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Add a new managers layer #528

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imedina opened this issue Feb 11, 2020 · 1 comment
Open

Add a new managers layer #528

imedina opened this issue Feb 11, 2020 · 1 comment
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@imedina @julie-sullivan
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in progress work in progress, under active development
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v5.0.0

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@imedina
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imedina commented Feb 11, 2020

The current design consists of two layers: REST and DBAdapators. It would be great to add a new manager layer for different reasons.
@imedina imedina added this to the v5.0.0 milestone Feb 11, 2020
imedina added a commit that referenced this issue Feb 11, 2020
@imedina
lib: initial work in new managers layer #528
20c6f6d
@julie-sullivan julie-sullivan added the in progress work in progress, under active development label Feb 12, 2020
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  • DBAdaptor - should only be executing queries. Logic should be in manager
  • REST API - should only handle the requests/responses. Logic should be in the manager.

julie-sullivan added a commit that referenced this issue Feb 12, 2020
@julie-sullivan
use utils groupby method instead of local one. they are identical. #528
e7e9c3e
julie-sullivan added a commit that referenced this issue Feb 12, 2020
@julie-sullivan
move logic to live in the new managers #528
5c1587b
julie-sullivan added a commit that referenced this issue Feb 12, 2020
@julie-sullivan
Migrate clinical, gene, protein, transcript and region logic from RES…
9d37740 
…T to manager. Doesn't compile. #528
julie-sullivan added a commit that referenced this issue Feb 13, 2020
@julie-sullivan
add xref manager. #528
0c1d06a
julie-sullivan added a commit that referenced this issue Feb 14, 2020
@julie-sullivan
add repeats, migrate more methods from dbadaptors. #528
e4cb407
julie-sullivan added a commit that referenced this issue Feb 14, 2020
@julie-sullivan
keep list of managers by species and assembly. lots of classes compil…
df69d64 
…e now. #528
julie-sullivan added a commit that referenced this issue Feb 17, 2020
@julie-sullivan
add metamanager, checkstyle #528
39c430b
julie-sullivan added a commit that referenced this issue Feb 18, 2020
@julie-sullivan
refactor monitor to live in lib instead of core. extract inner classe…
f782f0f 
…s. update metamanager. #528
julie-sullivan added a commit that referenced this issue Feb 18, 2020
@julie-sullivan
try adding genequery object. #528
fd8a667
julie-sullivan added a commit that referenced this issue Feb 19, 2020
@julie-sullivan
move parseQueryParams() to be gene query constructor instead. #528
3d01a40
julie-sullivan added a commit that referenced this issue Feb 20, 2020
@julie-sullivan
add two new classes for query options. use reflection to create query…
bc35aa0 
… objects #528
julie-sullivan added a commit that referenced this issue Feb 21, 2020
@julie-sullivan
convert multivalue map to regular map. parse regions. #528
9b70f37
julie-sullivan added a commit that referenced this issue Feb 21, 2020
@julie-sullivan
add unit test for gene query #528
61ab2e3
julie-sullivan added a commit that referenced this issue Feb 21, 2020
@julie-sullivan
add unit test for gene query #528
35186fd
julie-sullivan added a commit that referenced this issue Feb 24, 2020
@julie-sullivan
string map instead of object map #528
306d6c5
julie-sullivan added a commit that referenced this issue Feb 24, 2020
@julie-sullivan
remove sort from gene info. doesn't make sense. add timeout and facet…
cc265c5 
… to queryoptions. add a temp toQueryoptions as that's what java commons lib needs. #528
julie-sullivan added a commit that referenced this issue Feb 25, 2020
@julie-sullivan
update parseQuery to parse genequery object. use text instead of Quer…
3b77e97 
…yParams because they may not always be the same. #528
julie-sullivan added a commit that referenced this issue Feb 25, 2020
@julie-sullivan
remove toMap, building the query manually as there are too many custo…
080ead7 
…m cases. #528
julie-sullivan added a commit that referenced this issue Feb 25, 2020
@julie-sullivan
check if param in map is in genequery object. throw exception if it's…
12b75a3 
… not recognised. use facet param to hold the groupby,distinct,aggregationstats fields. for /info loop though each ID and create and run each query -- in the REST class. #528
julie-sullivan added a commit that referenced this issue Mar 5, 2020
@julie-sullivan
fix xref search. remove test warning. implement count. fix REST respo…
6c5af9b 
…nses. rename method for clarity #528
julie-sullivan added a commit that referenced this issue Mar 5, 2020
@julie-sullivan
add validation for biotype in genequery #528
d3f21aa
julie-sullivan added a commit that referenced this issue Mar 5, 2020
@julie-sullivan
remove everything from /info except includes/excludes. leave the gene…
7a981c4 
…query for now until we decide what to do with queryoptions. #528
julie-sullivan added a commit that referenced this issue Mar 5, 2020
@julie-sullivan
disable querying TEMPORARILY on the command line to get things to com…
e970eb2 
…pile. TEMPORARILY add custom projection method, use the QueryUtils one in core instead. fix expression query. add cases for all query parameters. #528
julie-sullivan added a commit that referenced this issue Mar 6, 2020
@julie-sullivan
add protein and transcript queries. update gene query to extend trans…
3bfc8fd 
…cript. add order after sort always. #528
julie-sullivan added a commit that referenced this issue Mar 10, 2020
@julie-sullivan
add interfaces for common manager methods #528
d94df48
julie-sullivan added a commit that referenced this issue Mar 10, 2020
@julie-sullivan
add interfaces for common manager methods #528
18e0f6f
julie-sullivan added a commit that referenced this issue Mar 10, 2020
@julie-sullivan
add gene sequence end point. #528
6a7cd2c
julie-sullivan added a commit that referenced this issue Mar 11, 2020
@julie-sullivan
look in xrefs for genes, not gene value. gene value only has the HGNC…
bb19353 
… symbol, we want all gene identifiers #528
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