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Rm getters setters #7

Merged
merged 35 commits into from
Apr 18, 2016
Merged

Rm getters setters #7

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796c37d
Added property decorators to most evidence strings getters/setters to…
tomdcsmith Apr 6, 2016
a2eaf2e
Fixed setters.
tomdcsmith Apr 6, 2016
afc2595
db_xref_url decorators for genetics ev string
tomdcsmith Apr 6, 2016
7de59bb
Merge branch 'master' of https://github.com/EBIvariation/eva-cttv-pip…
tomdcsmith Apr 6, 2016
febf49e
Fixed recursion errors with getter/setter decorators.
tomdcsmith Apr 6, 2016
b1823d5
Decorators for urls, accessions and dates- and altered tests.
tomdcsmith Apr 6, 2016
7a5f765
Fixed test_unique_reference test. Fixed date setting.
tomdcsmith Apr 6, 2016
c0c44c8
Moved more evidence strings setters to pythonic decorated setters. Wr…
tomdcsmith Apr 7, 2016
80c251c
Tested most of CTTVEvidenceString class. Added eq and ne functions to…
tomdcsmith Apr 7, 2016
b4cd7d5
- Removed set_pubmed_refs, not used in code and not in latest evidenc…
tomdcsmith Apr 7, 2016
3baf576
Set target test
tomdcsmith Apr 7, 2016
e9c9480
Changed some clinvar_record getters to properties.
tomdcsmith Apr 7, 2016
cb5c024
Remaining clinvar_record getters to properties
tomdcsmith Apr 8, 2016
dbf83e1
Removed details
tomdcsmith Apr 8, 2016
b9de38d
EFOTerm getter to property. Start of efo term tests.
tomdcsmith Apr 14, 2016
5000619
Finished efoterm tests.
tomdcsmith Apr 14, 2016
009c066
Testing set_known_mutations
tomdcsmith Apr 14, 2016
336a3f2
Testing add and set known mutations.
tomdcsmith Apr 14, 2016
dc16834
- Removed _process_consequence_type_file_xls, no longer needed.
tomdcsmith Apr 14, 2016
5ea14e5
Chaged so_term rank and accession to properties.
tomdcsmith Apr 14, 2016
71590e6
-ensembl_gene_ids to property
tomdcsmith Apr 15, 2016
5b760a4
-Simplified so_terms attribute
tomdcsmith Apr 15, 2016
98640bc
Removed unused "get_ranked_so_names"
tomdcsmith Apr 15, 2016
a692889
Merge branch 'master' of https://github.com/EBIvariation/eva-cttv-pip…
tomdcsmith Apr 15, 2016
194dbe4
-Uncommented get_evidence_strings tests
tomdcsmith Apr 15, 2016
4d23080
-changed test dict in testing evidence string
tomdcsmith Apr 15, 2016
0df92e1
-Added maxdiff to see difference
tomdcsmith Apr 15, 2016
589de33
Comparing evidence strings rather than evidence strings and dicts
tomdcsmith Apr 15, 2016
cbdfae7
Changed calls to super classes in evidence_strings.
tomdcsmith Apr 15, 2016
73759d3
Changed to inherit from userdict instead.
tomdcsmith Apr 15, 2016
6321824
Print statement to view on travis
tomdcsmith Apr 15, 2016
a2a0999
Print statement to view on travis, 2
tomdcsmith Apr 15, 2016
aff63b5
Dynamically create timestamp for evidence string in test
tomdcsmith Apr 15, 2016
64e5e6e
Removed print statements in test
tomdcsmith Apr 15, 2016
6e435dd
Renamed ClinvarRecord.acc to accession for clarity.
tomdcsmith Apr 18, 2016
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Changed to inherit from userdict instead.
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@tomdcsmith
tomdcsmith committed Apr 15, 2016
commit 73759d3826e4ef2b5a1b4030c014637cbe78e756
9 changes: 5 additions & 4 deletions eva_cttv_pipeline/evidence_strings.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
from collections import UserDict
import json

import jsonschema
Expand All @@ -14,9 +15,9 @@
SOM_SCHEMA_FILE = utilities.get_resource_file(__package__, config.local_schema + "/src/literature_curated.json")


class CTTVEvidenceString(dict):
class CTTVEvidenceString(UserDict):
def __init__(self, a_dictionary):
super(CTTVEvidenceString, self).__init__(a_dictionary)
super().__init__(a_dictionary)
# dict.__init__(a_dictionary)

def add_unique_association_field(self, key, value):
Expand Down Expand Up @@ -144,7 +145,7 @@ def __init__(self):
}

# CTTVEvidenceString.__init__(self, a_dictionary)
super(CTTVGeneticsEvidenceString, self).__init__(a_dictionary)
super().__init__(a_dictionary)

@property
def db_xref_url(self):
Expand Down Expand Up @@ -296,7 +297,7 @@ def __init__(self):
}
# CTTVEvidenceString.__init__(self,a_dictionary)

super(CTTVSomaticEvidenceString, self).__init__(a_dictionary)
super().__init__(a_dictionary)

@property
def db_xref_url(self):
Expand Down