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initial plugin scaffolding script might be useful now while we expand it... #3

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293045f
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
boycer Oct 2, 2013
c22679e
delete new plugin folders
Oct 3, 2013
fc0b25b
delete irrelevant files
Oct 3, 2013
0370a8a
delete irrelevant files
Oct 3, 2013
fc0d9ea
cleclean up layout of form, redesign card and tile
Oct 11, 2013
8bbe28a
add class diagram into Design forlder for editing Wiki
ningyifan Nov 13, 2013
b92face
refectoring on MSPLsAnnotation by creating a new Interface
ningyifan Nov 14, 2013
3eba902
add two images for editing wiki spls model
ningyifan Nov 15, 2013
4b7fa08
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
boycer Nov 15, 2013
72a1de8
added an annotated image to the design folder
boycer Nov 15, 2013
579d202
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
ningyifan Nov 16, 2013
7269b0c
add dailymed static pages and plugin project
ningyifan Nov 22, 2013
d26d1aa
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
ningyifan Nov 22, 2013
1c931cd
add program at annotation.spls.util for load annotation into persiste…
ningyifan Dec 23, 2013
1d157ca
removing unecessary files from the test file repository
rkboyce Dec 31, 2013
b94eda3
removing some other files that are not useful to the project or locat…
rkboyce Dec 31, 2013
f77e666
moved the test SPL pages for warfarin and clopidogrel
rkboyce Dec 31, 2013
23200d3
adjusted the oracle code to use only the two test HTML pages for now
rkboyce Dec 31, 2013
e1f5d9f
Revert 1d157ca..23200d3
Jan 10, 2014
4f5fcaf
Revert 1c931cd..e1f5d9f
Jan 10, 2014
89be62e
Revert e1f5d9f..4f5fcaf
Jan 10, 2014
6386cbe
Revert 1c931cd..89be62e
Jan 10, 2014
63ca8af
Revert 23200d3..6386cbe
Jan 11, 2014
4360fea
ce
Jan 16, 2014
49784bc
fixed bugs on SPLS ui.form ui.card and ui.tile
Jan 22, 2014
eeb4e99
minor change to git-helps
rkboyce Jan 22, 2014
5db4681
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Jan 22, 2014
c4ee8d2
added a local library path that will hopefully not screw up the other…
rkboyce Jan 22, 2014
260b6c8
fixed bugs in spls ui.card and ui.tile
Jan 22, 2014
b0a932d
Merge branch 'master' of http://github.com/rkboyce/DomeoClient
Jan 22, 2014
5ea7c6d
added biomarkers and created a new text area for medical conditions
rkboyce Jan 23, 2014
351540e
for real...added biomarkers and created a new text area for medical c…
rkboyce Jan 23, 2014
3d1272f
add radio buton by value none, fix bug on form persistence
Jan 24, 2014
20bb77f
add rest of none value of radio button, add drug of interest, modifie…
Jan 28, 2014
b9920ec
minor cleanup on the SPL pharmgx UI
rkboyce Jan 29, 2014
842c897
fixed conflicts with the previous upstream merge
rkboyce Jan 31, 2014
7ce213c
UNTESTED: added in the code for 'unmarshalling' SPL annotations
rkboyce Jan 31, 2014
ee9f5a2
temporary commenting out of code in the unmarshaller for testing purp…
rkboyce Jan 31, 2014
f50f155
improved the layout so that items are not cut-off. Unfortunately, mes…
rkboyce Feb 1, 2014
fecb764
improved the layout further and fixed persistence issue - the GWT XML…
rkboyce Feb 1, 2014
9c6f166
created some test code for debugging the deserialization issues
rkboyce Feb 1, 2014
95b2303
continued debugging of deserialization
rkboyce Feb 1, 2014
40a3008
fix bug on TILE and delete unnecessary package spls/util
Feb 2, 2014
2a90648
delete unnecessary package plugins/annotation/spls/util
Feb 2, 2014
bbcabd7
implemented suggestions from Paulo to address demarshalling issue
rkboyce Feb 8, 2014
efd9a4b
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Feb 8, 2014
f07a97c
merging this rkboyce fork with the parent
rkboyce Feb 8, 2014
4b52e9e
abbreviate label of tile, identifies creator for card
Feb 10, 2014
2a1454c
expand card perfectly
Feb 11, 2014
e47923e
removing the logging from a plugin where it is not needed
rkboyce Feb 11, 2014
4b47cc4
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Feb 11, 2014
fb30268
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Feb 11, 2014
7422c7b
rearranged tile and relocated card popup position
Feb 11, 2014
635e643
progress on understanding demarshalling but no substantial changes
rkboyce Feb 13, 2014
f64ef3b
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Feb 13, 2014
e7e7809
change style for labels in tile
Feb 13, 2014
e0d6dc8
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Feb 13, 2014
a7dae88
first working complete retrieval of a custom body element from the da…
rkboyce Feb 14, 2014
548af8f
refactored the JsonSPLsAnnotationSerializer FSPLsForm and USPLJsonUnm…
rkboyce Feb 15, 2014
e443ca4
revised the marshalling and unmarshalling code to handle multiple sem…
rkboyce Feb 15, 2014
2b57fc9
added drug selection recommendation to the marshall and unmarshaller
rkboyce Feb 18, 2014
b6b6a90
test loading annotation by import for all of labels
Feb 19, 2014
97fe514
completed showing all of labels by test of import existing annotation
Feb 20, 2014
702f632
modifies textarea other variant and other test in FORM and CARD
Feb 21, 2014
4ef81fc
add a activity diagram for domeo wiki
Feb 27, 2014
b086c70
preselect no mention in form, shutdown useless plugin, changes for co…
Mar 2, 2014
fd036d7
add dia project in design, add rest of spls in SPL-annotation, modifi…
Mar 3, 2014
32d9cb7
add product label selection, rest style of dropdown listbox and make …
Mar 4, 2014
5e1ef9d
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Mar 4, 2014
7113129
persistence product label selection
Mar 4, 2014
8f535f0
test code for the new labeling dropdown and data element
Mar 5, 2014
495fabf
change uri for drug and biomarker
Mar 7, 2014
6f7625c
extract prefix to interface, move uri mapping list to model, fix bug …
Mar 7, 2014
13194a0
fix the bug trigger by wrong-spelling drug name abacavir
Mar 12, 2014
b1f39a4
enabled the Micropublication plugin
rkboyce Apr 8, 2014
36ea127
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Apr 8, 2014
69330fc
add HGNCGene field in form tile and card, besides, test marshalling a…
Apr 10, 2014
4f351ff
test function for new json string with new field HGNCGene
Apr 10, 2014
a3fb2bb
add new plugin PDDI, redesign form
Apr 10, 2014
7c0a42c
reorganized gorm, change fields name, add required fields validation
Apr 10, 2014
f57fb43
revised PDDI plugin ui
Apr 11, 2014
b258566
reorganize SPLs form
Apr 11, 2014
45fd883
enabling the qualifers plugin
rkboyce Apr 11, 2014
3cbac83
plugin name changes for ddi and fields name changes for spl
Apr 11, 2014
64e4782
merge domeoclient to upstream
Apr 14, 2014
3560f92
added the CMAP file for the pharmgx model
boycer Apr 14, 2014
8a646bd
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
boycer Apr 14, 2014
362a960
initial start on a test 'connector' using python
rkboyce Apr 14, 2014
fc94eca
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Apr 14, 2014
626dbdf
add revised PGx model in design folder
Apr 14, 2014
08f15aa
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Apr 14, 2014
2d55b31
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Apr 14, 2014
1878ec8
changed the PGx Model design file
boycer Apr 14, 2014
1ea1960
add idendifier of sio into PGx model
Apr 14, 2014
ba7d193
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Apr 14, 2014
87faac3
revised PGx model in design folder
Apr 15, 2014
7042a8c
widening drop down list box and fix index bug of HGNCGeneSymbol bug
Apr 18, 2014
5ef708c
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Apr 18, 2014
aefd01c
create model for DDI, coding in DDI form
Apr 23, 2014
397ca64
build PDDI plugin, almostly finish marshaling and unmarshaling
Apr 25, 2014
070799b
add search function for spl to search by all value of fields, also do…
Apr 29, 2014
1e9d66b
coding to marshals ddi annotation
Apr 29, 2014
c39c3e2
revised json serializer in DDI plugin
May 1, 2014
14e87ee
finished DDI marshalling
May 6, 2014
55858b8
finished plugin DDI unmarshalling, tested in facade
May 6, 2014
01e35db
clean the code, remove useless <import> statements
May 6, 2014
a37524f
finished unmarshalling for ddi plugin, tested in complied mode yet
May 7, 2014
ed2a614
add clinical trial, reformat drug label section, extends timeout period
May 19, 2014
787ac9c
for DDI, add select all, rename label and style for card, add list bo…
May 28, 2014
d864533
fix the bug wthat add null into drugs's list box, auto select role
May 28, 2014
db2dea8
test DDI plugin, change the code that add highlighted drug name into …
May 29, 2014
17abac4
set profile for spl and ddi plugin user, highlight current drug menti…
Jun 9, 2014
96a4396
highlight two drug mentions in form
Jun 9, 2014
d0d07e4
for spls plugin, update LOINC code selections in product lable section
Jun 10, 2014
56661c3
for DDI plugin, validate required fields, fix bug triggers in serailizer
Jun 12, 2014
00fffec
for DDI plugin, fix bug triggered by sets conflicts
Jun 12, 2014
ddb9917
For DDI, add validations for statement and modality
Jun 13, 2014
de0f98e
For DDI plugin, preselect drug type
Jun 16, 2014
5b9d840
first working script that pulls back annotations from the elastic sea…
rkboyce Jun 20, 2014
874caa5
now the body resources are converted to RDF
rkboyce Jun 20, 2014
f1ca8f1
now writing out a file with the data and preparing to test in Virtuoso
rkboyce Jun 20, 2014
0edf87f
added a name to conjuntive graph. I think that the script works but t…
rkboyce Jun 20, 2014
9857613
fix bugs in highlight durgs in sentences span, eable edit sentence sp…
Jun 20, 2014
a511d68
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Jun 20, 2014
e828bc3
a new script that copies the general convert script but executes a qu…
rkboyce Jun 20, 2014
30753c9
set query results to have a very large limit so that we would not tru…
rkboyce Jun 20, 2014
308d67a
added a namespace to the script that pulls annotations from Elasticse…
boycer Jun 23, 2014
ab2f3f9
trivial changes
rkboyce Jun 23, 2014
208d1a4
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Jun 23, 2014
11562c4
stage chengs in Design/python-SPL-connector/convertJsonLDToRDF.py
Jun 23, 2014
6eba04e
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Jun 23, 2014
be39843
modifications in DDI marshalling process
Jun 23, 2014
3a25c86
merging changes with Yifan
rkboyce Jun 24, 2014
7de3c08
fix search component for spl plugin
Jun 24, 2014
74a1cfd
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Jun 24, 2014
eea7064
added ability to pass parameters to the JSON-LD conversion script
rkboyce Jun 25, 2014
27a1034
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
rkboyce Jun 25, 2014
e195c7c
trivial change to store correct query strings for different agents
rkboyce Jun 25, 2014
c5a3f75
fix the drug mentions highlight bug in DDI plugin, comment out some d…
Jun 26, 2014
419bd69
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Jun 26, 2014
bba4912
trivials
Jul 3, 2014
e89c20c
updated to Yifan's version of the code
rkboyce Jul 3, 2014
2ac36b9
porting the DDI model to a corrected version
rkboyce Jul 3, 2014
cf7d065
for DDI plugin, make a test sample in facade to test unmarshaller and…
Jul 3, 2014
da7f79b
add good query for original DDI
Jul 3, 2014
4d62c00
replce empty nodes, works for changed DDI sets
Jul 3, 2014
6d04961
replace one more set of empty nodes, works for changed DDI sets
Jul 3, 2014
7664f96
revise sparql queries in txt and made modifications to replace all em…
Jul 3, 2014
69b9d04
updated documentation of the query script
rkboyce Jul 4, 2014
f4a459a
added another uuid for a user to the conversion script
Jul 4, 2014
bec53d8
removed an unused bit of code
rkboyce Jul 4, 2014
7261459
updated the documentation for the query script and edited the queries…
rkboyce Jul 4, 2014
ab91d67
remove comment from DDI form
Jul 8, 2014
90c1368
for ddi plugin, fixed bug that triggers by single character highlight
Jul 8, 2014
77fad0a
add sparql query for pharmgx plugin
Jul 9, 2014
e9951b6
add parameter elastico-collection for two convert scripts
Jul 9, 2014
4ba897f
revise script to allow to get rdf only for last version of annotation…
Jul 11, 2014
74c1846
add pharmgx data from icode-01, update queries in txt
Jul 11, 2014
b6d9af6
add sparql query for pharmacogenomics data, trivial changes for SPL form
Jul 15, 2014
c86fed6
add DDI study data
Jul 21, 2014
01717c0
add new product labels in folder SPL-Annotations-2
Jul 21, 2014
8d20e81
revise query for pharmgx data to add url that can jump back to sets i…
Jul 22, 2014
fde788d
add csv format of DDI sets - nonexpert1
Aug 12, 2014
87f021b
optimize pharmgx query
Aug 22, 2014
7c92f55
add DDI sets for nonexpert3 at 08282014
Sep 1, 2014
e117ae8
add DDI study sets for all annotators at 09022014
Sep 3, 2014
feee57d
update pharmgx data from 5 annotators
Sep 12, 2014
b29d0a7
edit query to get timestamp for DDI sets
Sep 22, 2014
5f42278
add query to get ddi sets in order of last saved time
Sep 29, 2014
5ba2f37
add new queries used for the reformatted pgx data graph
Oct 6, 2014
48eea57
revise reformatted pgx consensus data to OA standard
Oct 6, 2014
cf5524c
revised sparql queries to work with latest version of rebuilded conse…
Oct 7, 2014
edf43cd
revise parse script to pull annotations from all pharmacists
Nov 18, 2014
a20804c
add csv format spls annotations from all pharmacists
Nov 18, 2014
7f01609
add section labels for plugin DDI
Nov 24, 2014
862341f
add new field 'is drug indication' for test recommendation
Dec 4, 2014
080bb69
add query for creating csv that feeds IAA script
Dec 9, 2014
66f3fcf
remove old datasets
Feb 5, 2015
41b9343
clean DDIs example queries
Feb 5, 2015
be2d0aa
add post processed pgx annotations that comes from domeo dump out
Mar 4, 2015
75cabfd
rename graph name for pgx queries
Mar 4, 2015
023c1f5
clean old DDIs sets
Mar 11, 2015
5e774b7
revise ddis query to filter out preload NLPs
Mar 12, 2015
81fa64c
add query that pulls all annotations from specified label and annotator
Mar 19, 2015
8f3f8fb
add ddi new plugin mockup
Apr 15, 2015
c8a92bd
add mockup for pk ddi plugin
Apr 16, 2015
d3e0ece
update domeo new plugin mockups
Apr 21, 2015
eb2a4a1
finished UI design on DDI plugin (add increase Auc)
Apr 30, 2015
cea0071
refactors pddi plugin, increase Auc usecase
May 5, 2015
7ed5384
add script parse ddi annotation from elastico
May 7, 2015
bb7c795
fix annotation persistence bug on ddi plugin (drug-drug-interaction a…
May 13, 2015
644ea2b
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
May 13, 2015
1a7a812
add confirmation box for switch assertion type, ui changes
May 15, 2015
5537130
trivial changes
May 15, 2015
b0c0bef
ui changes on DDI form
May 21, 2015
a55fd31
add new query and annotation parse program for new ddi plugin
May 22, 2015
0992369
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
May 22, 2015
5f0a961
add drug group to type, rename plugin
May 27, 2015
5b42b73
extend annotation retrieve timeout limit from 20 secs to 40 secs, han…
Jun 2, 2015
8d560e5
clean eclipse hidden files
Jun 3, 2015
0b67fe9
add comment textarea to pk_ddi
Jun 12, 2015
c499871
clean folder
Jun 15, 2015
01a065b
add PK DDI sets, revise sparql query
Jun 30, 2015
b85f4aa
put domeo.html back
Jul 1, 2015
475fb7d
add new types of assertion, rename increase auc, add dosing regimens
Jul 1, 2015
1aaeb5c
add cleaned dataset
Jul 1, 2015
c9238db
revert war folder to recovery htmls
Jul 1, 2015
49ad517
Merge branch 'master' of https://github.com/rkboyce/DomeoClient
Jul 1, 2015
79b1dbe
add gitignore
Jul 2, 2015
697bdb7
untrack eclipse hidden files
Jul 2, 2015
75b04fd
redesign pk ddi form for dose
Jul 2, 2015
d1026dd
add pgx consensus annotation set for pgx prototype query purpose
Jul 6, 2015
6f18a85
add pgx annotation in csv
Jul 7, 2015
47dcb1c
fix hidden file classpath to libs
Jul 20, 2015
5353959
change DDI model, finish marshalling & unmarshalling of PK_DDI plugin
Jul 23, 2015
af19cd6
redesign DDI form to add dosing duration, auc direction, and cl fields
Aug 11, 2015
515aa0b
add pk-ddi cmap model to design, finish marshalling and unmarshalling…
Aug 12, 2015
b9ca464
fix new line character escapse for wins ex.\r \t - testing
Aug 17, 2015
e3c61b2
handle win new line character \r\n - testing
Aug 17, 2015
85fa8ec
fix win new line character \r\n - testing
Aug 17, 2015
2a7899d
replace \r \n \t to whitespace to handle win's newline character
Aug 17, 2015
fef270a
revise cmax and t12 in DDI form, add formulation for dose
Aug 19, 2015
6270b4e
remove replace <> when annotate text
Aug 19, 2015
73a121e
add duration days in pk_ddi form
Aug 27, 2015
68068e8
replace tablet to Oral
Aug 27, 2015
9817d3a
add pkddi retrieved annotation set for 10 out of 67 labels
Sep 16, 2015
bc61cf1
add katrina's annotation set on 10 of 67 pkddi labels
Sep 16, 2015
2c49e32
add cleaned pkddi sets for labels 10 out of 67
Sep 17, 2015
7abdc33
add annotation retrieve info to log to Domeo.log for debug purpose
Sep 22, 2015
f6ff0a9
disable delete button on card and tile
Oct 6, 2015
b0813c3
fix the bug that dosuage role switched
Oct 6, 2015
a8d177f
debug clinical trial - drug dosuage
Oct 8, 2015
4d7fa6e
add test set
Oct 14, 2015
9fd76b8
trivial
Oct 14, 2015
853c796
add debug message in ddiform-editor
Oct 19, 2015
f54ac5b
trivial
Oct 19, 2015
2d0465f
debug experiment
Oct 19, 2015
da4cd09
add query to get pkddi sets for preloading purpose
Oct 21, 2015
79c7952
add annotation preload program
Oct 26, 2015
d394c6e
rename python connector to export tool
Oct 26, 2015
6d8b366
clean repository
Oct 26, 2015
4e2ddcb
fix the bug that whitespace append on url
Oct 26, 2015
7793e71
reorganize dailymed label parsing program
Oct 26, 2015
f092369
ignore .class
Oct 26, 2015
39daeee
edit README, add pkddi sets in csv
Oct 26, 2015
63e2ee5
add all NER sets
Oct 26, 2015
94d1ae4
trivial
Oct 27, 2015
f445365
add cmin to pkddi plugin
Oct 29, 2015
0677416
move domeo tools out to repostitory domeo-tools
Nov 19, 2015
f247733
add test label for dev mode
Nov 19, 2015
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Binary file added .DS_Store
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9 changes: 0 additions & 9 deletions .classpath

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5 changes: 5 additions & 0 deletions .gitignore
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<!DOCTYPE html>

<html lang="en">

<head>

<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<meta charset="utf-8">

</head>

<body><br><br><p><br><br>In a placebo-controlled trial in normal volunteers, the administration of two doses of sertraline did not significantly alter steady-state lithium levels or the renal clearance of lithium.<br></p><br><br></body>

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<!DOCTYPE html>

<html lang="en">

<head>

<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<meta charset="utf-8">

</head>

<body><br><br><p><br><br>In three separate in vivo interaction studies, sertraline was co-administered with cytochrome P450 3A4 substrates, terfenadine, carbamazepine, or cisapride under steady-state conditions. The results of these studies indicated that sertraline did not increase plasma concentrations of terfenadine, carbamazepine, or cisapride. These data indicate that sertraline’s extent of inhibition of P450 3A4 activity is not likely to be of clinical significance. Results of the interaction study with cisapride indicate that sertraline 200 mg (q.d.) induces the metabolism of cisapride (cisapride AUC and Cmax were reduced by about 35%).<br></p><br><br></body>

</html>

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test test
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# Module domeo
# RPC service class, partial path of RPC policy file
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