcagagtgta agagttcgtt agtgtttctt aaggaaagca atggcaagtt
- 661 ctcttacaaa tggacaaaat aatcttgtat gtctgaagtg atagtgtaca gtacaggaaa
- 721 tgtagctgtt actgagctat aatgggggct tggttctacc atatctctac tttgtgttta
- 781 tgtttgtgta tgcatgtact ccaaagtctt tctaatgttg ctttaatttc caaaaatgta
- 841 tgcattgctt taacaataca tgtgatgtgt catattacag atggggtcac agtggttata
- 901 aagagttata ccctgaagaa tttgaaacag acaggtaagg aaaataggct tactgaaaga
- 961 aactaagatg gtacaaaatc tgtattataa attgatttct taacttttac gaagaatata
- 1021 cttgccatca aaaatgtagc tagagaaaca ataggtgatt tagttaggag gtgatccctg
- 1081 ttttcccatt ctctggttga tgtttggcat gtctgtaagc attttggttt ttatatatag
- 1141 tattccatac agtaactcag tatggcagct tagaattttt accttcattt taaagatgag
- 1201 gaaacaaaaa ctcaatgaga atattaaagt gttaaagtat acattaaagt gcttatttaa
- 1261 aattcagatg ttaacctcaa ttttttaatc tagaatgcaa aatattaaaa taatacgctt
- 1321 tttttttaca taaaagcttc tattttttaa cttttcttat tagtagtgat cagcaagata
- 1381 ttaccaacgg gaagaaaaca tctccccagg taaagtcatc tacccatgaa tcccgcaaac
- 1441 acaagaagtc aaagaaatcc cacaaaaaaa agcagaaaaa aaggtcacac aaaaaacaga
- 1501 agaaaagcaa aaaggaagcc acagatataa cagcagattc ctcgagtgag ttctcagaag
- 1561 aaactggggc ttctggtaca aggaaaggga aacaaccaca taaacgcaag aaaaaatcca
- 1621 ggaaaaagtc tctcaaaaaa cctgctttat tcttagaggc agaaagtaac acttcacatt
- 1681 cagatgattc agcatccagc agttctgagg aaagtgagga aagagacact aagaaaacca
- 1741 aaaggaaaaa gagagagaaa aaagcccata cctctgtagc caacaatgaa atacaggaga
- 1801 ggacaaacaa acgcacaaat tggaaagtag ctacagatga aaggtctgct gagagctcag
- 1861 aggatgacta aatgggaaac acttttgttt tccacatgac tgtggatatt tacagttctt
- 1921 actccttgtg gttttgccag tgactcttgt tcagcacggg gcctgaggtc agagctgtct
- 1981 tgtgccatct gtatgttctg acagacgtct tgtcttctat tttggcgtta agcttgatcc
- 2041 ccttttcttg ttaaaaggga atctggtatt ttgttatgaa ggtttcttga agagattatt
- 2101 tttttttgca attaattacg tttagtgtag agtgcatata cagcaaatta aaggacccag
- 2161 aaagctggat ccaatagtga cctgggtaca ccaatcggaa tattgaattt ggggaagtca
- 2221 agggctggga tcaagaggtg gattggaact aatgccatgt aggatggtat gacaaggcaa
- 2281 cactgtattg ctctctgttt atatagcagg tgtcacaact aacttgtctt tagccttggt
- 2341 gctttgatcc ttctatattt tgaccccaca ggtgtggtcc ggtttactta atcaggacat
- 2401 gggcctaaga acaaaccttt tcccttcatg ataacatcca tagacaactt attagaaggg
- 2461 actagagttt ttgcaaattt ccctgctgga tggggcctat agctatactt agtatatgcc
- 2521 taaacatggt aattggatag taaatggttt tctagttcca ttgctgtata tttgcctaaa
- 2581 tggacttgtg ttcaaattat ttcttcaatt gtcatagata atcctgtacc aaatggggaa
- 2641 gaattaggaa ataatcatgt tgtctaatgg tactctggat tcagggcagc aactgccatt
- 2701 taaatgttgt cttgttcatt tctaaatctg ttcatgaagt ttaggttttc cctgaaacta
- 2761 agttgaatta tttccaaaat gaaacaggct tctcagggac atatccactt cttcccagtc
- 2821 tgcctttgga ttaaagcacc aagcagagac cacattaatt ccctttgcta tactgtgatc
- 2881 cttagtatgt taattcttaa gaaaccaaca tatcactgaa agaaggctgg cagaacgcaa
- 2941 gtgcattttt tcactgtggg aagaaagatc aagtgacgta ttattttttc ctggttgtca
- 3001 cttaatgggc tgagtaaaaa gcttgaaaac tcagactttc ggtcttggtt ctgccactca
- 3061 ttggttatga ggaggcccag agcaggtaag ttcaccttcc tggccttact ttcctgatgt
- 3121 gtaatacgga attacttcac agtagcatga cagtataaga caccagcagt agatacaact
- 3181 atgatgacat tccatgagtt ggtattttta gttctaactg ctaaatttgt tctctttacg
- 3241 ggacagattt ctaataaagt gcttggtctt aaaatacatg gttggacaga gtgccctatc
- 3301 ccttaactat gagcaggtgc taccttttgg gatatttatt ttaaatttta atactttggt
- 3361 actcaattgt cagtgttcca tggtgtgtat ttttattttt gggattagtg ggggtctaaa
- 3421 gggagaagaa tagtctctaa ttactacctc ttaacctaaa gcaattattt tgttcctgga
- 3481 gcaagttaaa tctttgttgg aaggagcttt ggccatatat tttttagcat gcattgtttc
- 3541 tgtgccctga aagtacctga aaggttttaa gcacagactc aggaaaatgt gccagtagaa
- 3601 caggccatct ccaggaaatt ggctctattt gggtcctgac cttcccttcc tcccaagtta
- 3661 gcaggcttgt tcttttgcaa ggaatacaca tcttgccttt tttttttttt tttttttgcc
- 3721 atgttttcct tttcttggtc atgtataagc aataaagctg ttttttgttc ttcatctttc
- 3781 ttaaccccaa attttcttct atgccttagg cttcgatggt tcttccaacc cccttaatat
- 3841 ggcttagggt ggtttttcaa aacctacaat cccccatttg cactactggc catggaacat
- 3901 ttatttctag tgttcctgcc aatcagagat ctctatatta aattctaaaa tgggattaaa
- 3961 agaagagttg gagaattcac acttattgag taactgatgt catacaacct ggaatttctg
- 4021 aattccaaat aaataaattt cactctttga acatttcatc ttttactttt tagcaccaac
- 4081 agacttgata acagcctgat gctgatctga caatgggttg atagccttcc cccactgacc
- 4141 cttaaatctg cttagtaaca agtcctttgc ttctgtcatt ctcctggggg atggcctact
- 4201 gccctccttt ctgtacaatc tgggcaaacc gactggtgat ggcaagagtg gtgtcaatga
- 4261 agcggtctac acagctggag agacaatttt cagtgcgaga gtctaggcga ttccctggct
- 4321 tctccacaca tttatcccaa cataactcca tgaagtgatg cacctaaaag gaaagaaaaa
- 4381 tagtaaccat tggggtctgc agataggcct aactcttgtt tattaacttc tcactttttg
- 4441 acacctgaca aaaccattct ttaaatcaac cacggagtca ctttgggctc ttctctttct
- 4501 tcatttccta attagtcacc aatattgatc cagatcctcg tccctacaga ttgtacattc
- 4561 tcaggtagga ctaataacct tttatattcc ccaaagtagc tagcaccatt gtgaaccaac
- 4621 tagggaacca attaattttc ccaaactatt gcactcattt tattccaaac ctatccccta
- 4681 gacaaggtaa ttcttccatt aaccttttgg gggttatgga tccactcccc agaaaaatgc
- 4741 acatacaggc acagaaatta tgtgcactgt cattagaatg ttcagggccc aaagatttct
- 4801 agccagggtt cttgctggtc atccgagcac cctcttcctc ccacccaaaa ggaaaaaacc
- 4861 attttaccaa gagcttacta tttgtgaggc tgggtactaa gaaatcagtt ctctctaagg
- 4921 tcctcaagga tagctgtcat cacctcccat ttaagaggcg tgattatgta gtccaaggtc
- 4981 atgtagccag caagaagtca ggccgcgtta gaaccatgtc cgaagggctc caaacccttg
- 5041 ttctacatcc atagtctaca gcgactactt cagagtccac cttcctccga taatgttcta
- 5101 gtcgttttca aatacattgt cgcatatgat cctcacaatc cagtgaggca gtggggtgac
- 5161 ggcgaaacca aaacccacag tggatgagta tcttttctac gggcacgtgg cctgcaagga
- 5221 gcagagggag gatgagaacc cagatctttc gaatgccagc ccagtcatgt cgccggctaa
- 5281 ctagtctccc gtacccttgc gtcgcccaaa tcttccctgc tttacacctt ttcttttctc
- 5341 cacgctacgc ttatatacct ggcacctgag cactaccggt caccagggac aggagagcca
- 5401 taactttgtc tttcgtgagg ggaatgggat gcagccggga tcgagcacca gtgagccgcc
- 5461 agtgtacaga cctccgagcg tgcccaggac caccaaggaa ggtgaaactt cctttccctt
- 5521 caccctcccc gtccccgcac ctgtgcagta aactgcgcct tctgctgctc ggcggccacc
- 5581 aggcgctgca actccgcttc atcggcttcg cccagctccg ccattgttcg cctcaggctc
- 5641 gccaccttcc gacagctgtg tttgcgcatg cgcgacgggt gtgcaccgcc tctcgacttc
- 5701 cggttcaccc agcatttcct cttccctgtt ttctttcgtc gtcgtgggtg ggaattgtcg
- 5761 cctaagtggt tccgggttgg tggatgacct tgagccctca ggaacgagat ggcggttctc
- 5821 tggaggctga gtgccgtttg cggtgcccta ggaggccgag gtgaggggtc ttcccaccct
- 5881 gaggtgctta gcgtagcctc cagccaggga aggggatgga agtgaggact catctgccgg
- 5941 gtgggagatc tcttgaggag aagaaaatac cgaaatcaca gcaatgacca ctgtagtcta
- 6001 ggggtccaga tgtttacccg aaggtatatt tcacttgctg tgagctgacg agttgaggga
- 6061 ataatcagaa agagagctcc ctctggaagt cgcagtcctg atgaggctaa tccacatagc
- 6121 agttctgttt tctccccgtt cactgtccct agaatgctcc ccactcgctc ccaccctgag
- 6181 tcgggaaaga gggttaggag cttgcccatt tcttctggag ttggtgtgtt tggatgtggg
- 6241 agtggagggg ggatcagttc gaaaatcatt taacctgggc atttgtgtta cctcaggtac
- 6301 tgtagtaatg ctaggataca aatgtgaaga aaacgtagtt cccgccctca acgagctttc
- 6361 attctgatga ggaaaacact gtcatagtag tccgggcaag atgaggtcct gaactaggaa
- 6421 agtagcacaa agaaaagaag attgtctcaa gaactgttaa agagatacgc caataggatt
- 6481 tggcgattga atttagggga aaagtctctc atgatttcca gattactgag ttaggttaaa
- 6541 gaatgcctga ggtgtcatta aataaagtag ggaacatgca gatgttccct ggtcttaact
- 6601 tcacagtaac cccagtgaaa tagatgctat cttcatttta caaataagat gttatcccct
- 6661 atttattgtt aagtagctta cctatggtca tttagaaagt ttgtcagtcc tgttaaagga
- 6721 gaggttctta tgatcatcct aatgactctt tcctcagctc tgttgcttcg aactccagtg
- 6781 gtcagacctg ctcatatctc agcatttctt caggaccgac ctatcccaga atggtgtgga
- 6841 gtgcagcaca tacacttgtc accgagccac cattgtatgt tctctccatc gctgctgctt
- 6901 tctgggctct agccatcttt accttcacta atggtcatgc ctttagcagg acttcctacc
- 6961 tgtagggggg actcttgtgt ccaactttgt caaatgaaga cctagtttac acctttgggc
- 7021 agacagtgcc attatggttg aatgatgcca tttataatca tagaagacct tctagcctaa
- 7081 gtctttacaa atttttttct tttgttttct ttttttttga gacagagtct cgctctgtta
- 7141 tgcaggctgg agtgcagtgg tgcgatctcg gctcactgca acctccacct tctgagttca
- 7201 agcaattctc ctgcccctgc ctcccgacta gctgggatta caggcgccca ccaccatgcc
- 7261 cagctaagtt ttgtactttt agtagagacg ggtttcaccg tgttggccgg gctggtctca
- 7321 aactcctgac ctcctcaaac tcctgacctc aggtgatctg cccacctcag cctcccaaag
- 7381 tgctgggatt gcaggcgtga gccaccacgc ctggaccact aacttacatt cataaggtgt
- 7441 ctgttcactt cactgaacca agactggctt aattctgtag caatacagca attctgtttt
- 7501 ttatccatct tcttggatct gtcttctaat caatatgtag gcattgagat acccttgtgc
- 7561 taaaagactt caaaaaacag agataaagcc ttcaaaaaac agagatagct tctctcaact
- 7621 actattttga tattttactt cctttgtact cagagttata tcctatatgt acactgcctg
- 7681 tcagtttggg ttactgtgtg gcatatgttg aacatgaaag atgtgtgttt ctcacatcaa
- 7741 cttttatgaa tctggtcctt tttgtagctg gctccaaggc tgcatctctc cactggacta
- 7801 gcgagagggt tgtcagtgtt ttgctcctgg gtctgcttcc ggctgcttat ttgaatcctt
- 7861 gctctgcgat ggactattcc ctggctgcag ccctcactct tcatggtcac tggcaagtat
- 7921 agcaattcca aatatagttg tctgctcagt ttgtttgctg tgagcttgtc ttatgtatta
- 7981 tatatgaggg agaagttgat tgaaatgccc taaatttgtt gaaaacttta aaatatatat
- 8041 aaaatatgta tatgcctaga tttatatatc tgcctgccta ttcaatgtct ttcaattcga
- 8101 tttccgtatc taatagcatt ttgaatgtag cctgtcaaac tgaatttctg atctccccta
- 8161 atctgttcct cctgcactct tgccccatct gaattaatgg catttccagt tttctctttg
- 8221 ttcaagtcta aacctggtaa gctccaaact tggtcattat ccttgactct agtagtagtc
- 8281 tcctaactgg ttcccatttg tgttcattcc caacacagca tacccagtga tcctgttaaa
- 8341 atgttaatta gaataagaca ttccccttct caaaacccta ttttgtctct tcatgttact
- 8401 caaagtcaga attcttaggg ttgtctgtag actctacatg attgaaccac cctgtttctt
- 8461 ccctcatttt tagctgctct ctctctcatt cacactgcct tccttgagat tccttgaaca
- 8521 tgccagggac attccaggtc tcagggcttc tcttaactgc ttctgcctga aactcttttt
- 8581 ctagctatac acttggcttg ttccttcatc tccttcaggt cttgaatgcc attctctcaa
- 8641 caaagccttc cctaaccact tattcaaaat tgcagtttct gtcctgccat tccttatctc
- 8701 tcttgcttgt tttatttttc tcaatagtac ttactgcctt ctaatatact acatcatctg
- 8761 ttcattattt tatatagtaa ttgcttcctt gcattttatc acccaaatgt atatccctaa
- 8821 atagtatagt ttattcttgc ctcttaaaaa aaaaaaagag atgtatgtgg gtggattatt
- 8881 ttgttatttt tactgtattt gtttgctgtt gtgcctctag agcctagaac tactctctgg
- 8941 tacgtgacat atagcactca gtaaatactt gctgaatgaa tgagcatcca gcgcctgttt
- 9001 gtttgtttgt ttgtttgttt attttttgag acagagtctc gctctgttgc ccaggctgga
- 9061 gtgcaatggt gtgatctcag ctcaccacaa cctccgcctc ccaggtacaa gcgattctcc
- 9121 ctgcctcagc ctcccaagta gctgggatta caggcgtgca ccaccacatc cggctaattt
- 9181 ttttgtattt ttagtagaga cggggtttcg ccattttggc caggctggtc tggaactcct
- 9241 gacctcaggt gatctgcccg cttcagcctc ctaaagtgct gggattacag gcgtgagcca
- 9301 ccatgtccgg cccagctttt gtttatttta tctggtatag tttgtatgac tttctacgta
- 9361 atgaaccttc taaaatgagg gtaaatgaca ggttgggttc cttgagttgt tctttttaag
- 9421 ttttgcaagg gacaatatgt tgtcattgtg gggggtaggg agccactttc ggattgttga
- 9481 aactggaagt actttggaga gtatcttaac caactctttt attttacaga tttggaaact
- 9541 aagacccagg gaggttaagt gacttgtcag aatcattttc tagctagtgt taaagatttt
- 9601 ttttttcttt tttttttggg acggagtctc actctcaccc aggctggagt gcagtggtgt
- 9661 gatcttggtt cactgcaacc tctgcctcct gggttcaagc aattctcatg cctcagcctc
- 9721 ccaagcagct gggattacag gcatgcgcca gcacacctgg ctcagttttg tattttaaat
- 9781 cgagacgggg tttcaccatg ttgtccaggc tggtcttgga ctcctgacct caagtgatcc
- 9841 tcccaccttg gcctcccaaa gtgctgggat tataggtgtg aaccaccgtg cccagcctaa
- 9901 aggggtttta attatctggt tttgtaggac tggttaggag aatgagttgt tgttgttgat
- 9961 gttgtttttt aaccacacag acctttccaa ataaaagatt ccagttgcat atgaaatatt
- 10021 agatcacaag tacagtaagt aatatttctc taacatgtca tccctcttga aggagctgtc
- 10081 tataatgtgc tccacttcct caacactgag tctcttttag cctgtattaa ttggggtctt
- 10141 atcccaacta tataacttag gttattctta ccaagggcac tgaaggcctt catctttcca
- 10201 aatccggttg tctattttct gccctccact tgcttgaagt ctcagccgcc ttcaactcaa
- 10261 ttaacaattc tccccataag tcacttttct ttggctttcc agatgcatag aagtctcctc
- 10321 tgccagatcc ttctcctctt gtctgacctc gagatgacaa aatctccagg gctgagtcat
- 10381 ggccttctta atttctccat ctgtaccctt ttttaggtga gctcagatct gacctgtttt
- 10441 tctgagctgc agacttgttt atctaattgt ctaattgaca tccacttgga tgtctgatag
- 10501 ttatcccaga tctaacattg gccaaatcgc tcttttttcc ccccaaatct cccttgattt
- 10561 ctcctttaaa acccccttct caaagctatg ctcaaactaa aattcttagg agtcattcta
- 10621 gatatttctt tttgttctta ccccacttat tccatcagtt ctgttctttc tttaaaaaat
- 10681 agtctgaatc ggccaggcgt ggtctcacgc ctgtaatcct agcactttgg gaggccgagg
- 10741 cgggcggatc atgaggtcag gagtttgaga ccagcctggc caatatggtg aaaccttgtc
- 10801 tctactaata atacaaaaat taagctgggc gtggtggcac acgcctttag tcccagctac
- 10861 ttgggagact gaggcagaag aaccgctgga acccaggagg tggaggttgt agtgagccaa
- 10921 gatcgtgcca ctgcactcca gcctgggtga cagagtgaga ctctgtctca aaaaaacaaa
- 10981 actctgaatc ggtcgagggg aaggggaggg agagcactag gataaatacc taatgcacgc
- 11041 ggagcttaaa ccctagatga cgggttgata ggtgcagcaa accaccatgg cacatgtata
- 11101 cctgtgtaac aaacctgcac gttcagcaca tgtatcccag aacttaaagt acaagaagaa
- 11161 aaaaaaaaag gaaaatggac attattagaa aaaaaaatag tctgaattgt cactttgcac
- 11221 cctgtcacca gcctaggtta agacaacagt ctcacgtagg ctacttcggt tgccttctaa
- 11281 ctagtttcct cttcagttgt tgctctgtcc cccacccact ctgttcattc atcacactac
- 11341 agccatagtg acctttttaa aacgtaaaat tatattcctc caaagtagat atacaaatgg
- 11401 ccaataagca catcagaaat tgctcagcat catttgtcat tagagaaatg caaatcaaca
- 11461 ccacaatgag atgccacctc acaccccatt aggatggctg taataaaaga tgggcagttt
- 11521 taagtgttgc tgaggacttg gagaaattgg aaccctcgtg gttctgctgg gaatataaaa
- 11581 cgtttcaatc actttggaaa acattctggc agttacaaca aaaagttaac cttagagtta
- 11641 ccatctgact cggcgatcta cttttaggtg tatacccaag agaactgaaa acgtgtccac
- 11701 gcaaaaaact tgtacaggaa tgatcatagc agcattattt ataatagcca aagagtggaa
- 11761 acaatccaaa tggctgtcag tggatgaata gctaaacaaa atatggtgta ttcatacaat
- 11821 agaatattat tcagccatac aaaggaatga tgtattgata aatgctatga catggatgaa
- 11881 cattgaaaac attatgctaa gttgacacaa aggccatata ttgtatggct tttttttttt
- 11941 tttttttttt tttgagacag agttttgctc ttgtcgctca ggctggagtg caatggtgcg
- 12001 atcttggctc ggcacgatct cggctcagca cgatctcggc ttactgcaac ctccgccttt
- 12061 cgggttcaag cgattctcct gcctcagcct cccaagtagc tggcattaca ggcatgtgcc
- 12121 accacgcctg gctaattttg tattttttgt agagatgggg tttctccttg ttggtcaggc
- 12181 tggtcttgaa ctcccaacat caggtgatcc gcccacttca cccacccaaa gtgctgggat
- 12241 tacaggtgtg agccaccacg cccagtggtg tatgggttct tttatatgaa atgtctagaa
- 12301 caggcaaagc catagagaca gaaagtaaat ttgtagttgg gtagtgggct aagaggtaga
- 12361 gggtttcttt ttggggtaat gagaatgttc tggaattaaa tgatgattgc acaactcaat
- 12421 atactaaaaa ccagtggatt atatactaaa aagcgtgaat tttttctggc gtttgactta
- 12481 cattgcaata aaactgttat aaaaatagta aaattaggtc actcctaatc tcaggcactc
- 12541 cctgcttaaa atgtatcagt ggtttcctat tatatttcat ataaaattca gattccttat
- 12601 catgaccttc aaagacccta tgcaaccgac ccctgccttc ctctgatctc tgcttcaccc
- 12661 atgtgctcca gccacacaaa atcttactat tcattagaga tgccactttg gtttggatgt
- 12721 tctcattcat gtcttccttt ctaaagtgtt tcttctcagt aacatatata tttacttttt
- 12781 ccttctcatt cactagtata ttccataagg gtagggatgc tgtctcactt actatactcc
- 12841 caacatttat gacagattct ggcacatgat atctacttaa taaattcttt ttgaattaat
- 12901 taaaaatact gtagagtttt agttattttt agttattggg gcgaaaggat cacttgcagc
- 12961 caagagttca agaccagcct gggcatcatg gtgagaccgc atctttaaag aaataaaaaa
- 13021 caggccaggc gcagtagctc acgcctgtag tcccaacact ttgggaggct gaggtgggcg
- 13081 gatcacaagg tcaggagttc gagaccagcc tggccaatat ggtgaaaccc tgtctctact
- 13141 aaaaatacaa aaattagctg ggtgtggtgg tgggcgcctg tagtcccagc tacttgggag
- 13201 gctggggcag gagaatcact tgaacccggg aggcggaggt tgtagtgagc cgagatcgtg
- 13261 ccactgcact ccagcctggg caaaagagcg agactctgtc tcaataaata aataaataaa
- 13321 taaataaata gaaggaaata aaaaacaatt agccgggcat ggaggcatgc tcctatagtc
- 13381 ccagctactt gggaggctga ggcaggagga tcacttgagc tcaggagttc gaggctgtag
- 13441 tgagctatga tcaggccact gcactccagc gtgggcaaca gagtaagact ttgtctctaa
- 13501 agaaaagtca ctagaaatag acttactgac atacacacgc aaaaggctat acagaatccc
- 13561 ctaaagaagc aaacagtgac agtggagtgg caaatggaga cattgcattt gaacttgaca
- 13621 gattgttttt ttgcagccaa gttatctgta tagtcttcta atttcactgt ggttttttat
- 13681 tgatgttatg attttttctt tttctttagg ggccttggac aagttgttac tgactatgtt
- 13741 catggggatg ccttgcagaa agctgccaag gcagggcttt tggcactttc agctttaacc
- 13801 tttgctgggc tttgctattt caactatcac gatgtgggca tctgcaaagc tgttgccatg
- 13861 ctgtggaagc tctgaccttt ttgacttcat actttgaaga attgatgtat gcctctttgc
- 13921 ctctgctttg tcatgccatt aagctcacaa taaggaagaa ataacagata agtccattgg
- 13981 tggacagcct tcttctctta atcacaagat tattttcaga atttaatctt tgaggaaaag
- 14041 gtttgagagg aattatatct aagttgtgag actgagttct atattctggt gagttaatgg
- 14101 ggttgcctcc cagcttctta taagactcac agtataacta aacatgatat atcagctttt
- 14161 gcctttcaat ttatcaatct cttaaagaga atccaacttt attacgatta gtatatgatc
- 14221 aaacttccat atttgccttg ggaataatgg acaaagggaa atactcttaa ttcatgaata
- 14281 aaaactttgc agaaaattag acagtgttta attttcgaaa acttccctct ctagacagta
- 14341 gataccacct actgatggtt acatatacta gggaaatttt aaaattagga aatgctgata
- 14401 gctcatatta taaatttcta aatcctagga agaaacgctt ggagtgcttc tgaatataca
- 14461 gaagttccat ttaagggcaa gtttccccgt agatgtatca aaatactacc aactgtaaat
- 14521 tgagatttaa ttcccaaatg tattctactt gttctaaaac aatctgtcca caaatataaa
- 14581 actataagta ataaattgtt attttcgcac aatgggaatc tctaatgtga aaatgtattc
- 14641 tatgaaaata atttttttaa ataaaatgtt atataataaa agtgtcttct atgcttttat
- 14701 atattagcta tcagtagttt tattcattag aattaggtgt ccattgcatc cacagcatga
- 14761 aaacaaaatt gggttttttt tttttttttg agacggagtc gcactctgtc acccaggttg
- 14821 gagtgcagtg gcatgatctc ggagcactgc aagctccgcc tcccaggttc atgtcattct
- 14881 cctgcctcag ccccccgagt aactgggatt acaggcaccc accaccacgc ccagctaata
- 14941 ttttgtattt tcagtggaca tggggtttca ccgtgttagc aaggatggtc tcgaactgct
- 15001 gacctcgtga tccacccatc ttggcctccc agagtgctgg gattacaggc atgagccacc
- 15061 ccgcccagcc aaaattgagt gtttaaattt tcttctgggg cttagcagtt aggtaaatca
- 15121 gacacaaagt actggaaaac aaaaaggact tgtaataggc agaaaaatac caagtgtata
- 15181 agtaatttgg tataaacaga gtataaggtt tagtatttag gaataagaac tatgtccaga
- 15241 ttatggtgtt ctgtgaatac cagcctttgg aattcatatt atgttctatg tgtatttagt
- 15301 ctggtctaag agttgagtgt aaggcatgat gctgtcttct atcaatatag agtaactggg
- 15361 actaagcaca ttttactcac caaggacctt actgggaagc tgaggcaaag gaagagtatg
- 15421 tgtttatgaa tgtgtactag gggttaaaga catgctctcc ttgatgtgcc tgtggtcttg
- 15481 tagagactca agtgtgcatt agggtttagg aagaggtgat taattctgtt ttggggtggg
- 15541 taaaaggttt caaaagaggg tgatgcctga atagcagtgg cacaccaaca gatagtggtg
- 15601 gtgggaccag tccaccctgg tgggagagaa tatataaaca atattctgac attgtttaga
- 15661 attgctgatg cttgatgatg ataaaaaaca aatggactaa aagtcaattt tattgtttta
- 15721 aaattctcta tagacgatcc cctccccacc ttgtagtgtc attccttccc ttccctagct
- 15781 ctcagtatac tgctgctgta gagtggagtg atgaaatgga gtcttccata aagtcaaaat
- 15841 ggggatggca gtgactctgg ataatatggg aatccatagc tatctctagt accatcagat
- 15901 cctagatata caaggctgtc tagtgctaat aagcttcatt agatggtgaa cgaagttgga
- 15961 gtggaggctg gttgggcact gcctgcccca tgtccctgct ggtttggtca ttaggatgga
- 16021 gctgagctgt ctttgggaag tcagtaggtt gctgtgagct gctggaaaat gaggcaagat
- 16081 tccggaaggg tgctgtggct catgcctgta atcccagcac tttgggaggc tgaggcagta
- 16141 ggattgcttg aggccaggag tttaaaacca gcgtgggcaa catagcaaga ccctgtctct
- 16201 acaaaaatac aataaaacaa aaaaaagatt agccggcatc actagcagtg gcatgtgcct
- 16261 gtagttctag ctaacttggg agccgagtgg gagaattgtt tgagtcccag gagtttgaga
- 16321 ttacaatgag ctatgatcat accaccgcac tccagcttag gtgacagagt gaaatcttgt
- 16381 ctctttaaaa aaaaaaaaaa tccaagggct aacagcaata gtagtttctg acggtaagca
- 16441 ggacatgatc agaactgtgc tttagaaata atttgggtac cattaggtgg gttaataagc
- 16501 tagaggtaga aggacatgtg aggggataga gacagaataa agggcctgaa ctttgagagt
- 16561 agcagtggaa gtaggagtca atctcaaaag gtattgtaga agtcaaaaac attaattcat
- 16621 tcatttgata gatactaagt acctcatgta atcagcactg tgccaggtac tgtggataac
- 16681 gataaaattt tacctgcctt tgaagggaat tcatagtcta attggggcaa cagaagaatg
- 16741 actgcaatac ggtgtagtaa gtgcagtgat ggtgaagcac gtcatgcgct gtgatgtaac
- 16801 aaagggtgca gtaaggattt gcctgcaagt ttcctggaag agaagatttg taacctgggt
- 16861 tttgaaagat aaggagctga cagtggctgg ggaagctggg atgaggtgta gggttgactg
- 16921 gaggatggca gatcaagcaa aagatgatat gtagtttggt atgacccagc acagggaggg
- 16981 actgattgta gaggacctta tatgccacga taagtaattg aaactttatc tttttttttt
- 17041 ttttttgaga cagagtctga ctctgtggcc caggctggaa tgtagtggcg cgatcttggc
- 17101 tcactgcaac ctctgcctcc catactcaag acatcctccc acctcagcct cttgagtagc
- 17161 tgggactaca ggcacatgcc accatccctg gctaattttt gtattttttg tagagatggg
- 17221 gtcttgctct gttgcccagg ctggtctcaa actcctggcc tcaagtgatt cacccacctc
- 17281 cgcctcccaa agggctggga tttcaggcgt gagccactgt gcctggcctg cgactttatc
- 17341 ttgacagcaa tatggagtta ctgaagactt aattatgcaa acggcatgat ccaattttta
- 17401 ttttaaatag gttttgctga cagctatgta aagaatggat ttgtgggagg taagcatgga
- 17461 aacagattat tttagtgacc cagaaaagaa ataatgaatt gtgaaggcaa ttgtagctag
- 17521 aatgaaggag agaacaaatt taagaaatat ttagaactta gaatcaatga gagttatact
- 17581 aagatgtgaa cgcttgaggg aggaaggagc tttgctcaat tttttgttgt aaataggtgg
- 17641 atgggaggta gtgtcattaa agaaaaatgt tgaaggaaaa ttagatatgg tactggaatc
- 17701 agtaactact gaagttttgg atttgtgaga cggctaggaa gagatagaat ttgtagactt
- 17761 ctattttttg gcaatatggc agactcaatt ttagaaagta tttactttga tatgaagcct
- 17821 gttagaatgt taaacaagaa cacctttaaa aatatttcat ttatttattt gggacggagt
- 17881 ttcactcttg ttgcccaggc tggagtgcaa tggcatgatc tcggctcact gcaacctccg
- 17941 cttcctgggt tcaagcggtt ctcctgcctc aacctcctga gtagctggga ttacaggtgc
- 18001 ccacaagcac acctggctaa tttttgtatt tttagtagag atggggtttc agctatgttg
- 18061 gccaggctgg tctcaaaact cctgacctca ggtgatccac ccacctcggc ctcccaaagt
- 18121 gctgggatta cagaccactg cacccggcca aaacatatta tttagtttgc aaaaagaaat
- 18181 cttctggagc cagaccaaag taagtctgca gctagggagg taagcaagtg cttagggtat
- 18241 cagttgcccc taagagtatc tactaagccc aggtggccca gagttctagt cttcttcttc
- 18301 ttattattat tattatatat atatttttga gacagagtct cgctctgtca cccaggctgg
- 18361 agtgcagtgg tgcgatcttg gctcactgca agctccgcct gccaggttca caccattctc
- 18421 ccacctcagc ctctggagta gctgggacta caggcgcctg ccaccatgcc cggctaattt
- 18481 tgttttcata tttttagtag agacggggtt tcaccgtgtc agccaggatg gtcttgatct
- 18541 cctgacctca tgatccgcct gcctcggcct cccaaagtgc taggattaca ggcatgagcc
- 18601 accacgccta gccattatta tatttttttg agtcagaatc acgctctgtt gtccaggttg
- 18661 gagtgcagtg gcgtgatc
-//
-
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diff --git a/tests/fixtures.py b/tests/fixtures.py
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+++ b/tests/fixtures.py
@@ -0,0 +1,641 @@
+"""
+Fixtures for unit tests.
+
+Each fixture is defined by a function which when called sets up the fixture.
+The order of calling can be important (e.g., fixtures using the database such
+as :func:`hg19` must be called after the :func:`database` fixture).
+"""
+
+
+import os
+import shutil
+
+from mutalyzer.config import settings
+from mutalyzer.db import Base, session
+from mutalyzer.db.models import (Assembly, Chromosome, Reference,
+ TranscriptMapping, TranscriptProteinLink)
+
+
+#: Reference definitions for use with the :func:`cache` fixture.
+REFERENCES = {
+ 'AB026906.1': {'filename': 'AB026906.1.gb.bz2',
+ 'checksum': '29b003d5a71af74dc61a92d2ef5cd5d9',
+ 'geninfo_id': '5295993'},
+ 'AL449423.14': {'filename': 'AL449423.14.gb.bz2',
+ 'checksum': '00a014242818a3b003b4c077af9e10e0',
+ 'geninfo_id': '16944057'},
+ 'NM_000059.3': {'filename': 'NM_000059.3.gb.bz2',
+ 'checksum': 'f93216b3a596adab279ebd7903258548',
+ 'geninfo_id': '119395733'},
+ 'NM_003002.2': {'filename': 'NM_003002.2.gb.bz2',
+ 'checksum': '990aa672364937335365609617df3050',
+ 'geninfo_id': '222352156'},
+ 'NG_012772.1': {'filename': 'NG_012772.1.gb.bz2',
+ 'checksum': '163881f00c9c26516d52a4ddb34f941f',
+ 'geninfo_id': '256574794',
+ 'links': [('NM_052818', 'NP_438169'),
+ ('NM_001079691', 'NP_001073159'),
+ ('NM_000059', 'NP_000050'),
+ ('NM_001136571', 'NP_001130043')]},
+ 'AA010203.1': {'filename': 'AA010203.1.gb.bz2',
+ 'checksum': '57cee03becb77ce68a225b9c844afb24',
+ 'geninfo_id': '1471230'},
+ 'NM_000088.3': {'filename': 'NM_000088.3.gb.bz2',
+ 'checksum': '5d1f23e3c1799bdb5586c6786b5d5744',
+ 'geninfo_id': '110349771'},
+ 'NM_000143.3': {'filename': 'NM_000143.3.gb.bz2',
+ 'checksum': 'c91799f40fdc0466bf7702af14cf070a',
+ 'geninfo_id': '299758401'},
+ 'NM_002001.2': {'filename': 'NM_002001.2.gb.bz2',
+ 'checksum': '7fd5aa4fe864fd5193f224fca8cea70d',
+ 'geninfo_id': '31317229'},
+ 'NG_008939.1': {'filename': 'NG_008939.1.gb.bz2',
+ 'checksum': '114a03e16ad2f63531d796c2fb0d7039',
+ 'geninfo_id': '211938431',
+ 'links': [('NM_000532', 'NP_000523')]},
+ 'NM_000193.2': {'filename': 'NM_000193.2.gb.bz2',
+ 'checksum': '86d03e1cf38c1387d90116539ea0678f',
+ 'geninfo_id': '21071042'},
+ 'NP_064445.1': {'filename': 'NP_064445.1.gb.bz2',
+ 'checksum': '33ea9315882b4a9d8c33018a201be2fa',
+ 'geninfo_id': '9910526'},
+ 'L41870.1': {'filename': 'L41870.1.gb.bz2',
+ 'checksum': '91b1e539a053f731f95d230a06710897',
+ 'geninfo_id': '793994'},
+ 'NG_009105.1': {'filename': 'NG_009105.1.gb.bz2',
+ 'checksum': 'f2579e6c4a8ead4566e485aad493ef7e',
+ 'geninfo_id': '216548283',
+ 'links': [('NM_020061', 'NP_064445')]},
+ 'AF230870.1': {'filename': 'AF230870.1.gb.bz2',
+ 'checksum': '9fefa34f40d94910edb5de34a3f98910',
+ 'geninfo_id': '7739657'},
+ 'NG_012337.1': {'filename': 'NG_012337.1.gb.bz2',
+ 'checksum': 'ad712f4f225398d2b11b4f08110c70e6',
+ 'geninfo_id': '254039638',
+ 'links': [('NM_018195', 'NP_060665'),
+ ('NM_001082969', 'NP_001076438'),
+ ('NM_001082970', 'NP_001076439'),
+ ('NM_003002', 'NP_002993'),
+ ('NM_012459', 'NP_036591')]},
+ 'NM_203473.1': {'filename': 'NM_203473.1',
+ 'checksum': 'ec8fbdeda11ef8ec953e4ed39e9a84e5',
+ 'geninfo_id': '45439330'},
+ 'NM_000132.3': {'filename': 'NM_000132.3.gb.bz2',
+ 'checksum': '94569bee76d7c8b1168e17df4fe1dcb4',
+ 'geninfo_id': '192448441'},
+ 'LRG_1': {'filename': 'LRG_1.xml.bz2',
+ 'checksum': '5b8f5a39fcd9e3005688eddffd482746'},
+ 'DMD': {'accession': 'UD_139015194859',
+ 'filename': 'UD_139015194859.gb.bz2',
+ 'checksum': '2cc769c3f636c722142c0aae12662bd4',
+ 'links': [('NM_000109', 'NP_000100'),
+ ('NM_004006', 'NP_003997'),
+ ('NM_004009', 'NP_004000'),
+ ('NM_004010', 'NP_004001'),
+ ('NM_004007', None),
+ ('NM_004011', 'NP_004002'),
+ ('NM_004012', 'NP_004003'),
+ ('NM_004023', 'NP_004014'),
+ ('NM_004020', 'NP_004011'),
+ ('NM_004022', 'NP_004013'),
+ ('NM_004021', 'NP_004012'),
+ ('NM_004013', 'NP_004004'),
+ ('NM_004014', 'NP_004005'),
+ ('NM_004018', 'NP_004009'),
+ ('NM_004017', 'NP_004008'),
+ ('NM_004016', 'NP_004007'),
+ ('NM_004015', 'NP_004006'),
+ ('NM_004019', 'NP_004010')]},
+ 'DPYD': {'accession': 'UD_139015208095',
+ 'filename': 'UD_139015208095.gb.bz2',
+ 'checksum': 'b2b9d402a6e43f80ce1e9bbb72a3c0c6',
+ 'links': [('NR_046590', None),
+ ('XM_005270562', 'XP_005270619'),
+ ('NM_000110', 'NP_000101'),
+ ('XM_005270561', 'XP_005270618'),
+ ('XM_005270563', 'XP_005270620'),
+ ('XM_005270564', 'XP_005270621'),
+ ('NM_001160301', 'NP_001153773')]},
+ 'MARK1': {'accession': 'UD_139015213982',
+ 'filename': 'UD_139015213982.gb.bz2',
+ 'checksum': '0d63a8fe5beddeb793940f6ae194b985',
+ 'links': [('NM_018650', 'NP_061120'),
+ ('XM_005273133', None),
+ ('XM_005273134', 'XP_005273191'),
+ ('XM_005273135', None),
+ ('XM_005273136', None)]},
+ 'A1BG': {'accession': 'UD_139015218717',
+ 'filename': 'UD_139015218717.gb.bz2',
+ 'checksum': 'e179de8b248806815394c4f7496ba872',
+ 'links': [('NM_001207009', 'NP_001193938'),
+ ('NM_198458', 'NP_940860'),
+ ('XM_005258578', 'XP_005258635'),
+ ('XM_005258577', 'XP_005258634'),
+ ('NR_015380', None),
+ ('NM_130786', 'NP_570602'),
+ ('XM_005258393', 'XP_005258450')]},
+ 'chr9_reverse': {'accession': 'UD_139015349377',
+ 'filename': 'UD_139015349377.gb.bz2',
+ 'checksum': 'd21f92d09116c4831ce8d3ef832aa281',
+ 'links': [('NM_001195250', 'NP_001182179'),
+ ('NR_036576', None),
+ ('NR_036577', None),
+ ('NM_001195252', 'NP_001182181'),
+ ('NM_001195248', 'NP_001182177'),
+ ('NM_175069', 'NP_778239'),
+ ('NM_175073', 'NP_778243'),
+ ('NM_001195251', 'NP_001182180'),
+ ('NM_001195254', 'NP_001182183'),
+ ('NR_036578', None),
+ ('NR_036579', None),
+ ('NM_001195249', 'NP_001182178')]},
+ 'COL1A1': {'accession': 'UD_139022298843',
+ 'filename': 'UD_139022298843.gb.bz2',
+ 'checksum': '815517e36fb380b52842ace6a6e78637',
+ 'links': [('XM_005257059', 'XP_005257116'),
+ ('XM_005257058', 'XP_005257115'),
+ ('NM_000088', 'NP_000079')]}}
+
+
+def database():
+ """
+ Fixture for database table definitions.
+ """
+ Base.metadata.create_all(session.get_bind())
+ session.commit()
+
+
+def hg19():
+ """
+ Fixture for GRCh37/hg19 genome assembly with chromosomes.
+ """
+ assembly = Assembly('GRCh37', 9606, 'Homo sapiens', alias='hg19')
+ session.add(assembly)
+
+ session.add_all(Chromosome(assembly, name, accession, organelle_type)
+ for accession, name, organelle_type in [
+ ('NC_000001.10', 'chr1', 'chromosome'),
+ ('NC_000002.11', 'chr2', 'chromosome'),
+ ('NC_000003.11', 'chr3', 'chromosome'),
+ ('NC_000004.11', 'chr4', 'chromosome'),
+ ('NC_000005.9', 'chr5', 'chromosome'),
+ ('NC_000006.11', 'chr6', 'chromosome'),
+ ('NC_000007.13', 'chr7', 'chromosome'),
+ ('NC_000008.10', 'chr8', 'chromosome'),
+ ('NC_000009.11', 'chr9', 'chromosome'),
+ ('NC_000010.10', 'chr10', 'chromosome'),
+ ('NC_000011.9', 'chr11', 'chromosome'),
+ ('NC_000012.11', 'chr12', 'chromosome'),
+ ('NC_000013.10', 'chr13', 'chromosome'),
+ ('NC_000014.8', 'chr14', 'chromosome'),
+ ('NC_000015.9', 'chr15', 'chromosome'),
+ ('NC_000016.9', 'chr16', 'chromosome'),
+ ('NC_000017.10', 'chr17', 'chromosome'),
+ ('NC_000018.9', 'chr18', 'chromosome'),
+ ('NC_000019.9', 'chr19', 'chromosome'),
+ ('NC_000020.10', 'chr20', 'chromosome'),
+ ('NC_000021.8', 'chr21', 'chromosome'),
+ ('NC_000022.10', 'chr22', 'chromosome'),
+ ('NC_000023.10', 'chrX', 'chromosome'),
+ ('NC_000024.9', 'chrY', 'chromosome'),
+ ('NT_167244.1', 'chr6_apd_hap1', 'chromosome'),
+ ('NT_113891.2', 'chr6_cox_hap2', 'chromosome'),
+ ('NT_167245.1', 'chr6_dbb_hap3', 'chromosome'),
+ ('NT_167246.1', 'chr6_mann_hap4', 'chromosome'),
+ ('NT_167247.1', 'chr6_mcf_hap5', 'chromosome'),
+ ('NT_167248.1', 'chr6_qbl_hap6', 'chromosome'),
+ ('NT_167249.1', 'chr6_ssto_hap7', 'chromosome'),
+ ('NT_167250.1', 'chr4_ctg9_hap1', 'chromosome'),
+ ('NT_167251.1', 'chr17_ctg5_hap1', 'chromosome'),
+ ('NC_012920.1', 'chrM', 'mitochondrion')])
+
+ session.commit()
+
+
+def hg19_transcript_mappings():
+ """
+ Fixture for some selected transcript mappings in the GRCh37/hg19 genome
+ assembly. Depends on the :func:`hg19` fixture.
+ """
+ chromosome_1 = Chromosome.query.filter_by(accession='NC_000001.10').one()
+ chromosome_3 = Chromosome.query.filter_by(accession='NC_000003.11').one()
+ chromosome_6 = Chromosome.query.filter_by(accession='NC_000006.11').one()
+ chromosome_7 = Chromosome.query.filter_by(accession='NC_000007.13').one()
+ chromosome_8 = Chromosome.query.filter_by(accession='NC_000008.10').one()
+ chromosome_11 = Chromosome.query.filter_by(accession='NC_000011.9').one()
+ chromosome_20 = Chromosome.query.filter_by(accession='NC_000020.10').one()
+ chromosome_22 = Chromosome.query.filter_by(accession='NC_000022.10').one()
+ chromosome_x = Chromosome.query.filter_by(accession='NC_000023.10').one()
+ chromosome_mt = Chromosome.query.filter_by(accession='NC_012920.1').one()
+
+ session.add_all([chromosome_1, chromosome_6, chromosome_8, chromosome_11,
+ chromosome_20, chromosome_22, chromosome_mt])
+
+ session.add(TranscriptMapping(
+ chromosome_11,
+ 'refseq',
+ 'NM_003002',
+ 'SDHD',
+ 'forward',
+ 111957571,
+ 111966518,
+ [111957571, 111958581, 111959591, 111965529],
+ [111957683, 111958697, 111959735, 111966518],
+ 'ncbi',
+ transcript=1,
+ cds=(111957632, 111965694),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_11,
+ 'refseq',
+ 'NR_028383',
+ 'TIMM8B',
+ 'reverse',
+ 111955524,
+ 111957522,
+ [111955524, 111956702, 111957364],
+ [111956186, 111957034, 111957522],
+ 'ncbi',
+ transcript=1,
+ cds=None,
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_6,
+ 'refseq',
+ 'NM_000500',
+ 'CYP21A2',
+ 'forward',
+ 32006082,
+ 32009419,
+ [32006082, 32006499, 32006871, 32007133, 32007323, 32007526,
+ 32007782, 32008183, 32008445, 32008646],
+ [32006401, 32006588, 32007025, 32007234, 32007424, 32007612,
+ 32007982, 32008361, 32008548, 32009419],
+ 'ncbi',
+ transcript=1,
+ cds=(32006200, 32008911),
+ select_transcript=False,
+ version=5))
+ session.add(TranscriptMapping(
+ chromosome_22,
+ 'refseq',
+ 'NM_001145134',
+ 'CPT1B',
+ 'reverse',
+ 51007290,
+ 51017096,
+ [51007290, 51007765, 51008005, 51008722, 51009320, 51009587,
+ 51009804, 51010435, 51010632, 51011304, 51011949, 51012764,
+ 51012922, 51014464, 51014627, 51015286, 51015753, 51016204,
+ 51016978],
+ [51007510, 51007850, 51008097, 51008835, 51009472, 51009721,
+ 51009968, 51010551, 51010737, 51011489, 51012144, 51012848,
+ 51013029, 51014541, 51014764, 51015463, 51015892, 51016363,
+ 51017096],
+ 'ncbi',
+ transcript=1,
+ cds=(51007767, 51016344),
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_22,
+ 'refseq',
+ 'NR_021492',
+ 'LOC100144603',
+ 'forward',
+ 51021455,
+ 51022356,
+ [51021455, 51022027],
+ [51021752, 51022356],
+ 'ncbi',
+ transcript=1,
+ cds=None,
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_1,
+ 'refseq',
+ 'NM_001007553',
+ 'CSDE1',
+ 'reverse',
+ 115259538,
+ 115300624,
+ [115259538, 115261234, 115262200, 115263160, 115266504, 115267842,
+ 115268832, 115269604, 115272879, 115273129, 115275225, 115276353,
+ 115276610, 115277063, 115279379, 115280092, 115280584, 115282313,
+ 115292442, 115300546],
+ [115260837, 115261366, 115262363, 115263338, 115266623, 115267954,
+ 115269007, 115269711, 115273043, 115273269, 115275437, 115276478,
+ 115276738, 115277144, 115279476, 115280184, 115280693, 115282511,
+ 115292828, 115300624],
+ 'ncbi',
+ transcript=1,
+ cds=(115260790, 115282511),
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_1,
+ 'refseq',
+ 'NM_001130523',
+ 'CSDE1',
+ 'reverse',
+ 115259538,
+ 115300671,
+ [115259538, 115261234, 115262200, 115263160, 115266504, 115267842,
+ 115268832, 115269604, 115272879, 115273129, 115275225, 115276353,
+ 115276610, 115277063, 115279379, 115280584, 115282313, 115284148,
+ 115292442, 115300546],
+ [115260837, 115261366, 115262363, 115263338, 115266623, 115267954,
+ 115269007, 115269711, 115273043, 115273269, 115275437, 115276478,
+ 115276738, 115277144, 115279476, 115280693, 115282511, 115284294,
+ 115292828, 115300671],
+ 'ncbi',
+ transcript=1,
+ cds=(115260790, 115284285),
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_1,
+ 'refseq',
+ 'NM_002241',
+ 'KCNJ10',
+ 'reverse',
+ 160007257,
+ 160040051,
+ [160007257, 160039812],
+ [160012322, 160040051],
+ 'ncbi',
+ transcript=1,
+ cds=(160011183, 160012322),
+ select_transcript=False,
+ version=4))
+ session.add(TranscriptMapping(
+ chromosome_20,
+ 'refseq',
+ 'NM_001162505',
+ 'TMEM189',
+ 'reverse',
+ 48740274,
+ 48770335,
+ [48740274, 48744512, 48746083, 48747402, 48760039, 48770054],
+ [48741716, 48744724, 48746227, 48747484, 48760158, 48770335],
+ 'ncbi',
+ transcript=1,
+ cds=(48741595, 48770174),
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_8,
+ 'refseq',
+ 'NM_017780',
+ 'CHD7',
+ 'forward',
+ 61591339,
+ 61779465,
+ [61591339, 61653818, 61693559, 61707545, 61712947, 61714087,
+ 61720776, 61728946, 61732566, 61734349, 61734583, 61735062,
+ 61736399, 61741222, 61742881, 61748632, 61749376, 61750227,
+ 61750635, 61754203, 61754406, 61757423, 61757809, 61761074,
+ 61761610, 61763052, 61763591, 61763821, 61764578, 61765057,
+ 61765388, 61766922, 61768534, 61769004, 61773463, 61774755,
+ 61775107, 61777575],
+ [61591641, 61655656, 61693989, 61707686, 61713084, 61714152,
+ 61720831, 61729060, 61732649, 61734486, 61734704, 61735305,
+ 61736575, 61741365, 61743136, 61748842, 61749571, 61750394,
+ 61750814, 61754313, 61754611, 61757622, 61757968, 61761163,
+ 61761713, 61763181, 61763663, 61763878, 61764806, 61765265,
+ 61766059, 61767082, 61768761, 61769447, 61773684, 61774895,
+ 61775211, 61779465],
+ 'ncbi',
+ transcript=1,
+ cds=(61653992, 61778492),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_mt,
+ 'refseq',
+ 'NC_012920',
+ 'ND4',
+ 'forward',
+ 10760,
+ 12137,
+ [10760],
+ [12137],
+ 'reference',
+ transcript=1,
+ cds=(10760, 12137),
+ select_transcript=True,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_1,
+ 'refseq',
+ 'NM_002001',
+ 'FCER1A',
+ 'forward',
+ 159259504,
+ 159278014,
+ [159259504, 159272096, 159272644, 159273718, 159275778, 159277538],
+ [159259543, 159272209, 159272664, 159273972, 159276035, 159278014],
+ 'ncbi',
+ transcript=1,
+ cds=(159272155, 159277722),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_7,
+ 'refseq',
+ 'XM_001715131',
+ 'LOC100132858',
+ 'reverse',
+ 19828,
+ 36378,
+ [19828, 20834, 31060, 32957, 35335, 36224],
+ [19895, 21029, 31437, 33107, 35541, 36378],
+ 'ncbi',
+ transcript=1,
+ cds=(19828, 36378),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_x,
+ 'refseq',
+ 'NM_004011',
+ 'DMD',
+ 'reverse',
+ 31137345,
+ 32430371,
+ [31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
+ 31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
+ 31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
+ 31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
+ 31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
+ 31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
+ 32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
+ 32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
+ 32408188, 32429869, 32430279],
+ [31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
+ 31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
+ 31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
+ 31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
+ 31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
+ 31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
+ 32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
+ 32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
+ 32408298, 32430030, 32430371],
+ 'ncbi',
+ transcript=1,
+ cds=(31140036, 32430326),
+ select_transcript=False,
+ version=3))
+ session.add(TranscriptMapping(
+ chromosome_x,
+ 'refseq',
+ 'NM_004019',
+ 'DMD',
+ 'reverse',
+ 31196312,
+ 31285024,
+ [31196312, 31198487, 31200855, 31222078, 31224699, 31227615,
+ 31241164, 31279072, 31284927],
+ [31196922, 31198598, 31201021, 31222235, 31224784, 31227816,
+ 31241238, 31279133, 31285024],
+ 'ncbi',
+ transcript=1,
+ cds=(31196782, 31284946),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_x,
+ 'refseq',
+ 'NM_004007',
+ 'DMD',
+ 'reverse',
+ 31137345,
+ 33038317,
+ [31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
+ 31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
+ 31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
+ 31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
+ 31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
+ 31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
+ 32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
+ 32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
+ 32408188, 32429869, 32456358, 32459297, 32466573, 32472779,
+ 32481556, 32482703, 32486615, 32490281, 32503036, 32509394,
+ 32519872, 32536125, 32563276, 32583819, 32591647, 32591862,
+ 32613874, 32632420, 32662249, 32663081, 32715987, 32717229,
+ 32827610, 32834585, 32841412, 32862900, 32867845, 33038256],
+ [31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
+ 31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
+ 31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
+ 31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
+ 31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
+ 31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
+ 32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
+ 32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
+ 32408298, 32430030, 32456507, 32459431, 32466755, 32472949,
+ 32481711, 32482816, 32486827, 32490426, 32503216, 32509635,
+ 32519959, 32536248, 32563451, 32583998, 32591754, 32591963,
+ 32613993, 32632570, 32662430, 32663269, 32716115, 32717410,
+ 32827728, 32834757, 32841504, 32862977, 32867937, 33038317],
+ 'ncbi',
+ transcript=1,
+ cds=(31140036, 32834745),
+ select_transcript=False,
+ version=2))
+ session.add(TranscriptMapping(
+ chromosome_x,
+ 'refseq',
+ 'NM_203473',
+ 'PORCN',
+ 'forward',
+ 48367371,
+ 48379202,
+ [48367371, 48368172, 48369683, 48370280, 48370714, 48370977,
+ 48371223, 48372628, 48372913, 48374105, 48374278, 48374449,
+ 48375571, 48378763],
+ [48367491, 48368344, 48369875, 48370323, 48370895, 48371107,
+ 48371240, 48372753, 48373013, 48374181, 48374341, 48374534,
+ 48375681, 48379202],
+ 'ncbi',
+ transcript=1,
+ cds=(48368209, 48378864),
+ select_transcript=False,
+ version=1))
+ session.add(TranscriptMapping(
+ chromosome_x,
+ 'refseq',
+ 'NM_000132',
+ 'F8',
+ 'reverse',
+ 154064063,
+ 154250998,
+ [154064063, 154088707, 154089993, 154091358, 154124352, 154128141,
+ 154129646, 154130326, 154132181, 154132571, 154133086, 154134695,
+ 154156846, 154175973, 154182167, 154185232, 154189350, 154194245,
+ 154194701, 154197606, 154212962, 154215512, 154221211, 154225248,
+ 154227754, 154250685],
+ [154066027, 154088883, 154090141, 154091502, 154124507, 154128226,
+ 154129717, 154130442, 154132363, 154132799, 154133298, 154134848,
+ 154159951, 154176182, 154182317, 154185446, 154189443, 154194416,
+ 154194962, 154197827, 154213078, 154215580, 154221423, 154225370,
+ 154227875, 154250998],
+ 'ncbi',
+ transcript=1,
+ cds=(154065872, 154250827),
+ select_transcript=False,
+ version=3))
+ session.add(TranscriptMapping(
+ chromosome_3,
+ 'refseq',
+ 'NM_000249',
+ 'MLH1',
+ 'forward',
+ 37034841,
+ 37092337,
+ [37034841, 37038110, 37042446, 37045892, 37048482, 37050305,
+ 37053311, 37053502, 37055923, 37058997, 37061801, 37067128,
+ 37070275, 37081677, 37083759, 37089010, 37090008, 37090395,
+ 37091977],
+ [37035154, 37038200, 37042544, 37045965, 37048554, 37050396,
+ 37053353, 37053590, 37056035, 37059090, 37061954, 37067498,
+ 37070423, 37081785, 37083822, 37089174, 37090100, 37090508,
+ 37092337],
+ 'ncbi',
+ transcript=1,
+ cds=(37035039, 37092144),
+ select_transcript=False,
+ version=3))
+
+ session.commit()
+
+
+def cache(*references):
+ """
+ Returns a cache fixture for the given references.
+ """
+ def cache_with_references():
+ for reference in references:
+ entry = REFERENCES[reference]
+ try:
+ accession = entry['accession']
+ except KeyError:
+ accession = reference
+ geninfo_id = entry.get('geninfo_id')
+
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ entry['filename'])
+ shutil.copy(path, settings.CACHE_DIR)
+
+ session.add(Reference(accession, entry['checksum'],
+ geninfo_identifier=geninfo_id))
+
+ for transcript, protein in entry.get('links', []):
+ session.add(TranscriptProteinLink(transcript, protein))
+
+ session.commit()
+
+ return cache_with_references
diff --git a/tests/test_crossmap.py b/tests/test_crossmap.py
index 2fdeffadb4ed6ae843623cd4f5273326b72bf6d8..d15009994edc64a6a64dd8d86528f8c162e57446 100644
--- a/tests/test_crossmap.py
+++ b/tests/test_crossmap.py
@@ -8,19 +8,13 @@ from nose.tools import *
from mutalyzer.Crossmap import Crossmap
-import utils
+from utils import MutalyzerTest
-class TestCrossmap():
+class TestCrossmap(MutalyzerTest):
"""
Test the Crossmap class.
"""
- def setup(self):
- utils.create_test_environment(database=True)
-
- def teardown(self):
- utils.destroy_environment()
-
def test_splice_sites(self):
"""
Check whether the gene on the forward strand has the right splice
diff --git a/tests/test_describe.py b/tests/test_describe.py
index c922deed7a4e71a559c09875c2d1459c4eb49d75..8a7967a29f615007a460e09158d79fb7e0797a1d 100644
--- a/tests/test_describe.py
+++ b/tests/test_describe.py
@@ -10,19 +10,13 @@ from nose.tools import *
import mutalyzer
from mutalyzer import describe
-import utils
+from utils import MutalyzerTest
-class TestDescribe():
+class TestDescribe(MutalyzerTest):
"""
Test the mytalyzer.describe module.
"""
- def setup(self):
- utils.create_test_environment()
-
- def teardown(self):
- utils.destroy_environment()
-
def test1(self):
"""
Test 1.
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 3253ad773cba96293a6e6cbfb1e7c8eb06581e7c..f9bf9ec9c637355bfa8abcef5a73afc353b8b38f 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -11,24 +11,18 @@ import mutalyzer
from mutalyzer.grammar import Grammar
from mutalyzer.output import Output
-import utils
+from utils import MutalyzerTest
-class TestGrammar():
+class TestGrammar(MutalyzerTest):
"""
Test the mytalyzer.grammar module.
"""
def setup(self):
- """
- Initialize test Grammar instance.
- """
- utils.create_test_environment()
+ super(TestGrammar, self).setup()
self.output = Output(__file__)
self.grammar = Grammar(self.output)
- def teardown(self):
- utils.destroy_environment()
-
def _parse(self, description):
"""
Parse a variant description.
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 4287d2f49e3654a4895c22c5e8f1d3f46eb2d8a9..4b2af7d4107dd44309012ee0f40ebbd5dcd2d8f1 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -5,33 +5,34 @@ Tests for the mapping module.
#import logging; logging.basicConfig()
from nose.tools import *
+from sqlalchemy import or_
from mutalyzer.db.models import Assembly
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
-import utils
+from fixtures import database, hg19, hg19_transcript_mappings
+from utils import MutalyzerTest
-class TestConverter():
+class TestConverter(MutalyzerTest):
"""
Test the Converter class.
"""
+ fixtures = (database, hg19, hg19_transcript_mappings)
+
def setup(self):
- """
- Initialize test converter module.
- """
- utils.create_test_environment(database=True)
+ super(TestConverter, self).setup()
self.output = Output(__file__)
- def teardown(self):
- utils.destroy_environment()
-
- def _converter(self, build):
+ def _converter(self, assembly_name_or_alias):
"""
- Create a Converter instance for a given build.
+ Create a Converter instance for a given genome assembly.
"""
- assembly = Assembly.query.first()
+ assembly = Assembly.query \
+ .filter(or_(Assembly.name == assembly_name_or_alias,
+ Assembly.alias == assembly_name_or_alias)) \
+ .one()
return Converter(assembly, self.output)
def test_converter(self):
@@ -80,6 +81,11 @@ class TestConverter():
See also bug #58.
"""
+ # Todo: This test is bogus now that we use a fixture that has just the
+ # mapping to chromosome 6. However, I think we only get this mapping
+ # from our current source (NCBI seq_gene.md) anyway, so I'm not sure
+ # where we got the other mappings from in the past (but haven't
+ # investigated really).
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_000500.5:c.92C>T')
assert_equal(genomic, 'NC_000006.11:g.32006291C>T')
@@ -105,15 +111,10 @@ class TestConverter():
is exactly on the border of an exon.
Bug reported February 24, 2012 by S Venkata Suresh Kumar.
-
- Note: You need the full hg18 and hg19 databases for these tests to
- pass (i.e. the one used on the production server, possibly
- updated with newer mappings from the NCBI).
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000001.10:g.115259837_115259837delT', 'list')
assert 'NM_001007553.1:c.3863delA' not in coding
- assert 'NM_001007553.2:c.3863delA' not in coding
assert 'NM_001007553.1:c.*953delA' in coding
assert 'NM_001130523.1:c.*953delA' in coding
@@ -127,9 +128,7 @@ class TestConverter():
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000001.10:g.160012314_160012329del16', 'list')
assert 'NM_002241.4:c.-27250-7_-27242del16' not in coding
- #assert 'NM_002241.3:c.-27340-7_-27332del16' not in coding
assert 'NM_002241.4:c.1-7_9del16' in coding
- #assert 'NM_002241.3:c.1-7_9del16' in coding
def test_range_order_forward_correct(self):
"""
diff --git a/tests/test_mutator.py b/tests/test_mutator.py
index cc15f0e3e91b38a03994782fad51aef09a9eb9d8..43117c693df524ef43bd4ea3c839417e570c8043 100644
--- a/tests/test_mutator.py
+++ b/tests/test_mutator.py
@@ -11,11 +11,10 @@ from nose.tools import *
from Bio.Seq import Seq
import mutalyzer
-from mutalyzer.util import skip
from mutalyzer.output import Output
from mutalyzer import mutator
-import utils
+from utils import MutalyzerTest
def _seq(length):
@@ -28,20 +27,14 @@ def _seq(length):
return Seq(sequence)
-class TestMutator():
+class TestMutator(MutalyzerTest):
"""
Test the mutator module.
"""
def setup(self):
- """
- Initialize test mutator module.
- """
- utils.create_test_environment()
+ super(TestMutator, self).setup()
self.output = Output(__file__)
- def teardown(self):
- utils.destroy_environment()
-
def _mutator(self, sequence):
"""
Create a Mutator instance for a given sequence.
@@ -202,13 +195,14 @@ class TestMutator():
m.deletion(12, 13) # g.12_13del
assert_equal(m.shift_sites(sites), [4, 9, 12, 15, 23, 25])
- @skip
def test_shift_sites_acc_del2_on(self):
"""
Deletion of 2 in intron/exon.
@note: This hits a splice site, so we don't really support it.
"""
+ return
+
l = 30
sites = [4, 9, 14, 17, 25, 27]
m = self._mutator(_seq(l))
@@ -235,13 +229,14 @@ class TestMutator():
m.deletion(16, 17) # g.16_17del
assert_equal(m.shift_sites(sites), [4, 9, 14, 15, 23, 25])
- @skip
def test_shift_sites_don_del2_on(self):
"""
Deletion of 2 in exon/intron.
@note: This hits a splice site, so we don't really support it.
"""
+ return
+
l = 30
sites = [4, 9, 14, 17, 25, 27]
m = self._mutator(_seq(l))
@@ -595,7 +590,6 @@ class TestMutator():
m.deletion(16, 17) # g.16_17del
assert_equal(m.shift_sites(sites), [4, 9, 10, 15, 16, 25])
- @skip
def test_shift_sites_adj_del2_on(self):
"""
Adjacent exons: deletion of 2 at exon/exon boundary.
@@ -603,6 +597,8 @@ class TestMutator():
@todo: This is a special case of bug #????. Once fixed, the two
exons will be joined to one new exon.
"""
+ return
+
l = 30
sites = [4, 9, 10, 17, 18, 27]
m = self._mutator(_seq(l))
diff --git a/tests/test_parsers_genbank.py b/tests/test_parsers_genbank.py
index ec8083b04c34c0394dfc4bdada5cf503f81bbf5d..d66ad1af3d519a615cd6b57b7137829c51da048a 100644
--- a/tests/test_parsers_genbank.py
+++ b/tests/test_parsers_genbank.py
@@ -8,23 +8,17 @@ from nose.tools import *
from mutalyzer.parsers import genbank
-import utils
+from utils import MutalyzerTest
-class TestMutator():
+class TestMutator(MutalyzerTest):
"""
Test the mutator module.
"""
def setup(self):
- """
- Initialize test mutator module.
- """
- utils.create_test_environment(database=True)
+ super(TestMutator, self).setup()
self.gb_parser = genbank.GBparser()
- def teardown(self):
- utils.destroy_environment()
-
def test_product_lists_mismatch(self):
"""
Test finding mismatches in some product lists.
diff --git a/tests/test_scheduler.py b/tests/test_scheduler.py
index 9c7467f2576b2fb458887c38a18273e556675dde..1fc3d5eeb95658330dc2895bf5e3d36f6ee5e1fb 100644
--- a/tests/test_scheduler.py
+++ b/tests/test_scheduler.py
@@ -3,10 +3,13 @@ Tests for the Scheduler module.
"""
+import bz2
import os
import StringIO
#import logging; logging.basicConfig()
+from Bio import Entrez
+from mock import patch
from nose.tools import *
from mutalyzer.config import settings
@@ -15,18 +18,16 @@ from mutalyzer import File
from mutalyzer import output
from mutalyzer import Scheduler
-import utils
+from fixtures import database, cache
+from utils import MutalyzerTest
+from utils import fix
-class TestScheduler():
+class TestScheduler(MutalyzerTest):
"""
Test the Scheduler class.
"""
- def setup(self):
- utils.create_test_environment(database=True)
-
- def teardown(self):
- utils.destroy_environment()
+ fixtures = (database, )
@staticmethod
def _batch_job(variants, expected, job_type, argument=None):
@@ -36,23 +37,19 @@ class TestScheduler():
batch_file = StringIO.StringIO('\n'.join(variants) + '\n')
job, columns = file_instance.parseBatchFile(batch_file)
result_id = scheduler.addJob('test@test.test', job, columns,
- None, job_type, argument)
+ job_type)
+
+ batch_job = BatchJob.query.filter_by(result_id=result_id).one()
- left = BatchQueueItem.query \
- .join(BatchJob) \
- .filter_by(result_id=result_id) \
- .count()
+ left = batch_job.batch_queue_items.count()
assert_equal(left, len(variants))
scheduler.process()
- left = BatchQueueItem.query \
- .join(BatchJob) \
- .filter_by(result_id=result_id) \
- .count()
+ left = batch_job.batch_queue_items.count()
assert_equal(left, 0)
- filename = 'Results_%s.txt' % result_id
+ filename = 'batch-job-%s.txt' % result_id
result = open(os.path.join(settings.CACHE_DIR, filename))
next(result) # Header.
@@ -69,8 +66,9 @@ class TestScheduler():
'OK'],
['AL449423.14(CDKN2A_v002):c.5_400del',
'OK']]
- self._batch_job(variants, expected, 'SyntaxChecker')
+ self._batch_job(variants, expected, 'syntax-checker')
+ @fix(cache('AB026906.1', 'NM_000059.3'))
def test_name_checker(self):
"""
Simple name checker batch job.
@@ -114,7 +112,7 @@ class TestScheduler():
'NM_000059.3(BRCA2_i001):p.(Asp224Tyr)',
'',
'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
- self._batch_job(variants, expected, 'NameChecker')
+ self._batch_job(variants, expected, 'name-checker')
def test_name_checker_altered(self):
"""
@@ -179,8 +177,21 @@ class TestScheduler():
'NM_000059.3(BRCA2_i001):p.(Asp224Tyr)',
'',
'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
- self._batch_job(variants, expected, 'NameChecker')
+ # Patch GenBankRetriever.fetch to return the contents of NM_000059.3
+ # for NM_000059.
+ def mock_efetch(*args, **kwargs):
+ if kwargs.get('id') != 'NM_000059':
+ return Entrez.efetch(*args, **kwargs)
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'NM_000059.3.gb.bz2')
+ return bz2.BZ2File(path)
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ self._batch_job(variants, expected, 'name-checker')
+
+ @fix(cache('NM_000059.3'))
def test_name_checker_skipped(self):
"""
Name checker job with skipped entries.
@@ -211,4 +222,12 @@ class TestScheduler():
'NM_000059.3(BRCA2_i001):p.(Asp224Tyr)',
'',
'BspHI,CviAII,FatI,Hpy188III,NlaIII']]
- self._batch_job(variants, expected, 'NameChecker')
+
+ # Patch GenBankRetriever.fetch to fail on NM_1234567890.3.
+ def mock_efetch(*args, **kwargs):
+ if kwargs.get('id') != 'NM_1234567890.3':
+ return Entrez.efetch(*args, **kwargs)
+ raise IOError()
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ self._batch_job(variants, expected, 'name-checker')
diff --git a/tests/test_services_json.py b/tests/test_services_json.py
index 9b2f4e8051bbf8baa5c061d4f2019205325c9cfa..f5b1a42c902f11ad78dc91ca3ed338c3a638ed1a 100644
--- a/tests/test_services_json.py
+++ b/tests/test_services_json.py
@@ -9,7 +9,9 @@ from spyne.server.null import NullServer
import mutalyzer
from mutalyzer.services.json import application
-import utils
+from fixtures import database, hg19, hg19_transcript_mappings
+from utils import MutalyzerTest
+from utils import fix
# Todo: We currently have no way of testing POST requests to the JSON API. We
@@ -20,20 +22,14 @@ import utils
# [2] https://github.com/LUMC/spyne/commit/58660dec28d47b1c3bf1e46d20f55a913ad036cd
-class TestServicesJson():
+class TestServicesJson(MutalyzerTest):
"""
Test the Mutalyzer HTTP/RPC+JSON interface.
"""
def setup(self):
- """
- Initialize test server.
- """
- utils.create_test_environment(database=True)
+ super(TestServicesJson, self).setup()
self.server = NullServer(application, ostr=True)
- def teardown(self):
- utils.destroy_environment()
-
def _call(self, method, *args, **kwargs):
r = getattr(self.server.service, method)(*args, **kwargs)
return json.loads(''.join(r))
@@ -64,6 +60,7 @@ class TestServicesJson():
#assert_equal(r['faultcode'], 'Client.ValidationError')
pass
+ @fix(database, hg19, hg19_transcript_mappings)
def test_transcriptinfo_valid(self):
"""
Running transcriptInfo with valid arguments should get us a Transcript
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index 13d0335c3e025413105dec6e614d475dce60c456..53344ca56e89efebfc8dc5204b51c0b1e57aa15b 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -3,24 +3,30 @@ Tests for the SOAP interface to Mutalyzer.
"""
+import bz2
import datetime
import logging
import os
import tempfile
-import time
+from Bio import Entrez
+from mock import patch
from nose.tools import *
from spyne.server.null import NullServer
from spyne.model.fault import Fault
from suds.client import Client
import mutalyzer
+from mutalyzer.config import settings
from mutalyzer.output import Output
from mutalyzer.services.soap import application
from mutalyzer.sync import CacheSync
-from mutalyzer.util import skip, slow
+from mutalyzer import Scheduler
+
+from fixtures import database, cache, hg19, hg19_transcript_mappings
+from utils import MutalyzerTest
+from utils import fix
-import utils
# Suds logs an awful lot of things with level=DEBUG, including entire WSDL
# files and SOAP responses. On any error, this is all dumped to the console,
@@ -44,15 +50,12 @@ def _write_wsdl(server):
return wsdl_filename
-class TestServicesSoap():
+class TestServicesSoap(MutalyzerTest):
"""
Test the Mutalyzer SOAP interface.
"""
def setup(self):
- """
- Initialize test server.
- """
- utils.create_test_environment(database=True)
+ super(TestServicesSoap, self).setup()
self.server = NullServer(application, ostr=True)
# Unfortunately there's no easy way to just give a SUDS client a
# complete WSDL string, it only accepts a URL to it. So we create one.
@@ -60,10 +63,7 @@ class TestServicesSoap():
self.client = Client('file://%s' % self.wsdl, cache=None)
def teardown(self):
- """
- Remove temporary file used for WSDL.
- """
- utils.destroy_environment()
+ super(TestServicesSoap, self).teardown()
os.unlink(self.wsdl)
def _call(self, method, *args, **kwargs):
@@ -106,6 +106,7 @@ class TestServicesSoap():
# See https://github.com/arskom/spyne/issues/318
self._call('checkSyntax')
+ @fix(database, hg19, hg19_transcript_mappings)
def test_transcriptinfo_valid(self):
"""
Running transcriptInfo with valid arguments should get us a Transcript
@@ -117,6 +118,7 @@ class TestServicesSoap():
assert_equal(r.trans_stop, 1066)
assert_equal(r.CDS_stop, 774)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_numberconversion_gtoc_valid(self):
"""
Running numberConversion with valid g variant should give a list of
@@ -127,6 +129,7 @@ class TestServicesSoap():
assert_equal(type(r.string), list)
assert 'NM_002001.2:c.1del' in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_numberconversion_ctog_valid(self):
"""
Running numberConversion with valid c variant should give a list of
@@ -137,22 +140,20 @@ class TestServicesSoap():
assert_equal(type(r.string), list)
assert 'NC_000001.10:g.159272155del' in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_numberconversion_gtoc_gene(self):
"""
Running numberConversion with valid g variant and a gene name should
give a list of c variant names on transcripts for the given gene.
"""
r = self._call('numberConversion',
- build='hg19', variant='NC_000011.9:g.111959693G>T', gene='C11orf57')
+ build='hg19', variant='NC_000023.10:g.32827640G>A', gene='DMD')
assert_equal(type(r.string), list)
- # Fix for r536: disable the -u and +d convention.
- #assert 'NM_001082969.1:c.*2178+d3819G>T' in r.string
- #assert 'NM_001082970.1:c.*2178+d3819G>T' in r.string
- #assert 'NM_018195.3:c.*2178+d3819G>T' in r.string
- assert 'NM_001082969.1:c.*5997G>T' in r.string
- assert 'NM_001082970.1:c.*5997G>T' in r.string
- assert 'NM_018195.3:c.*5997G>T' in r.string
+ assert 'NM_004007.2:c.250C>T' in r.string
+ assert 'NM_004011.3:c.-397314C>T' in r.string
+ assert 'NM_004019.2:c.-1542694C>T' in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_numberconversion_gtoc_no_transcripts(self):
"""
Running numberConversion with valid g variant but no transcripts
@@ -162,6 +163,7 @@ class TestServicesSoap():
build='hg19', variant='chr7:g.345T>C')
assert_false(r)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_numberconversion_gtoc_required_gene(self):
"""
Running numberConversion with valid g variant but no transcripts
@@ -175,6 +177,7 @@ class TestServicesSoap():
#assert 'XM_001715131.2:c.1155+d19483A>G' in r.string
assert 'XM_001715131.2:c.*19483A>G' in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_gettranscriptsbygenename_valid(self):
"""
Running getTranscriptsByGeneName with valid gene name should give a
@@ -183,15 +186,12 @@ class TestServicesSoap():
r = self._call('getTranscriptsByGeneName',
build='hg19', name='DMD')
assert_equal(type(r.string), list)
- for t in ['NM_004006.2',
- 'NM_000109.3',
- 'NM_004021.2',
- 'NM_004009.3',
- 'NM_004007.2',
- 'NM_004018.2',
- 'NM_004022.2']:
+ for t in ['NM_004011.3',
+ 'NM_004019.2',
+ 'NM_004007.2']:
assert t in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_gettranscriptsbygenename_invalid(self):
"""
Running getTranscriptsByGeneName with invalid gene name should not
@@ -201,6 +201,7 @@ class TestServicesSoap():
build='hg19', name='BOGUSGENE')
assert_false(r)
+ @fix(database, cache('AF230870.1'))
def test_gettranscriptsandinfo_valid(self):
"""
Running getTranscriptsAndInfo with a valid genomic reference should
@@ -213,7 +214,7 @@ class TestServicesSoap():
'mtmB2_v001']:
assert t in names
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database, cache('AL449423.14'))
def test_gettranscriptsandinfo_restricted_valid(self):
"""
Running getTranscriptsAndInfo with a valid genomic reference and a
@@ -232,21 +233,22 @@ class TestServicesSoap():
'C9orf53_v001']:
assert_false(t in names)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_gettranscriptsmapping(self):
"""
Running getTranscriptsMapping should give a list of
TranscriptMappingInfo objects.
"""
r = self._call('getTranscriptsMapping',
- 'hg19', 'chr16', 70680470, 70807150, 1)
+ 'hg19', 'chrX', 31200000, 31210000, 1)
assert_equal(type(r.TranscriptMappingInfo), list)
names = [t.name for t in r.TranscriptMappingInfo]
- for t in ('NM_152456',
- 'NM_138383',
- 'NM_018052',
- 'NR_034083'):
+ for t in ('NM_004011',
+ 'NM_004019',
+ 'NM_004007'):
assert t in names
+ @fix(database, hg19, hg19_transcript_mappings)
def test_mappinginfo(self):
"""
Running mappingInfo should give a Mapping object.
@@ -261,61 +263,68 @@ class TestServicesSoap():
assert_equal(r.startmain, 1388)
assert_equal(r.endmain, 1388)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_mappinginfo(self):
"""
Running mappingInfo should give a Mapping object.
"""
r = self._call('mappingInfo',
- '3.0-beta-06', 'hg19', 'NM_001008541.1', 'g.112039014G>T')
+ '3.0-beta-06', 'hg19', 'NM_002001.2', 'g.159272168G>T')
assert_equal(r.endoffset, 0)
- assert_equal(r.start_g, 112039014)
+ assert_equal(r.start_g, 159272168)
assert_equal(r.startoffset, 0)
assert_equal(r.mutationType, 'subst')
- assert_equal(r.end_g, 112039014)
- assert_equal(r.startmain, 175)
- assert_equal(r.endmain, 175)
+ assert_equal(r.end_g, 159272168)
+ assert_equal(r.startmain, 14)
+ assert_equal(r.endmain, 14)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_mappinginfo_compound(self):
"""
- Running mappingInfo with compound variant should give a Mapping object.
+ Running mappingInfo with compound variant should give a Mapping
+ object.
"""
r = self._call('mappingInfo',
- '3.0-beta-06', 'hg19', 'NM_001008541.1', 'g.[112039014G>T;112039018T>A]')
+ '3.0-beta-06', 'hg19', 'NM_002001.2', 'g.[159272168G>T;159272174T>A]')
assert_equal(r.endoffset, 0)
- assert_equal(r.start_g, 112039014)
+ assert_equal(r.start_g, 159272168)
assert_equal(r.startoffset, 0)
assert_equal(r.mutationType, 'compound')
- assert_equal(r.end_g, 112039018)
- assert_equal(r.startmain, 175)
- assert_equal(r.endmain, 179)
+ assert_equal(r.end_g, 159272174)
+ assert_equal(r.startmain, 14)
+ assert_equal(r.endmain, 20)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_mappinginfo_reverse(self):
"""
- Running mappingInfo on a reverse transcript should give a Mapping object.
+ Running mappingInfo on a reverse transcript should give a Mapping
+ object.
"""
r = self._call('mappingInfo',
- '3.0-beta-06', 'hg19', 'NM_000035.3', 'g.104184170_104184179del')
+ '3.0-beta-06', 'hg19', 'NM_004011.3', 'g.31152229_31152239del')
assert_equal(r.endoffset, 0)
- assert_equal(r.start_g, 104184170)
+ assert_equal(r.start_g, 31152229)
assert_equal(r.startoffset, 0)
assert_equal(r.mutationType, 'del')
- assert_equal(r.end_g, 104184179)
- assert_equal(r.startmain, 1016)
- assert_equal(r.endmain, 1007)
+ assert_equal(r.end_g, 31152239)
+ assert_equal(r.startmain, 6981)
+ assert_equal(r.endmain, 6971)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_mappinginfo_compound_reverse(self):
"""
- Running mappingInfo with compound variant on a reverse transcript should give a Mapping object.
+ Running mappingInfo with compound variant on a reverse transcript
+ should give a Mapping object.
"""
r = self._call('mappingInfo',
- '3.0-beta-06', 'hg19', 'NM_000035.3', 'g.[104184170_104184179del;104184182_104184183del]')
+ '3.0-beta-06', 'hg19', 'NM_004011.3', 'g.[31152229_31152232del;31152235_31152239del]')
assert_equal(r.endoffset, 0)
- assert_equal(r.start_g, 104184170)
+ assert_equal(r.start_g, 31152229)
assert_equal(r.startoffset, 0)
assert_equal(r.mutationType, 'compound')
- assert_equal(r.end_g, 104184183)
- assert_equal(r.startmain, 1016)
- assert_equal(r.endmain, 1003)
+ assert_equal(r.end_g, 31152239)
+ assert_equal(r.startmain, 6981)
+ assert_equal(r.endmain, 6971)
def test_info(self):
"""
@@ -325,6 +334,7 @@ class TestServicesSoap():
assert_equal(type(r.versionParts.string), list)
assert_equal(r.version, mutalyzer.__version__)
+ @fix(database, cache('AB026906.1', 'AL449423.14', 'NM_003002.2'))
def test_getcache(self):
"""
Running the getCache method should give us the expected number of
@@ -334,23 +344,31 @@ class TestServicesSoap():
output = Output(__file__)
sync = CacheSync(output)
- cache = sync.local_cache(created_since)
r = self._call('getCache', created_since)
- if len(cache) > 0:
- assert_equal(len(r.CacheEntry), len(cache))
+ assert_equal(len(r.CacheEntry), 3)
def test_getdbsnpdescriptions(self):
"""
Running getdbSNPDescriptions method should give us the expected HGVS
descriptions for the given dbSNP id.
"""
- r = self._call('getdbSNPDescriptions', 'rs9919552')
+ # Patch Retriever.snpConvert to return rs9919552.
+ def mock_efetch(*args, **kwargs):
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'rs9919552.xml.bz2')
+ return bz2.BZ2File(path)
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ r = self._call('getdbSNPDescriptions', 'rs9919552')
+
assert 'NC_000011.9:g.111959625C>T' in r.string
assert 'NG_012337.2:g.7055C>T' in r.string
assert 'NM_003002.3:c.204C>T' in r.string
assert 'NP_002993.1:p.Ser68=' in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_gettranscripts(self):
"""
Running getTranscripts should give a list of transcripts.
@@ -358,15 +376,11 @@ class TestServicesSoap():
r = self._call('getTranscripts',
build='hg19', chrom='chrX', pos=32237295)
assert_equal(type(r.string), list)
- for t in ['NM_000109',
- 'NM_004006',
- 'NM_004007',
- 'NM_004009',
- 'NM_004010',
- 'NM_004011',
- 'NM_004012']:
+ for t in ['NM_004011',
+ 'NM_004007']:
assert t in r.string
+ @fix(database, hg19, hg19_transcript_mappings)
def test_gettranscripts_with_versions(self):
"""
Running getTranscripts with versions=True should give a list
@@ -375,15 +389,11 @@ class TestServicesSoap():
r = self._call('getTranscripts',
build='hg19', chrom='chrX', pos=32237295, versions=True)
assert_equal(type(r.string), list)
- for t in ['NM_000109.3',
- 'NM_004006.2',
- 'NM_004007.2',
- 'NM_004009.3',
- 'NM_004010.3',
- 'NM_004011.3',
- 'NM_004012.3']:
+ for t in ['NM_004011.3',
+ 'NM_004007.2']:
assert t in r.string
+ @fix(database, cache('NM_003002.2'))
def test_runmutalyzer(self):
"""
Just a runMutalyzer test.
@@ -393,19 +403,33 @@ class TestServicesSoap():
assert_equal(r.genomicDescription, 'NM_003002.2:n.335G>T')
assert 'NM_003002.2(SDHD_v001):c.274G>T' in r.transcriptDescriptions.string
+ @fix(database)
def test_runmutalyzer_reference_info_nm(self):
"""
Get reference info for an NM variant without version.
"""
- r = self._call('runMutalyzer', 'NM_003002:c.274G>T')
+ # Patch GenBankRetriever.fetch to return the contents of NM_003002.2
+ # for NM_003002.
+ def mock_efetch(*args, **kwargs):
+ if kwargs.get('id') != 'NM_003002':
+ return Entrez.efetch(*args, **kwargs)
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'NM_003002.2.gb.bz2')
+ return bz2.BZ2File(path)
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ r = self._call('runMutalyzer', 'NM_003002:c.274G>T')
+
assert_equal(r.errors, 0)
- assert_equal(r.referenceId, 'NM_003002.3')
- assert_equal(r.sourceId, 'NM_003002.3')
+ assert_equal(r.referenceId, 'NM_003002.2')
+ assert_equal(r.sourceId, 'NM_003002.2')
assert_equal(r.sourceAccession, 'NM_003002')
- assert_equal(r.sourceVersion, '3')
- assert_equal(r.sourceGi, '452405284')
+ assert_equal(r.sourceVersion, '2')
+ assert_equal(r.sourceGi, '222352156')
assert_equal(r.molecule, 'n')
+ @fix(database, cache('NM_003002.2'))
def test_runmutalyzer_reference_info_nm_version(self):
"""
Get reference info for an NM variant with version.
@@ -419,23 +443,7 @@ class TestServicesSoap():
assert_equal(r.sourceGi, '222352156')
assert_equal(r.molecule, 'n')
- def test_runmutalyzer_reference_info_ud(self):
- """
- Get reference info for a UD variant after creating it.
-
- UD_129433404385: NC_000023.10 31135344 33362726 2 NULL 2011-10-04 13:15:04
- """
- ud = str(self._call('sliceChromosome',
- 'NC_000023.10', 31135344, 33362726, 2))
- r = self._call('runMutalyzer', ud + ':g.1del')
- assert_equal(r.errors, 0)
- assert_equal(r.referenceId, ud)
- assert_equal(r.sourceId, 'NC_000023.10')
- assert_equal(r.sourceAccession, 'NC_000023')
- assert_equal(r.sourceVersion, '10')
- assert_equal(r.sourceGi, '224589822')
- assert_equal(r.molecule, 'g')
-
+ @fix(database, cache('LRG_1'))
def test_runmutalyzer_reference_info_lrg(self):
"""
Get reference info for an LRG variant.
@@ -446,37 +454,51 @@ class TestServicesSoap():
assert_equal(r.sourceId, 'LRG_1')
assert_equal(r.molecule, 'g')
+ @fix(database, cache('NG_012772.1'))
def test_runmutalyzer_reference_info_ng(self):
"""
Get reference info for an NG variant without version.
"""
- r = self._call('runMutalyzer', 'NG_012772:g.18964del')
+ # Patch GenBankRetriever.fetch to return the contents of NG_012772.1
+ # for NG_012772.
+ def mock_efetch(*args, **kwargs):
+ if kwargs.get('id') != 'NG_012772':
+ return Entrez.efetch(*args, **kwargs)
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'NG_012772.1.gb.bz2')
+ return bz2.BZ2File(path)
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ r = self._call('runMutalyzer', 'NG_012772:g.18964del')
+
assert_equal(r.errors, 0)
- assert_equal(r.referenceId, 'NG_012772.3')
- assert_equal(r.sourceId, 'NG_012772.3')
+ assert_equal(r.referenceId, 'NG_012772.1')
+ assert_equal(r.sourceId, 'NG_012772.1')
assert_equal(r.sourceAccession, 'NG_012772')
- assert_equal(r.sourceVersion, '3')
- assert_equal(r.sourceGi, '388428999')
+ assert_equal(r.sourceVersion, '1')
+ assert_equal(r.sourceGi, '256574794')
assert_equal(r.molecule, 'g')
+ @fix(database, cache('NG_009105.1'))
def test_runmutalyzer_reference_info_ng_version(self):
"""
Get reference info for an NG variant with version.
"""
- r = self._call('runMutalyzer', 'NG_012772.3:g.18964del')
+ r = self._call('runMutalyzer', 'NG_009105.1:g.18964del')
assert_equal(r.errors, 0)
- assert_equal(r.referenceId, 'NG_012772.3')
- assert_equal(r.sourceId, 'NG_012772.3')
- assert_equal(r.sourceAccession, 'NG_012772')
- assert_equal(r.sourceVersion, '3')
- assert_equal(r.sourceGi, '388428999')
+ assert_equal(r.referenceId, 'NG_009105.1')
+ assert_equal(r.sourceId, 'NG_009105.1')
+ assert_equal(r.sourceAccession, 'NG_009105')
+ assert_equal(r.sourceVersion, '1')
+ assert_equal(r.sourceGi, '216548283')
assert_equal(r.molecule, 'g')
+ @fix(database, cache('NG_012772.1'))
def test_runmutalyzer_reference_info_gi(self):
"""
Get reference info for a GI variant.
"""
- self._call('runMutalyzer', 'NG_012772.1:g.1del') # Make sure the server has this reference cached
r = self._call('runMutalyzer', 'gi256574794:g.18964del')
assert_equal(r.errors, 0)
assert_equal(r.referenceId, 'NG_012772.1')
@@ -486,85 +508,121 @@ class TestServicesSoap():
assert_equal(r.sourceGi, '256574794')
assert_equal(r.molecule, 'g')
+ @fix(database, cache('NM_000143.3'))
def test_runmutalyzer_exons(self):
"""
Exon table in runMutalyzer output.
"""
- r = self._call('runMutalyzer', 'NM_004959.4:c.630_636del')
+ r = self._call('runMutalyzer', 'NM_000143.3:c.630_636del')
assert_equal(r.errors, 0)
- expected_exons = [(1, 172, '-187', '-16'),
- (173, 289, '-15', '102'),
- (290, 431, '103', '244'),
- (432, 1057, '245', '870'),
- (1058, 1177, '871', '990'),
- (1178, 1325, '991', '1138'),
- (1326, 3095, '1139', '*1522')]
+ expected_exons = [(1, 195, '-63', '132'),
+ (196, 330, '133', '267'),
+ (331, 441, '268', '378'),
+ (442, 618, '379', '555'),
+ (619, 801, '556', '738'),
+ (802, 967, '739', '904'),
+ (968, 1171, '905', '1108'),
+ (1172, 1299, '1109', '1236'),
+ (1300, 1453, '1237', '1390'),
+ (1454, 1867, '1391', '*271')]
assert_equal(len(r.exons.ExonInfo), len(expected_exons))
for exon, expected_exon in zip(r.exons.ExonInfo, expected_exons):
assert_equal((exon.gStart, exon.gStop, exon.cStart, exon.cStop),
expected_exon)
- def test_gettranscriptsandinfo_slice(self):
- """
- Running getTranscriptsAndInfo on a chromosomal slice should include
- chromosomal positions.
-
- slice: 48284003 - 48259456 (COL1A1 with 5001 and 2001 borders)
- translation start: 48284003 - 5001 + 1 = 48279003
- translation end: 48259456 + 2001 = 48261457
- """
- ud = str(self._call('sliceChromosomeByGene',
- 'COL1A1', 'human', 5000, 2000))
- r = self._call('getTranscriptsAndInfo', ud)
- assert_equal(type(r.TranscriptInfo), list)
- names = [t.name for t in r.TranscriptInfo]
- assert 'COL1A1_v001' in names
- for t in r.TranscriptInfo:
- if t.name != 'COL1A1_v001':
- continue
- assert_equal(t.cTransStart, '-129')
- assert_equal(t.gTransStart, 5001)
- assert_equal(t.chromTransStart, 48279003)
- assert_equal(t.cTransEnd, '*1406')
- assert_equal(t.gTransEnd, 22547)
- assert_equal(t.chromTransEnd, 48261457)
- assert_equal(t.sortableTransEnd, 4883)
- assert_equal(t.cCDSStart, '1')
- assert_equal(t.gCDSStart, 5130)
- assert_equal(t.chromCDSStart, 48278874)
- assert_equal(t.cCDSStop, '3477')
- assert_equal(t.gCDSStop, 21141)
- assert_equal(t.chromCDSStop, 48262863)
-
- @skip # Todo: AL449423.14 no longer contains gene annotations.
- @slow
+ @fix(database, cache('AB026906.1', 'NM_003002.2', 'AL449423.14'))
def test_batchjob(self):
"""
Submit a batch job.
"""
variants = ['AB026906.1(SDHD):g.7872G>T',
- 'NM_003002.1:c.3_4insG',
+ 'NM_003002.2:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- data = '\n'.join(variants).encode('base64')
+ data = '\n'.join(variants) + '\n' #.encode('base64')
result = self._call('submitBatchJob', data, 'NameChecker')
- job_id = int(result)
-
- for _ in range(50):
- try:
- result = self._call('getBatchJob', job_id)
- break
- except Fault:
- result = self._call('monitorBatchJob', job_id)
- assert int(result) <= len(variants)
- time.sleep(1)
- else:
- assert False
+ job_id = str(result)
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == len(variants)
+
+ scheduler = Scheduler.Scheduler()
+ scheduler.process()
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == 0
+
+ result = self._call('getBatchJob', job_id)
assert_equal(len(result.decode('base64').strip().split('\n')) - 1,
len(variants))
- @slow
+ @fix(database)
+ def test_batchjob_newlines_unix(self):
+ """
+ Submit a batch job with UNIX newlines.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.2:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ data = '\n'.join(variants) + '\n'
+
+ result = self._call('submitBatchJob', data, 'SyntaxChecker')
+ job_id = str(result)
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == len(variants)
+
+ scheduler = Scheduler.Scheduler()
+ scheduler.process()
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == 0
+
+ @fix(database)
+ def test_batchjob_newlines_mac(self):
+ """
+ Submit a batch job with Mac newlines.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.2:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ data = '\r'.join(variants) + '\r'
+
+ result = self._call('submitBatchJob', data, 'SyntaxChecker')
+ job_id = str(result)
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == len(variants)
+
+ scheduler = Scheduler.Scheduler()
+ scheduler.process()
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == 0
+
+ @fix(database)
+ def test_batchjob_newlines_windows(self):
+ """
+ Submit a batch job with Windows newlines.
+ """
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.2:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ data = '\r\n'.join(variants) + '\r\n'
+
+ result = self._call('submitBatchJob', data, 'SyntaxChecker')
+ job_id = str(result)
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == len(variants)
+
+ scheduler = Scheduler.Scheduler()
+ scheduler.process()
+
+ result = self._call('monitorBatchJob', job_id)
+ assert int(result) == 0
+
+ @fix(database)
def test_batchjob_toobig(self):
"""
Submit the batch name checker with a too big input file.
@@ -579,8 +637,8 @@ feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui
blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla
facilisi."""
data = seed
- # Very crude way of creating something at least 6MB in size
- while len(data) < 6000000:
+ # Very crude way of creating something big.
+ while len(data) <= settings.MAX_FILE_SIZE:
data += data
try:
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index a2ac64b847fd73974e8e874172e73b6f8b33860c..7049fc3fa1a93ec03f5377021b575857a1e81e5d 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -9,47 +9,33 @@ from nose.tools import *
from mutalyzer.output import Output
from mutalyzer.Retriever import GenBankRetriever
from mutalyzer.variantchecker import check_variant
-from mutalyzer.util import slow, skip
-import utils
+from fixtures import REFERENCES
+from fixtures import database, cache, hg19, hg19_transcript_mappings
+from utils import MutalyzerTest
+from utils import fix
-class TestVariantchecker():
+# Todo: We had a test for checking a variant on a CONTIG RefSeq reference
+# (NG_005990.1), but instead we should have separate tests for the retriever
+# module, including a test for fetching a CONTIG RefSeq reference.
+
+
+class TestVariantchecker(MutalyzerTest):
"""
Test the variantchecker module.
"""
+ fixtures = (database, )
+
def setup(self):
"""
Initialize test variantchecker module.
"""
- utils.create_test_environment(database=True)
+ super(TestVariantchecker, self).setup()
self.output = Output(__file__)
self.retriever = GenBankRetriever(self.output)
- def teardown(self):
- utils.destroy_environment()
-
- def _slice(self, chromosome, start, stop, orientation):
- """
- Get a UD slice.
-
- Orientation: 1 for forward, 2 for reverse.
- """
- return self.retriever.retrieveslice(chromosome, start, stop, orientation)
-
- def _slice_gene(self, gene, organism='human', upstream=5000, downstream=2000):
- """
- Get a UD slice for a gene.
- """
- return self.retriever.retrievegene(gene, organism, upstream, downstream)
-
- def _load_record(self, identifier):
- """
- Load a record in the database and cache.
- """
- return self.retriever.loadrecord(identifier)
-
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_in_frame(self):
"""
Simple in-frame deletion should give a simple description on protein
@@ -64,7 +50,7 @@ class TestVariantchecker():
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_insertion_in_frame(self):
"""
Simple in-frame insertion should give a simple description on protein
@@ -79,7 +65,7 @@ class TestVariantchecker():
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame(self):
"""
Simple in-frame deletion/insertion should give a simple description on
@@ -95,7 +81,7 @@ class TestVariantchecker():
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame_complete(self):
"""
Simple in-frame deletion/insertion should give a simple description on
@@ -111,6 +97,7 @@ class TestVariantchecker():
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
+ @fix(cache('NM_003002.2'))
def test_est_warning_nm_est(self):
"""
Warning for EST positioning on NM reference.
@@ -119,6 +106,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 1
+ @fix(cache('NM_003002.2'))
def test_no_est_warning_nm_c(self):
"""
No EST warning for c. positioning on NM reference.
@@ -127,6 +115,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 0
+ @fix(cache('NM_003002.2'))
def test_no_est_warning_nm_n(self):
"""
No EST warning for n. positioning on NM reference.
@@ -135,6 +124,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 0
+ @fix(cache('NG_012772.1'))
def test_est_warning_ng_est(self):
"""
Warning for EST positioning on NG reference.
@@ -143,6 +133,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 1
+ @fix(cache('NG_012772.1'))
def test_no_est_warning_ng_g(self):
"""
No EST warning for g. positioning on NG reference.
@@ -151,6 +142,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 0
+ @fix(cache('AA010203.1'))
def test_no_est_warning_est_est(self):
"""
No warning for EST positioning on EST reference.
@@ -159,6 +151,7 @@ class TestVariantchecker():
west = self.output.getMessagesWithErrorCode('WEST')
assert len(west) == 0
+ @fix(cache('NM_003002.2'))
def test_roll(self):
"""
Just a variant where we should roll.
@@ -167,6 +160,7 @@ class TestVariantchecker():
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert len(wroll) > 0
+ @fix(cache('NM_003002.2'))
def test_no_roll(self):
"""
Just a variant where we cannot roll.
@@ -175,6 +169,7 @@ class TestVariantchecker():
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert_equal(len(wroll), 0)
+ @fix(cache('NM_000088.3'))
def test_no_roll_splice(self):
"""
Here we can roll but should not, because it is over a splice site.
@@ -185,6 +180,7 @@ class TestVariantchecker():
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert_equal(len(wroll), 0)
+ @fix(cache('NM_000088.3'))
def test_partial_roll_splice(self):
"""
Here we can roll two positions, but should roll only one because
@@ -196,6 +192,7 @@ class TestVariantchecker():
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert len(wroll) > 0
+ @fix(cache('NM_000088.3'))
def test_roll_after_splice(self):
"""
Here we can roll and should, we stay in the same exon.
@@ -204,7 +201,7 @@ class TestVariantchecker():
wroll = self.output.getMessagesWithErrorCode('WROLLFORWARD')
assert len(wroll) > 0
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_roll_both_ins(self):
"""
Insertion that rolls should not use the same inserted sequence in
@@ -238,7 +235,7 @@ class TestVariantchecker():
assert_equal ('AL449423.14:g.65471_65472insACT', self.output.getIndexedOutput('genomicDescription', 0, ''))
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 1)
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_roll_reverse_ins(self):
"""
Insertion that rolls on the reverse strand should not use the same
@@ -249,7 +246,7 @@ class TestVariantchecker():
assert_equal ('AL449423.14:g.65471_65472insACT', self.output.getIndexedOutput('genomicDescription', 0, ''))
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 0)
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_roll_message_forward(self):
"""
Roll warning message should only be shown for currently selected
@@ -259,7 +256,7 @@ class TestVariantchecker():
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 1)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLREVERSE')), 0)
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_roll_message_reverse(self):
"""
Roll warning message should only be shown for currently selected
@@ -269,6 +266,7 @@ class TestVariantchecker():
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLFORWARD')), 0)
assert_equal(len(self.output.getMessagesWithErrorCode('WROLLREVERSE')), 1)
+ @fix(cache('NM_000143.3'))
def test_ins_cds_start(self):
"""
Insertion on CDS start boundary should not be included in CDS.
@@ -277,6 +275,7 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput("newprotein", 0), None)
# Todo: Is this a good test?
+ @fix(cache('NM_000143.3'))
def test_ins_cds_start_after(self):
"""
Insertion after CDS start boundary should be included in CDS.
@@ -285,6 +284,7 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput("newprotein", 0), '?')
# Todo: Is this a good test?
+ @fix(cache('NG_012772.1'))
def test_del_splice_site(self):
"""
Deletion hitting one splice site should not do a protein prediction.
@@ -296,6 +296,7 @@ class TestVariantchecker():
# prediction is done.
assert not self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_exon(self):
"""
Deletion of an entire exon should be possible.
@@ -307,6 +308,7 @@ class TestVariantchecker():
# prediction is done.
assert self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_exon_exact(self):
"""
Deletion of exactly an exon should be possible.
@@ -318,6 +320,7 @@ class TestVariantchecker():
# prediction is done.
assert self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_exon_in_frame(self):
"""
Deletion of an entire exon with length a triplicate should give a
@@ -335,6 +338,7 @@ class TestVariantchecker():
assert self.output.getOutput('newprotein')
# Todo: assert that protein products indeed have only this difference.
+ @fix(cache('NG_012772.1'))
def test_del_exons(self):
"""
Deletion of two entire exons should be possible.
@@ -346,6 +350,7 @@ class TestVariantchecker():
# prediction is done.
assert self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_intron(self):
"""
Deletion of an entire intron should be possible (fusion of remaining
@@ -358,6 +363,7 @@ class TestVariantchecker():
# prediction is done.
assert self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_intron_exact(self):
"""
Deletion of exactly an intron should be possible (fusion of flanking
@@ -373,6 +379,7 @@ class TestVariantchecker():
assert self.output.getOutput('oldprotein')
assert not self.output.getOutput('newprotein')
+ @fix(cache('NG_012772.1'))
def test_del_intron_in_frame(self):
"""
Deletion of an entire intron should be possible (fusion of remaining
@@ -386,6 +393,7 @@ class TestVariantchecker():
assert self.output.getOutput('newprotein')
# Todo: assert that protein products indeed have only this difference.
+ @fix(cache('NG_012772.1'))
def test_del_exon_unknown_offsets(self):
"""
Deletion of an entire exon with unknown offsets should be possible.
@@ -406,6 +414,7 @@ class TestVariantchecker():
# Todo: .c notation should still be c.632-?_681+?del, but what about
# other transcripts?
+ @fix(cache('NG_012772.1'))
def test_del_exon_unknown_offsets_in_frame(self):
"""
Deletion of an entire exon with unknown offsets and length a
@@ -429,6 +438,7 @@ class TestVariantchecker():
# Todo: .c notation should still be c.632-?_681+?del, but what about
# other transcripts?
+ @fix(cache('NG_012772.1'))
def test_del_exon_unknown_offsets_composed(self):
"""
Deletion of an entire exon with unknown offsets and another composed
@@ -449,7 +459,7 @@ class TestVariantchecker():
# Todo: .c notation should still be c.632-?_681+?del, but what about
# other transcripts?
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_del_exon_unknown_offsets_reverse(self):
"""
Deletion of an entire exon with unknown offsets should be possible,
@@ -470,6 +480,7 @@ class TestVariantchecker():
# Todo: .c notation should still be c.632-?_681+?del, but what about
# other transcripts?
+ @fix(cache('NM_000143.3'))
def test_del_exon_transcript_reference(self):
"""
Deletion of entire exon on a transcript reference should remove the
@@ -477,13 +488,15 @@ class TestVariantchecker():
of the flanking exons (as would happen using the mechanism for genomic
references).
"""
- check_variant('NM_018723.3:c.758_890del', self.output)
+ #check_variant('NM_018723.3:c.758_890del', self.output)
+ check_variant('NM_000143.3:c.739_904del', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('WOVERSPLICE')), 0)
assert_equal(self.output.getOutput('removedSpliceSites'), [2])
# Todo: For now, the following is how to check if protein
# prediction is done.
assert self.output.getOutput('newprotein')
+ @fix(cache('AB026906.1'))
def test_ins_range(self):
"""
Insertion of a range is not implemented yet.
@@ -491,6 +504,7 @@ class TestVariantchecker():
check_variant('AB026906.1:c.274_275ins262_268', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('AB026906.1'))
def test_delins_range(self):
"""
Deletion/insertion of a range is not implemented yet.
@@ -498,14 +512,6 @@ class TestVariantchecker():
check_variant('AB026906.1:c.274delins262_268', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
- def test_contig_reference(self):
- """
- Variant description on a CONTIG RefSeq reference.
- """
- check_variant('NG_005990.1:g.1del', self.output)
- assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
- 'NG_005990.1:g.1del')
-
def test_no_reference(self):
"""
Variant description without a reference.
@@ -513,6 +519,7 @@ class TestVariantchecker():
check_variant('g.244355733del', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOREF')), 1)
+ @fix(cache('NM_003002.2'), hg19, hg19_transcript_mappings)
def test_chromosomal_positions(self):
"""
Variants on transcripts in c. notation should have chromosomal positions
@@ -522,6 +529,7 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput('rawVariantsChromosomal', 0),
('chr11', '+', [('274G>T', (111959695, 111959695))]))
+ @fix(cache('NM_002001.2'))
def test_ex_notation(self):
"""
Variant description using EX notation should not crash but deletion of
@@ -530,6 +538,7 @@ class TestVariantchecker():
check_variant('NM_002001.2:c.EX1del', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('IDELSPLICE')), 1)
+ @fix(cache('LRG_1'))
def test_lrg_reference(self):
"""
We should be able to use LRG reference sequence without error.
@@ -540,30 +549,11 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
'LRG_1:g.6855G>T')
- def test_lrg_reference_new(self):
- """
- We should be able to use new LRG reference sequence without error.
-
- Note that all LRG sequences are now in a new format and essentially
- this test is no different from the previous, except that LRG_218 was
- not yet in our cache which makes it easier to test the new format.
- """
- check_variant('LRG_218:c.1786_1788delAAT', self.output)
- error_count, _, _ = self.output.Summary()
- assert_equal(error_count, 0)
-
- def test_non_numeric_locus_tag_ending(self):
- """
- Locus tag in NC_002128 does not end in an underscore and three digits
- but we should not crash on it.
- """
- check_variant('NC_002128(tagA):c.3del', self.output)
-
+ @fix(cache('NM_002001.2'))
def test_gi_reference_plain(self):
"""
Test reference sequence notation with GI number.
"""
- assert self._load_record('NM_002001.2') # Make sure it's in our database
check_variant('31317229:c.6del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -572,11 +562,11 @@ class TestVariantchecker():
assert '31317229(FCER1A_v001):c.6del' \
in self.output.getOutput('descriptions')
+ @fix(cache('NM_002001.2'))
def test_gi_reference_prefix(self):
"""
Test reference sequence notation with GI number and prefix.
"""
- assert self._load_record('NM_002001.2') # Make sure it's in our database
check_variant('GI31317229:c.6del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -585,11 +575,11 @@ class TestVariantchecker():
assert '31317229(FCER1A_v001):c.6del' \
in self.output.getOutput('descriptions')
+ @fix(cache('NM_002001.2'))
def test_gi_reference_prefix_colon(self):
"""
Test reference sequence notation with GI number and prefix with colon.
"""
- assert self._load_record('NM_002001.2') # Make sure it's in our database
check_variant('GI:31317229:c.6del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -598,6 +588,7 @@ class TestVariantchecker():
assert '31317229(FCER1A_v001):c.6del' \
in self.output.getOutput('descriptions')
+ @fix(cache('NM_002001.2'))
def test_nop_nm(self):
"""
Variant on NM without effect should be described as '='.
@@ -610,11 +601,12 @@ class TestVariantchecker():
assert 'NM_002001.2(FCER1A_v001):c.=' \
in self.output.getOutput('descriptions')
+ @fix(cache('DMD'))
def test_nop_ud(self):
"""
Variant on UD without effect should be described as '='.
"""
- ud = self._slice_gene('DMD')
+ ud = REFERENCES['DMD']['accession']
check_variant(ud + ':g.5T>T', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -625,12 +617,13 @@ class TestVariantchecker():
assert ud + '(DMD_v001):c.=' \
in self.output.getOutput('descriptions')
+ @fix(cache('DPYD'))
def test_ud_reverse_sequence(self):
"""
Variant on UD from reverse strand should have reverse complement
sequence.
"""
- ud = self._slice_gene('DPYD')
+ ud = REFERENCES['DPYD']['accession']
check_variant(ud + '(DPYD_v1):c.85C>T', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -641,11 +634,12 @@ class TestVariantchecker():
assert ud + '(DPYD_v001):c.85C>T' \
in self.output.getOutput('descriptions')
+ @fix(cache('MARK1'))
def test_ud_forward_sequence(self):
"""
Variant on UD from forward strand should have forward sequence.
"""
- ud = self._slice_gene('MARK1')
+ ud = REFERENCES['MARK1']['accession']
check_variant(ud + '(MARK1_v001):c.400T>C', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -656,12 +650,14 @@ class TestVariantchecker():
assert ud + '(MARK1_v001):c.400T>C' \
in self.output.getOutput('descriptions')
+ @fix(cache('chr9_reverse'))
def test_ud_reverse_range(self):
"""
Variant on UD from reverse strand should have reversed range
positions.
"""
- ud = self._slice('NC_000009.11', 32922603, 33006639, 2)
+ # This is just some slice on from the reverse strand of hg19 chr9.
+ ud = REFERENCES['chr9_reverse']['accession']
check_variant(ud + ':g.10624_78132del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -670,11 +666,12 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
ud + ':g.10624_78132del')
+ @fix(cache('MARK1'))
def test_ud_forward_range(self):
"""
Variant on UD from forward strand should have forward range positions.
"""
- ud = self._slice_gene('MARK1')
+ ud = REFERENCES['MARK1']['accession']
check_variant(ud + '(MARK1_v001):c.400_415del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -683,13 +680,15 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
ud + ':g.76614_76629del')
+ @fix(cache('chr9_reverse'))
def test_ud_reverse_del_length(self):
"""
Variant on UD from reverse strand should have reversed range
positions, but not reverse complement of first argument (it is not a
sequence, but a length).
"""
- ud = self._slice('NC_000009.11', 32922603, 33006639, 2)
+ # This is just some slice on from the reverse strand of hg19 chr9.
+ ud = REFERENCES['chr9_reverse']['accession']
check_variant(ud + ':g.10624_78132del67509', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -698,6 +697,7 @@ class TestVariantchecker():
assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
ud + ':g.10624_78132del')
+ @fix(cache('DPYD'))
def test_ud_reverse_roll(self):
"""
Variant on UD from reverse strand should roll the oposite direction.
@@ -709,7 +709,7 @@ class TestVariantchecker():
g. 748 749 750 751 752 753
chr g. 868 867 866 865 864 863
"""
- ud = self._slice_gene('DPYD')
+ ud = REFERENCES['DPYD']['accession']
check_variant(ud + '(DPYD_v001):c.104del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -720,6 +720,7 @@ class TestVariantchecker():
assert ud + '(DPYD_v001):c.105del' \
in self.output.getOutput('descriptions')
+ @fix(cache('MARK1'))
def test_ud_forward_roll(self):
"""
Variant on UD from forward strand should roll the same.
@@ -731,7 +732,7 @@ class TestVariantchecker():
g. 612 613 614 615 616
chr g. 179 180 181 182 183
"""
- ud = self._slice_gene('MARK1')
+ ud = REFERENCES['MARK1']['accession']
check_variant(ud + '(MARK1_v001):c.400del', self.output)
error_count, _, _ = self.output.Summary()
assert_equal(error_count, 0)
@@ -742,7 +743,7 @@ class TestVariantchecker():
assert ud + '(MARK1_v001):c.401del' \
in self.output.getOutput('descriptions')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_with_sequence_forward_genomic(self):
"""
Specify the deleted sequence in a deletion.
@@ -753,7 +754,7 @@ class TestVariantchecker():
assert 'AL449423.14(CDKN2A_v001):c.98_99del' \
in self.output.getOutput('descriptions')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_with_length_forward_genomic(self):
"""
Specify the deleted sequence length in a deletion.
@@ -764,7 +765,7 @@ class TestVariantchecker():
assert 'AL449423.14(CDKN2A_v001):c.98_99del' \
in self.output.getOutput('descriptions')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_with_sequence_reverse_coding(self):
"""
Specify the deleted sequence in a deletion on the reverse strand.
@@ -775,7 +776,7 @@ class TestVariantchecker():
assert 'AL449423.14(CDKN2A_v001):c.161_163del' \
in self.output.getOutput('descriptions')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(cache('AL449423.14'))
def test_deletion_with_length_reverse_coding(self):
"""
Specify the deleted sequence length in a deletion on the reverse strand.
@@ -786,6 +787,7 @@ class TestVariantchecker():
assert 'AL449423.14(CDKN2A_v001):c.161_163del' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
def test_deletion_with_sequence_reverse_ng_coding(self):
"""
Specify the deleted sequence in a deletion on the reverse strand
@@ -797,6 +799,7 @@ class TestVariantchecker():
assert 'NG_008939.1(PCCB_v001):c.155_157del' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
def test_deletion_with_length_reverse_ng_coding(self):
"""
Specify the deleted sequence length in a deletion on the reverse strand
@@ -808,6 +811,7 @@ class TestVariantchecker():
assert 'NG_008939.1(PCCB_v001):c.155_157del' \
in self.output.getOutput('descriptions')
+ @fix(cache('AB026906.1'))
def test_inversion(self):
"""
Inversion variant.
@@ -818,6 +822,7 @@ class TestVariantchecker():
assert 'AB026906.1(SDHD_v001):c.274_275inv' \
in self.output.getOutput('descriptions')
+ @fix(cache('NM_000193.2'))
def test_delins_with_length(self):
"""
Delins with explicit length of deleted sequence (bug #108).
@@ -825,6 +830,7 @@ class TestVariantchecker():
check_variant('NM_000193.2:c.108_109del2insG', self.output)
assert 'NM_000193.2(SHH_i001):p.(Lys38Serfs*2)' in self.output.getOutput('protDescriptions')
+ @fix(cache('NG_009105.1'))
def test_protein_level_description(self):
"""
Currently protein level descriptions are not implemented.
@@ -832,6 +838,7 @@ class TestVariantchecker():
check_variant('NG_009105.1(OPN1LW):p.=', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('NP_064445.1'))
def test_protein_reference(self):
"""
Currently protein references are not implemented.
@@ -839,28 +846,33 @@ class TestVariantchecker():
check_variant('NP_064445.1:p.=', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('A1BG'))
def test_wnomrna_other(self):
"""
Warning for no mRNA field on other than currently selected transcript
should give WNOMRNA_OTHER warning.
"""
- ud = self._slice_gene('A1BG') # Contains ZNF497 (v1 and v2) with no mRNA
+ # Contains ZNF497 (v1 and v2) with no mRNA
+ ud = REFERENCES['A1BG']['accession']
check_variant(ud + '(A1BG_v001):c.13del', self.output)
wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER')
assert len(wnomrna_other) == 3
+ @fix(cache('A1BG'))
def test_wnomrna(self):
"""
Warning for no mRNA field on currently selected transcript should give
WNOMRNA warning.
"""
- ud = self._slice_gene('A1BG') # Contains ZNF497 (v1 and v2) with no mRNA
+ # Contains ZNF497 (v1 and v2) with no mRNA
+ ud = REFERENCES['A1BG']['accession']
check_variant(ud + '(ZNF497_v001):c.13del', self.output)
wnomrna = self.output.getMessagesWithErrorCode('WNOMRNA')
wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER')
assert len(wnomrna) == 1
assert len(wnomrna_other) == 2
+ @fix(cache('L41870.1'))
def test_mrna_ref_adjacent_exons_warn(self):
"""
Warning for mRNA reference where exons are not adjacent.
@@ -871,10 +883,11 @@ class TestVariantchecker():
w_exon_annotation = self.output.getMessagesWithErrorCode('WEXON_ANNOTATION')
assert len(w_exon_annotation) == 1
+ @fix(cache('NM_003002.2'))
def test_mrna_ref_adjacent_exons_no_warn(self):
"""
No warning for mRNA reference where exons are adjacent.
"""
- check_variant('NM_133378.3:c.1del', self.output)
+ check_variant('NM_003002.2:c.1del', self.output)
w_exon_annotation = self.output.getMessagesWithErrorCode('WEXON_ANNOTATION')
assert len(w_exon_annotation) == 0
diff --git a/tests/test_website.py b/tests/test_website.py
index 797ef63d9c4c0ee9c1d74120652f300c02d2dc9a..13984378cb66ff7e950d85c5001954b0647df324 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -6,372 +6,236 @@ Tests for the WSGI interface to Mutalyzer.
#import logging; logging.basicConfig()
+import bz2
+import cgi
+import logging
+from mock import patch
import os
import re
-import urllib2
+from StringIO import StringIO
import time
-import web
-from nose.tools import *
-from webtest import TestApp
-import logging
import urllib
-import cgi
+import urllib2
-# Todo: Since the `mutalyzer.website` module accesses the configuration
-# settings at import time, we need to pre-populate those. This hack can
-# be removed once we moved from web.py to Flask and refactored the web
-# application into an application factory (which does not access the
-# configuration settings at import time).
-from mutalyzer.config import settings
-settings.configure(dict(
- DEBUG = True,
- TESTING = True,
- CACHE_DIR = None,
- DATABASE_URI = 'sqlite://',
- LOG_FILE = None))
+from Bio import Entrez
+import lxml.html
+from nose.tools import *
import mutalyzer
-from mutalyzer import website
-from mutalyzer.util import slow, skip
+from mutalyzer import Scheduler
+from mutalyzer.website import create_app
-import utils
+from fixtures import cache, database, hg19, hg19_transcript_mappings
+from utils import MutalyzerTest
+from utils import fix
BATCH_RESULT_URL = 'http://localhost/mutalyzer/Results_{id}.txt'
-class TestWSGI():
+class TestWebsite(MutalyzerTest):
"""
Test the Mutalyzer WSGI interface.
"""
def setup(self):
- """
- Initialize test application.
- """
- utils.create_test_environment(database=True)
- web.config.debug = False
- application = website.app.wsgifunc()
- self.app = TestApp(application)
-
- def teardown(self):
- utils.destroy_environment()
+ super(TestWebsite, self).setup()
+ self.app = create_app().test_client()
- def test_root(self):
- """
- Expect the index HTML page.
- """
- r = self.app.get('')
- assert_equal(r.status, '301 Moved Permanently')
- assert r.location.endswith('/')
- r = r.follow()
- assert_equal(r.status, '200 OK')
- # We check for <html> to make sure the menu template is included
- r.mustcontain('<html>',
- 'Welcome to the Mutalyzer website',
- '</html>')
-
- def test_index(self):
+ def test_homepage(self):
"""
Expect the index HTML page.
"""
r = self.app.get('/')
- assert_equal(r.status, '200 OK')
- # We check for <html> to make sure the menu template is included
- r.mustcontain('<html>',
- 'Welcome to the Mutalyzer website',
- '</html>')
-
- def test_index_explicit(self):
- """
- Expect the index HTML page.
- """
- r = self.app.get('/index')
- assert_equal(r.status, '200 OK')
- # We check for <html> to make sure the menu template is included
- r.mustcontain('<html>',
- 'Welcome to the Mutalyzer website',
- '</html>')
+ assert_equal(r.status_code, 200)
+ assert 'Welcome to the Mutalyzer website' in r.data
def test_about(self):
"""
- See if my name is on the About page ;)
+ See if people get proper credit.
"""
r = self.app.get('/about')
assert_equal(r.status, '200 OK')
- r.mustcontain('Martijn Vermaat')
+ assert 'Jonathan Vis' in r.data
def test_non_existing(self):
"""
Expect a 404 response.
"""
- r = self.app.get('/this/doesnotexist', status=404)
+ r = self.app.get('/this/doesnotexist')
+ assert_equal(r.status_code, 404)
+ @fix(database)
def test_menu_links(self):
"""
Test all links in the main menu.
"""
ignore = [] # This could contain relative links we want to skip
r = self.app.get('/')
- for link in r.lxml.cssselect('#menu a'):
+
+ dom = lxml.html.fromstring(r.data)
+
+ for link in dom.cssselect('#menu a'):
href = link.get('href')
- if href.startswith('http://') or href.startswith('https://') \
- or href in ignore:
+ if (href.startswith('http://') or
+ href.startswith('https://') or
+ href in ignore):
continue
if not href.startswith('/'):
href = '/' + href
- self.app.get(href)
+
+ r = self.app.get(href)
+ assert_equal(r.status_code, 200)
def test_description_extractor(self):
"""
Submit the variant description extractor.
"""
- r = self.app.get('/descriptionExtract')
- form = r.forms[0]
- form['referenceSeq'] = 'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA'
- form['variantSeq'] = 'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA'
- r = form.submit()
- r.mustcontain('g.[5_6insTT;17del;26A>C;35dup]')
+ r = self.app.get('/description-extractor', query_string={
+ 'reference_sequence': 'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA',
+ 'variant_sequence': 'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA'})
+ assert 'g.[5_6insTT;17del;26A>C;35dup]' in r.data
def test_checksyntax_valid(self):
"""
Submit the check syntax form with a valid variant.
"""
- r = self.app.get('/syntaxCheck')
- form = r.forms[0]
- form['variant'] = 'AB026906.1:c.274G>T'
- r = form.submit()
- r.mustcontain('The syntax of this variant is OK!')
+ r = self.app.get('/syntax-checker',
+ query_string={'description': 'AB026906.1:c.274G>T'})
+ assert 'The syntax of this variant is OK!' in r.data
def test_checksyntax_invalid(self):
"""
Submit the check syntax form with an invalid variant.
"""
- r = self.app.get('/syntaxCheck')
- form = r.forms[0]
- form['variant'] = 'AB026906.1:c.27'
- r = form.submit()
- r.mustcontain('Fatal',
- 'Details of the parse error')
+ r = self.app.get('/syntax-checker',
+ query_string={'description': 'AB026906.1:c.27'})
+ assert 'Fatal' in r.data
+ assert 'Details of the parse error' in r.data
+ @fix(database, cache('NM_002001.2'))
def test_check_valid(self):
"""
Submit the name checker form with a valid variant.
Should include form and main HTML layout.
"""
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'NM_002001.2:g.1del'
- r = form.submit()
- r.mustcontain('0 Errors',
- '0 Warnings',
- 'Raw variant 1: deletion of 1',
- '<a href="#bottom" class="hornav">go to bottom</a>',
- '<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">')
-
- def test_check_more_valid(self):
- """
- Test the name checker for some more variants.
- """
- def check_name(name):
- r = self.app.get('/check?name=%s' % name)
- r.mustcontain('0 Errors')
- names = ['NG_012337.1:g.7055C>T']
- for name in names:
- check_name(name)
-
- def test_check_post(self):
- """
- Test the name checker for a POST request.
-
- We accept POST requests for backwards compatibility.
- """
- def check_name(name):
- r = self.app.post('/check', {'name': name})
- assert_equal(r.status, '301 Moved Permanently')
- assert r.location.endswith('/check?name=%s' % urllib.quote(name))
- names = ['NG_012337.1:g.7055C>T']
- for name in names:
- check_name(name)
-
- def test_check_post_old(self):
- """
- Test the name checker for a POST request with the old parameter
- name.
-
- We accept POST requests for backwards compatibility.
- """
- def check_name(name):
- r = self.app.post('/check', {'mutationName': name})
- assert_equal(r.status, '301 Moved Permanently')
- assert r.location.endswith('/check?name=%s' % urllib.quote(name))
- names = ['NG_012337.1:g.7055C>T']
- for name in names:
- check_name(name)
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NM_002001.2:g.1del'})
+ assert '0 Errors' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Raw variant 1: deletion of 1' in r.data
+ assert '<a href="#bottom" class="hornav">go to bottom</a>' in r.data
+ assert '<input type="text" name="description" value="NM_002001.2:g.1del" style="width:100%">' in r.data
def test_check_invalid(self):
"""
Submit the name checker form with an invalid variant.
"""
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'NM_002001.2'
- r = form.submit()
- r.mustcontain('1 Error',
- '0 Warnings',
- 'Details of the parse error')
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NM_002001.2'})
+ assert '1 Error' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Details of the parse error' in r.data
+ @fix(database, cache('NP_064445.1'))
def test_check_protein_reference(self):
"""
Submit the name checker form with a protein reference sequence (not
supported).
"""
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'BAA81889.1:c.274G>T'
- r = form.submit()
- r.mustcontain('1 Error',
- '0 Warnings',
- 'Protein reference sequences are not supported')
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NP_064445.1:c.274G>T'})
+ assert '1 Error' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Protein reference sequences are not supported' in r.data
+ @fix(database, cache('NM_002001.2'))
def test_check_noninteractive(self):
"""
Submit the name checker form non-interactively.
Should not include form and main layout HTML.
"""
- r = self.app.get('/check?name=NM_002001.2:g.1del&standalone=1')
- assert_false('<a href="#bottom" class="hornav">go to bottom</a>' in r)
- assert_false('<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">' in r)
- r.mustcontain('0 Errors',
- '0 Warnings',
- 'Raw variant 1: deletion of 1',
- '<html>',
- '</html>')
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NM_002001.2:g.1del',
+ 'standalone': '1'})
+ assert '<a href="#bottom" class="hornav">go to bottom</a>' not in r.data
+ assert '<input type="text" name="description" value="NM_002001.2:g.1del" style="width:100%">' not in r.data
+ assert '0 Errors' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Raw variant 1: deletion of 1' in r.data
+ @fix(database, cache('NG_012772.1'))
def test_check_interactive_links(self):
"""
Submitting interactively should have links to transcripts also
interactive.
"""
- r = self.app.get('/check?name=%s' % urllib.quote('NG_012337.1:g.7055C>T'))
- r.mustcontain('0 Errors')
- r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1:g.7055C>T')))
- # Fix for r536: disable the -u and +d convention.
- #r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-30-u2103G>A')))
- r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-2133G>A')))
- r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(SDHD_v001):c.204C>T')))
-
- @skip
- def test_check_noninteractive_links(self):
- """
- Submitting non-interactively should have links to transcripts also
- non-interactive.
-
- Todo: This is hard to implement in TAL, do this when we move to
- another template language. See Trac issue #97.
- """
- r = self.app.get('/check?name=%s&standalone=1' % urllib.quote('NG_012337.1:g.7055C>T'))
- r.mustcontain('0 Errors')
- r.mustcontain('"check?name=%s&standalone=1"' % cgi.escape(urllib.quote('NG_012337.1:g.7055C>T')))
- r.mustcontain('"check?name=%s&standalone=1"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-30-u2103G>A')))
- r.mustcontain('"check?name=%s&standalone=1"' % cgi.escape(urllib.quote('NG_012337.1(SDHD_v001):c.204C>T')))
-
- def test_check_noninteractive_old(self):
- """
- Submit the name checker form non-interactively in the old style.
- Should redirect to new style.
- """
- r = self.app.get('/check?mutationName=NM_002001.2:g.1del')
- assert_equal(r.status, '301 Moved Permanently')
- assert r.location.endswith('/check?name=%s&standalone=1' % urllib.quote('NM_002001.2:g.1del'))
-
- def test_check_browser_link(self):
- """
- Submit the name checker form with a coding variant on a transcript.
- Should include link to UCSC Genome Browser.
- """
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'NM_003002.2:c.274G>T'
- r = form.submit()
- # Note: the r.environ does not work in versions higher than webob 1.1.1
- bed_track = urllib.quote(r.environ['wsgi.url_scheme'] + '://' + r.environ['HTTP_HOST'] + '/bed?name=' + urllib.quote('NM_003002.2:c.274G>T'))
- r.mustcontain('<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr11:111959685-111959705&hgt.customText=%s">View original variant in UCSC Genome Browser</a>' % bed_track)
-
- def test_checkforward(self):
- """
- A checkForward request should redirect to the name checker.
-
- This is for backwards compatibility with old bookmarks.
- """
- r = self.app.get('/checkForward?mutationName=%s' % urllib.quote('NM_002001.2:g.1del'))
- assert_equal(r.status, '301 Moved Permanently')
- assert r.location.endswith('/check?name=%s' % urllib.quote('NM_002001.2:g.1del'))
- r = r.follow()
- r.mustcontain('0 Errors',
- '0 Warnings',
- 'Raw variant 1: deletion of 1',
- '<a href="#bottom" class="hornav">go to bottom</a>',
- '<input type="text" name="name" value="NM_002001.2:g.1del" style="width:100%">')
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NG_012772.1:g.128del'})
+ assert '0 Errors' in r.data
+ assert 'href="/name-checker?description=NG_012772.1%3Ag.128del"' in r.data
+ assert 'href="/name-checker?description=NG_012772.1%28BRCA2_v001%29%3Ac.-5100del"' in r.data
def test_snp_converter_valid(self):
"""
Submit the SNP converter form with a valid SNP.
"""
- r = self.app.get('/snp')
- form = r.forms[0]
- form['rsId'] = 'rs9919552'
- r = form.submit()
- r.mustcontain('0 Errors',
- '0 Warnings',
- 'NC_000011.9:g.111959625C>T',
- 'NG_012337.2:g.7055C>T',
- 'NM_003002.3:c.204C>T',
- 'NP_002993.1:p.Ser68=')
+ # Patch Retriever.snpConvert to return rs9919552.
+ def mock_efetch(*args, **kwargs):
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'rs9919552.xml.bz2')
+ return bz2.BZ2File(path)
+
+ with patch.object(Entrez, 'efetch', mock_efetch):
+ r = self.app.get('/snp-converter',
+ query_string={'rs_id': 'rs9919552'})
+ assert '0 Errors' in r.data
+ assert '0 Warnings' in r.data
+ assert 'NC_000011.9:g.111959625C>T' in r.data
+ assert 'NG_012337.2:g.7055C>T' in r.data
+ assert 'NM_003002.3:c.204C>T' in r.data
+ assert 'NP_002993.1:p.Ser68=' in r.data
def test_snp_converter_invalid(self):
"""
Submit the SNP converter form with an invalid SNP.
"""
- r = self.app.get('/snp')
- form = r.forms[0]
- form['rsId'] = 'r9919552'
- r = form.submit()
- r.mustcontain('1 Error',
- '0 Warnings',
- 'Fatal',
- 'This is not a valid dbSNP id')
+ r = self.app.get('/snp-converter',
+ query_string={'rs_id': 'r9919552'})
+
+ assert '1 Error' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Fatal' in r.data
+ assert 'This is not a valid dbSNP id' in r.data
+ @fix(database, hg19, hg19_transcript_mappings)
def test_position_converter_c2g(self):
"""
Submit the position converter form with a valid variant.
"""
- r = self.app.get('/positionConverter')
- form = r.forms[0]
- form['assembly_name_or_alias'] = 'hg19'
- form['variant'] = 'NM_003002.2:c.204C>T'
- r = form.submit()
- r.mustcontain('NC_000011.9:g.111959625C>T')
+ r = self.app.get('/position-converter',
+ query_string={'assembly_name_or_alias': 'hg19',
+ 'description': 'NM_003002.2:c.204C>T'})
+ assert 'NC_000011.9:g.111959625C>T' in r.data
+ @fix(database, hg19, hg19_transcript_mappings)
def test_position_converter_g2c(self):
"""
Submit the position converter form with a valid variant.
"""
- r = self.app.get('/positionConverter')
- form = r.forms[0]
- form['assembly_name_or_alias'] = 'hg19'
- form['variant'] = 'NC_000011.9:g.111959625C>T'
- r = form.submit()
- r.mustcontain('NM_003002.2:c.204C>T')
+ r = self.app.get('/position-converter',
+ query_string={'assembly_name_or_alias': 'hg19',
+ 'description': 'NC_000011.9:g.111959625C>T'})
+ assert 'NM_003002.2:c.204C>T' in r.data
- @slow
- def _batch(self, batch_type='NameChecker', arg1=None, file="", size=0,
- header='', lines=None):
+ def _batch(self, job_type='name-checker', assembly_name_or_alias=None,
+ file="", size=0, header='', lines=None):
"""
Submit a batch form.
- @kwarg batch_type: Type of batch job to test. One of NameChecker,
- SyntaxChecker, PositionConverter.
- @kwarg arg1: Optional extra argument for the batch job.
+ @kwarg batch_type: Type of batch job to test. One of name-checker,
+ syntax-checker, position-converter.
+ @kwarg argument: Optional extra argument for the batch job.
@kwarg file: String with variants to use as input for the batch job.
@kwarg size: Number of variants in input.
@kwarg header: Message that must be found in the batch job result.
@@ -379,73 +243,71 @@ class TestWSGI():
@return: The batch result document.
@rtype: string
+ """
+ data = {'job_type': job_type,
+ 'email': 'test@test.test',
+ 'file': (StringIO(file), 'test.txt')}
+ if assembly_name_or_alias is not None:
+ data['assembly_name_or_alias'] = assembly_name_or_alias
+
+ r = self.app.post('/batch-jobs',
+ data=data)
+ progress_url = '/' + r.location.split('/')[-1]
+
+ r = self.app.get(progress_url)
+ assert '<div id="if_items_left">' in r.data
+ assert '<div id="ifnot_items_left" style="display:none">' in r.data
+ assert ('<span id="items_left">%d</span>' % size) in r.data
+
+ scheduler = Scheduler.Scheduler()
+ scheduler.process()
+
+ r = self.app.get(progress_url)
+ assert '<div id="if_items_left" style="display:none">' in r.data
+ assert '<div id="ifnot_items_left">' in r.data
+
+ dom = lxml.html.fromstring(r.data)
+ result_url = dom.cssselect('#ifnot_items_left a')[0].attrib['href']
- @note: Since the batch files are processed by a running batch daemon
- process, the result gets written to the directory defined by the
- system-wide configuration (e.g. /var/mutalyzer/cache), thus
- inaccessible for the TestApp instance under our current user.
- The 'solution' for this is to download the results via a running
- webserver that should be using the same configuration as the batch
- daemon. Yes, this is a hack.
- """
- r = self.app.get('/batch')
- form = r.forms[0]
- if arg1:
- form['arg1'] = arg1
- form['batchType'] = batch_type
- form['batchEmail'] = 'test@test.test'
- form.set('batchFile', ('test_%s.txt' % batch_type,
- file))
- r = form.submit()
- id = r.lxml.cssselect('#jobID')[0].get('value')
- max_tries = 60
- for i in range(max_tries):
- r = self.app.get('/progress?jobID=' + id + '&totalJobs=' + str(size) + '&ajax=1')
- assert_equal(r.content_type, 'text/plain')
- #print '%s: %s' % (batch_type, r.body)
- if r.body == 'OK': break
- assert re.match('[0-9]+', r.body)
- time.sleep(2)
- assert_equal(r.body, 'OK')
- # Actually, this only means the last entry was taken from the database
- # queue. It might still be processing, in which case we miss some
- # expected output. So let's wait a few seconds.
- time.sleep(2)
- # This is a hack to get to the batch results (see @note above).
- response = urllib2.urlopen(BATCH_RESULT_URL.format(id=id))
- assert_equal(response.info().getheader('Content-Type'), 'text/plain')
- result = response.read()
- assert header in result
if not lines:
lines = size
- assert_equal(len(result.strip().split('\n')) - 1, lines)
- return result
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ r = self.app.get(result_url)
+ assert 'text/plain' in r.headers['Content-Type']
+ assert header in r.data
+ assert_equal(len(r.data.strip().split('\n')) - 1, lines)
+
+ return r.data
+
+ @fix(database, cache('AB026906.1', 'NM_003002.2', 'AL449423.14'))
def test_batch_namechecker(self):
"""
Submit the batch name checker form.
"""
variants=['AB026906.1(SDHD):g.7872G>T',
- 'NM_003002.1:c.3_4insG',
+ 'NM_003002.2:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- self._batch('NameChecker',
+ self._batch('name-checker',
file='\n'.join(variants),
size=len(variants),
- header='Input\tErrors | Messages')
+ header='Input\tErrors and warnings')
+ @fix(database)
def test_batch_namechecker_extra_tab(self):
"""
- Submit the batch name checker form with lines ending with tab
+ Submit the batch syntax checker form with lines ending with tab
characters.
"""
- variants=['AB026906.1(SDHD):g.7872G>T\t']
- self._batch('NameChecker',
+ variants=['AB026906.1(SDHD):g.7872G>T\t',
+ 'AB026906.1(SDHD):g.7872G>T\t',
+ 'AB026906.1(SDHD):g.7872G>T\t']
+ self._batch('syntax-checker',
file='\n'.join(variants),
- size=len(variants),
- header='Input\tErrors | Messages')
+ size=len(variants) * 2,
+ lines=len(variants),
+ header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker(self):
"""
Submit the batch syntax checker form.
@@ -453,67 +315,67 @@ class TestWSGI():
variants = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\n'.join(variants),
size=len(variants),
header='Input\tStatus')
+ @fix(database, hg19, hg19_transcript_mappings)
def test_batch_positionconverter(self):
"""
Submit the batch position converter form.
"""
variants = ['NM_003002.2:c.204C>T',
'NC_000011.9:g.111959625C>T']
- self._batch('PositionConverter',
- arg1='hg19',
+ self._batch('position-converter',
+ assembly_name_or_alias='hg19',
file='\n'.join(variants),
size=len(variants),
header='Input Variant')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_unix(self):
"""
- Submit the batch syntax checker form with unix line endings.
+ Submit batch syntax checker job with Unix line endings.
"""
variants = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\n'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_mac(self):
"""
- Submit the batch syntax checker form with mac line endings.
+ Submit batch syntax checker job with Mac line endings.
"""
variants = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\r'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_windows(self):
"""
- Submit the batch syntax checker form with windows line endings.
+ Submit batch syntax checker job with Windows line endings.
"""
variants = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
'AL449423.14(CDKN2A_v002):c.5_400del']
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\r\n'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_big_unix(self):
"""
- Submit the batch syntax checker form with unix line ending
- styles and a big input file.
+ Submit big batch syntax checker job with Unix line endings.
"""
samples = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
@@ -522,16 +384,15 @@ class TestWSGI():
# Create 240 variants out of 3 samples
for i in range(80):
variants.extend(samples)
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\n'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_big_mac(self):
"""
- Submit the batch syntax checker form with mac line ending
- styles and a big input file.
+ Submit big batch syntax checker job with Mac line endings.
"""
samples = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
@@ -540,16 +401,15 @@ class TestWSGI():
# Create 240 variants out of 3 samples
for i in range(80):
variants.extend(samples)
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\r'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_newlines_big_windows(self):
"""
- Submit the batch syntax checker form with windows line ending
- styles and a big input file.
+ Submit big batch syntax checker job with Windows line endings.
"""
samples = ['AB026906.1(SDHD):g.7872G>T',
'NM_003002.1:c.3_4insG',
@@ -558,12 +418,12 @@ class TestWSGI():
# Create 240 variants out of 3 samples
for i in range(80):
variants.extend(samples)
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\r\n'.join(variants),
size=len(variants),
header='Input\tStatus')
- @skip # Todo: AL449423.14 no longer contains gene annotations.
+ @fix(database)
def test_batch_syntaxchecker_oldstyle(self):
"""
Submit the batch syntax checker form with old style input file.
@@ -572,60 +432,28 @@ class TestWSGI():
'AB026906.1\tSDHD\tg.7872G>T',
'NM_003002.1\t\tc.3_4insG',
'AL449423.14\tCDKN2A_v002\tc.5_400del']
- self._batch('SyntaxChecker',
+ self._batch('syntax-checker',
file='\n'.join(variants),
size=len(variants)-1,
header='Input\tStatus')
- @slow
+ @fix(database, cache('AB026906.1'))
def test_batch_namechecker_restriction_sites(self):
"""
Submit the batch name checker form and see if restriction site effects
are added.
-
- Note that we use the @slow decorator here even though it is already
- applied to self._batch. The reason is that we use the result from
- self._batch, which does not exist if @slow checks are disabled.
"""
variants=['AB026906.1:c.274G>T',
'AB026906.1:c.[274G>T;143A>G;15G>T]']
- results = self._batch('NameChecker',
+ results = self._batch('name-checker',
file='\n'.join(variants),
size=len(variants),
- header='Input\tErrors | Messages').strip().split('\n')
+ header='Input\tErrors and warnings').strip().split('\n')
assert 'Restriction Sites Created\tRestriction Sites Deleted' in results[0]
assert 'CviQI,RsaI\tBccI' in results[1]
assert 'CviQI,RsaI;HhaI,HinP1I;SfcI\tBccI;;BpmI,BsaXI (2),MnlI' in results[2]
- @slow
- def test_batch_syntaxchecker_toobig(self):
- """
- Submit the batch syntax checker with a too big input file.
- """
- seed = """
-Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
-nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi
-enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis
-nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in
-hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu
-feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui
-blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla
-facilisi."""
- file = seed
- # Very crude way of creating something at least 6MB in size
- while len(file) < 6000000:
- file += file
- r = self.app.get('/batch')
- form = r.forms[0]
- form['batchType'] = 'SyntaxChecker'
- form['batchEmail'] = 'm.vermaat.hg@lumc.nl'
- form.set('batchFile', ('test_batch_toobig.txt',
- file))
- r = form.submit(status=413)
- assert_equal(r.content_type, 'text/plain')
-
- @skip # Todo: AL449423.14 no longer contains gene annotations.
- @slow
+ @fix(database)
def test_batch_multicolumn(self):
"""
Submit the batch syntax checker with a multiple-colums input file.
@@ -635,7 +463,7 @@ facilisi."""
variants = [('AB026906.1(SDHD):g.7872G>T', 'NM_003002.1:c.3_4insG'),
('NM_003002.1:c.3_4insG', 'AB026906.1(SDHD):g.7872G>T'),
('AL449423.14(CDKN2A_v002):c.5_400del', 'AL449423.14(CDKN2A_v002):c.5_400del')]
- result = self._batch('SyntaxChecker',
+ result = self._batch('syntax-checker',
file='\n'.join(['\t'.join(r) for r in variants]),
size=len(variants) * 2,
header='Input\tStatus',
@@ -647,198 +475,219 @@ facilisi."""
"""
Download a Python example client for the web service.
"""
- r = self.app.get('/download/client-suds.py')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('#!/usr/bin/env python')
+ r = self.app.get('/downloads/client-suds.py')
+ assert 'text/plain' in r.headers['Content-Type']
+ assert '#!/usr/bin/env python' in r.data
def test_download_rb(self):
"""
Download a Ruby example client for the web service.
"""
- r = self.app.get('/download/client-savon.rb')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('#!/usr/bin/env ruby')
+ r = self.app.get('/downloads/client-savon.rb')
+ assert 'text/plain' in r.headers['Content-Type']
+ assert '#!/usr/bin/env ruby' in r.data
def test_download_cs(self):
"""
Download a C# example client for the web service.
"""
- r = self.app.get('/download/client-mono.cs')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('public static void Main(String [] args) {')
+ r = self.app.get('/downloads/client-mono.cs')
+ assert_equal(r.headers['Content-Type'], 'text/plain')
+ assert 'public static void Main(String [] args) {' in r.data
def test_download_php(self):
"""
Download a PHP example client for the web service.
"""
- r = self.app.get('/download/client-php.php')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('<?php')
+ r = self.app.get('/downloads/client-php.php')
+ assert 'text/plain' in r.headers['Content-Type']
+ assert '<?php' in r.data
def test_downloads_batchtest(self):
"""
Download the batch test example file.
"""
r = self.app.get('/downloads/batchtestnew.txt')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('NM_003002.1:c.3_4insG')
+ assert 'text/plain' in r.headers['Content-Type']
+ assert 'NM_003002.1:c.3_4insG' in r.data
def test_annotated_soap_api(self):
"""
Test the SOAP documentation generated from the WSDL.
"""
r = self.app.get('/soap-api')
- assert_equal(r.content_type, 'text/html')
- r.mustcontain('Web Service: Mutalyzer')
+ assert 'text/html' in r.headers['Content-Type']
+ assert 'Web Service: Mutalyzer' in r.data
+ @fix(database, cache('NG_012337.1'))
def test_getgs(self):
"""
Test the /getGS interface used by LOVD2.
"""
- r = self.app.get('/getGS?variantRecord=NM_003002.2&forward=1&mutationName=NG_012337.1:g.7055C%3ET')
- r.mustcontain('0 Errors',
- '0 Warnings',
- 'Raw variant 1: substitution at 7055')
- assert_equal(r.body.find('go to bottom'), -1)
- assert_equal(r.body.find('<input'), -1)
-
+ r = self.app.get('/getGS',
+ query_string={'variantRecord': 'NM_003002.2',
+ 'forward': '1',
+ 'mutationName': 'NG_012337.1:g.7055C>T'},
+ follow_redirects=True)
+ assert '0 Errors' in r.data
+ assert '0 Warnings' in r.data
+ assert 'Raw variant 1: substitution at 7055' in r.data
+ assert 'go to bottom' not in r.data
+ assert '<input' not in r.data
+
+ @fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_g2c(self):
"""
Test the /Variant_info interface used by LOVD2 (g to c).
"""
- r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=g.48374289_48374389del')
- assert_equal(r.content_type, 'text/plain')
+ r = self.app.get('/Variant_info',
+ query_string={'LOVD_ver': '2.0-29',
+ 'build': 'hg19',
+ 'acc': 'NM_203473.1',
+ 'var': 'g.48374289_48374389del'})
+ assert 'text/plain' in r.headers['Content-Type']
expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
- assert_equal(r.body, expected)
+ assert_equal(r.data, expected)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_c2g(self):
"""
Test the /Variant_info interface used by LOVD2 (c to g).
"""
- r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1020_1072%2B48del')
- assert_equal(r.content_type, 'text/plain')
+ r = self.app.get('/Variant_info',
+ query_string={'LOVD_ver': '2.0-29',
+ 'build': 'hg19',
+ 'acc': 'NM_203473.1',
+ 'var': 'c.1020_1072+48del'})
+ assert 'text/plain' in r.headers['Content-Type']
expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
- assert_equal(r.body, expected)
+ assert_equal(r.data, expected)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_c2g_downstream(self):
"""
Test the /Variant_info interface used by LOVD2 (c variant downstream
notation to g).
"""
- r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1709%2Bd187del')
- assert_equal(r.content_type, 'text/plain')
+ r = self.app.get('/Variant_info',
+ query_string={'LOVD_ver': '2.0-29',
+ 'build': 'hg19',
+ 'acc': 'NM_203473.1',
+ 'var': 'c.1709+d187del'})
+ assert 'text/plain' in r.headers['Content-Type']
expected = '\n'.join(['1709', '187', '1709', '187', '48379389', '48379389', 'del'])
- assert_equal(r.body, expected)
+ assert_equal(r.data, expected)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_no_variant(self):
"""
Test the /Variant_info interface used by LOVD2 (without variant).
"""
- r = self.app.get('/Variant_info?LOVD_ver=2.0-32&build=hg19&acc=NM_001083962.1')
+ r = self.app.get('/Variant_info',
+ query_string={'LOVD_ver': '2.0-29',
+ 'build': 'hg19',
+ 'acc': 'NM_203473.1'})
+ assert 'text/plain' in r.headers['Content-Type']
assert_equal(r.content_type, 'text/plain')
- expected = '\n'.join(['-612', '7720', '2016'])
- assert_equal(r.body, expected)
+ expected = '\n'.join(['-158', '1709', '1371'])
+ assert_equal(r.data, expected)
+ @fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_ivs(self):
"""
Test the /Variant_info interface used by LOVD2 (with IVS positioning).
"""
- r = self.app.get('/Variant_info?LOVD_ver=2.0-33&build=hg19&acc=NM_000249.3&var=c.IVS10%2B3A%3EG')
- assert_equal(r.content_type, 'text/plain')
+ r = self.app.get('/Variant_info',
+ query_string={'LOVD_ver': '2.0-33',
+ 'build': 'hg19',
+ 'acc': 'NM_000249.3',
+ 'var': 'c.IVS10+3A>G'})
+ assert 'text/plain' in r.headers['Content-Type']
expected = '\n'.join(['884', '3', '884', '3', '37059093', '37059093', 'subst'])
- assert_equal(r.body, expected)
+ assert_equal(r.data, expected)
+ @fix(database)
def test_upload_local_file(self):
"""
Test the genbank uploader.
+ """
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'AB026906.1.gb.bz2')
+ r = self.app.post('/reference-loader',
+ data={'method': 'upload',
+ 'file': (bz2.BZ2File(path), 'AB026906.1.gb')})
+ assert 'Your reference sequence was loaded successfully.' in r.data
+
+ dom = lxml.html.fromstring(r.data)
+ reference_url = dom.cssselect('#reference_download')[0].attrib['href']
- @todo: Use another genbank file to get a UD number and check that
- we can then check variants using that UD number.
- @todo: This genbank file location is bogus. The tests directory is not
- included with the package installation.
- """
- test_genbank_file = os.path.join(os.path.realpath(os.path.dirname(__file__)),
- 'data', 'AB026906.1.gb')
- r = self.app.get('/upload')
- form = r.forms[0]
- form['invoermethode'] = 'file'
- form.set('bestandsveld', ('test_upload.gb',
- open(test_genbank_file, 'r').read()))
- r = form.submit()
- r.mustcontain('Your reference sequence was loaded successfully.')
+ r = self.app.get(reference_url)
+ assert_equal(r.data, bz2.BZ2File(path).read())
+ @fix(database)
def test_upload_local_file_invalid(self):
"""
Test the genbank uploader with a non-genbank file.
-
- @note: We add the current time to the file contents to make sure it is
- not recognized by its hash.
"""
- r = self.app.get('/upload')
- form = r.forms[0]
- form['invoermethode'] = 'file'
- form.set('bestandsveld', ('test_upload.gb',
- 'this is not a genbank file (%s)\n' % time.ctime()))
- r = form.submit()
- r.mustcontain('The file could not be parsed.')
- print r.body
+ r = self.app.post('/reference-loader',
+ data={'method': 'upload',
+ 'file': (StringIO('this is not a genbank file'), 'AB026906.1.gb')})
+ assert 'Your reference sequence was loaded successfully.' not in r.data
+ assert 'The file could not be parsed.' in r.data
+ @fix(database, cache('NM_002001.2'))
def test_reference(self):
"""
Test if reference files are cached.
"""
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'AB026906.1:c.274G>T'
- r = form.submit()
- r.mustcontain('0 Errors',
- '1 Warning',
- 'Raw variant 1: substitution at 7872',
- '<a href="#bottom" class="hornav">go to bottom</a>',
- '<input type="text" name="name" value="AB026906.1:c.274G>T" style="width:100%">')
- r = self.app.get('/Reference/AB026906.1.gb')
- assert_equal(r.content_type, 'text/plain')
- assert_equal(r.content_length, 26427)
- r.mustcontain('ggaaaaagtc tctcaaaaaa cctgctttat')
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NM_002001.2:g.1del'})
+ assert '0 Errors' in r.data
+ r = self.app.get('/reference/NM_002001.2.gb')
+ path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+ 'data',
+ 'NM_002001.2.gb.bz2')
+ assert_equal(r.data, bz2.BZ2File(path).read())
+
+ @fix(database, cache('NM_002001.2'))
def test_reference_head(self):
"""
Test if reference files are cached, by issuing a HEAD request.
+ """
+ r = self.app.get('/name-checker',
+ query_string={'description': 'NM_002001.2:g.1del'})
+ assert '0 Errors' in r.data
- Note: The WebTest module also checks that the response to a HEAD
- request is empty, as it should be.
- """
- r = self.app.get('/check')
- form = r.forms[0]
- form['name'] = 'AB026906.1:c.274G>T'
- r = form.submit()
- r.mustcontain('0 Errors',
- '1 Warning',
- 'Raw variant 1: substitution at 7872',
- '<a href="#bottom" class="hornav">go to bottom</a>',
- '<input type="text" name="name" value="AB026906.1:c.274G>T" style="width:100%">')
- r = self.app.head('/Reference/AB026906.1.gb')
- assert_equal(r.content_type, 'text/plain')
+ r = self.app.head('/reference/NM_002001.2.gb')
+ assert_equal(r.status_code, 200)
+ @fix(database)
def test_reference_head_none(self):
"""
Test if non-existing reference files gives a 404 on a HEAD request.
"""
- r = self.app.head('/Reference/AB026906.78.gb', status=404)
+ r = self.app.head('/reference/NM_002001.2.gb')
+ assert_equal(r.status_code, 404)
+ @fix(database, hg19, hg19_transcript_mappings, cache('NM_003002.2'))
def test_bed(self):
"""
BED track for variant.
"""
- r = self.app.get('/bed?name=NM_003002.2%3Ac.274G%3ET')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('\t'.join(['chr11', '111959694', '111959695', '274G>T', '0', '+']))
+ r = self.app.get('/bed',
+ query_string={'description': 'NM_003002.2:c.274G>T'})
+ assert 'text/plain' in r.headers['Content-Type']
+ assert '\t'.join(['chr11', '111959694', '111959695', '274G>T', '0', '+']) in r.data
+ @fix(database, hg19, hg19_transcript_mappings, cache('NM_000132.3'))
def test_bed_reverse(self):
"""
BED track for variant on reverse strand.
"""
- r = self.app.get('/bed?name=NM_000132.3%3Ac.%5B4374A%3ET%3B4380_4381del%5D')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain('\t'.join(['chrX', '154157690', '154157691', '4374A>T', '0', '-']))
- r.mustcontain('\t'.join(['chrX', '154157683', '154157685', '4380_4381del', '0', '-']))
+ r = self.app.get('/bed',
+ query_string={'description': 'NM_000132.3:c.[4374A>T;4380_4381del]'})
+ assert 'text/plain' in r.headers['Content-Type']
+ assert '\t'.join(['chrX', '154157690', '154157691', '4374A>T', '0', '-']) in r.data
+ assert '\t'.join(['chrX', '154157683', '154157685', '4380_4381del', '0', '-']) in r.data
diff --git a/tests/utils.py b/tests/utils.py
index 93c6aab52c3684d40e9316f0411994aaacd07d04..befa5d72859279140211ad412fa2920fce8961d6 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -1,36 +1,68 @@
+"""
+Utilities for unit tests.
+"""
+
+
+from functools import wraps
import os
import shutil
import tempfile
from mutalyzer.config import settings
-from mutalyzer.db import models
-# Todo: Refactor creating and destroying environment into a context manager.
+class TestEnvironment(object):
+ """
+ Configure Mutalyzer for unit tests. All storage is transient and isolated.
+ """
+ def __init__(self, fixtures=None):
+ fixtures = fixtures or []
+
+ self.cache_dir = tempfile.mkdtemp()
+ log_handle, self.log_file = tempfile.mkstemp()
+ os.close(log_handle)
-def create_test_environment(database=False):
+ settings.configure({'DEBUG': False,
+ 'TESTING': True,
+ 'CACHE_DIR': self.cache_dir,
+ 'REDIS_URI': None,
+ 'DATABASE_URI': 'sqlite://',
+ 'LOG_FILE': self.log_file})
+
+ for fixture in fixtures:
+ fixture()
+
+ def destroy(self):
+ """
+ Destroy all storage defined in the current environment.
+ """
+ shutil.rmtree(self.cache_dir)
+ os.unlink(self.log_file)
+
+
+class MutalyzerTest(object):
"""
- Configure Mutalyzer for unit tests. All storage is transient and isolated.
+ Test class providing an isolated test environment for each test.
"""
- log_handle, log_filename = tempfile.mkstemp()
- os.close(log_handle)
+ fixtures = ()
- settings.configure(dict(
- DEBUG = False,
- TESTING = True,
- CACHE_DIR = tempfile.mkdtemp(),
- REDIS_URI = None,
- DATABASE_URI = 'sqlite://',
- LOG_FILE = log_filename))
+ def setup(self):
+ self.environment = TestEnvironment(fixtures=self.fixtures)
- if database:
- models.create_all()
+ def teardown(self):
+ self.environment.destroy()
-def destroy_environment():
+def fix(*fixtures):
"""
- Destroy all storage defined in the current environment.
+ Decorator for a unit test setting up the specified fixtures.
"""
- shutil.rmtree(settings.CACHE_DIR)
- os.unlink(settings.LOG_FILE)
+ def decorator(f):
+ @wraps(f)
+ def fixed_f(*args, **kwargs):
+ for fixture in fixtures:
+ fixture()
+ return f(*args, **kwargs)
+ return fixed_f
+ return decorator