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feat: remove RNAseq data handling and related components
1 parent 86a0fbb commit 3d85bf7

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10 files changed

+31
-97
lines changed

10 files changed

+31
-97
lines changed

‎src/backend/api/endpoints/curator_dashboard.py‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -127,7 +127,6 @@ def get_all_yes_no_data_types(self, paper_id):
127127
afp_newantibody_checked, afp_newantibody_details = self.get_class_author_sub_val("afp_antibody", paper_id)
128128
afp_siteaction_checked, afp_siteaction_details = self.get_class_author_sub_val("afp_siteaction", paper_id)
129129
afp_timeaction_checked, afp_timeaction_details = self.get_class_author_sub_val("afp_timeaction", paper_id)
130-
afp_rnaseq_checked, afp_rnaseq_details = self.get_class_author_sub_val("afp_rnaseq", paper_id)
131130
afp_chemphen_checked, afp_chemphen_details = self.get_class_author_sub_val("afp_chemphen", paper_id)
132131
afp_envpheno_checked, afp_envpheno_details = self.get_class_author_sub_val("afp_envpheno", paper_id)
133132
afp_catalyticact_checked, afp_catalyticact_details = self.get_class_author_sub_val("afp_catalyticact", paper_id)
@@ -140,7 +139,6 @@ def get_all_yes_no_data_types(self, paper_id):
140139
"afp_newantibody_checked": afp_newantibody_checked, "afp_newantibody_details": afp_newantibody_details,
141140
"afp_siteaction_checked": afp_siteaction_checked, "afp_siteaction_details": afp_siteaction_details,
142141
"afp_timeaction_checked": afp_timeaction_checked, "afp_timeaction_details": afp_timeaction_details,
143-
"afp_rnaseq_checked": afp_rnaseq_checked, "afp_rnaseq_details": afp_rnaseq_details,
144142
"afp_chemphen_checked": afp_chemphen_checked, "afp_chemphen_details": afp_chemphen_details,
145143
"afp_envpheno_checked": afp_envpheno_checked, "afp_envpheno_details": afp_envpheno_details,
146144
"afp_catalyticact_checked": afp_catalyticact_checked, "afp_catalyticact_details":
@@ -269,7 +267,6 @@ def on_post(self, req, resp, req_type):
269267
'"afp_newantibody_checked": "{}", "afp_newantibody_details": {}, ' \
270268
'"afp_siteaction_checked": "{}", "afp_siteaction_details": {}, ' \
271269
'"afp_timeaction_checked": "{}", "afp_timeaction_details": {}, ' \
272-
'"afp_rnaseq_checked": "{}", "afp_rnaseq_details": {}, ' \
273270
'"afp_chemphen_checked": "{}", "afp_chemphen_details": {}, ' \
274271
'"afp_envpheno_checked": "{}", "afp_envpheno_details": {}, ' \
275272
'"afp_humdis_checked": "{}", "afp_humdis_details": {}, ' \
@@ -279,7 +276,6 @@ def on_post(self, req, resp, req_type):
279276
other_yn["afp_newantibody_checked"], json.dumps(other_yn["afp_newantibody_details"]),
280277
other_yn["afp_siteaction_checked"], json.dumps(other_yn["afp_siteaction_details"]),
281278
other_yn["afp_timeaction_checked"], json.dumps(other_yn["afp_timeaction_details"]),
282-
other_yn["afp_rnaseq_checked"], json.dumps(other_yn["afp_rnaseq_details"]),
283279
other_yn["afp_chemphen_checked"], json.dumps(other_yn["afp_chemphen_details"]),
284280
other_yn["afp_envpheno_checked"], json.dumps(other_yn["afp_envpheno_details"]),
285281
other_yn["afp_humdis_checked"], json.dumps(other_yn["afp_humdis_details"]),

‎src/backend/api/endpoints/submission_form.py‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -181,8 +181,6 @@ def on_post(self, req, resp):
181181
self.db.afp.set_submitted_site_action(site_action=req.media["site_action"], paper_id=paper_id)
182182
if "time_action" in req.media:
183183
self.db.afp.set_submitted_time_action(time_action=req.media["time_action"], paper_id=paper_id)
184-
if "rnaseq" in req.media:
185-
self.db.afp.set_submitted_rnaseq(rnaseq=req.media["rnaseq"], paper_id=paper_id)
186184
if "additional_expr" in req.media:
187185
self.db.afp.set_submitted_additional_expr(additional_expr=req.media["additional_expr"],
188186
paper_id=paper_id)

‎src/frontend/curator_dashboard/src/pages/paper_lists/PapersFilters.js‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -144,8 +144,6 @@ const PapersFilters = ({papersPerPage, setNumPapersPerPageCallback}) => {
144144
onChange={() => dispatch(togglePaperListFilter("siteaction", "manual"))}/>
145145
<Form.Check checked={paperListFilters.manualFilters.has("timeaction")} type="checkbox" label="Time of action data"
146146
onChange={() => dispatch(togglePaperListFilter("timeaction", "manual"))}/>
147-
<Form.Check checked={paperListFilters.manualFilters.has("rnaseq")} type="checkbox" label="RNAseq data"
148-
onChange={() => dispatch(togglePaperListFilter("rnaseq", "manual"))}/>
149147
<Form.Check checked={paperListFilters.manualFilters.has("chemphen")} type="checkbox" label="Chemically induced phenotype"
150148
onChange={() => dispatch(togglePaperListFilter("chemphen", "manual"))}/>
151149
<Form.Check checked={paperListFilters.manualFilters.has("envpheno")} type="checkbox" label="Environmental induced phenotype"
@@ -193,8 +191,6 @@ const PapersFilters = ({papersPerPage, setNumPapersPerPageCallback}) => {
193191
onChange={() => dispatch(togglePaperListFilter("siteaction", "curation"))}/>
194192
<Form.Check checked={paperListFilters.curationFilters.has("timeaction")} type="checkbox" label="Time of action data"
195193
onChange={() => dispatch(togglePaperListFilter("timeaction", "curation"))}/>
196-
<Form.Check checked={paperListFilters.curationFilters.has("rnaseq")} type="checkbox" label="RNAseq data"
197-
onChange={() => dispatch(togglePaperListFilter("rnaseq", "curation"))}/>
198194
<Form.Check checked={paperListFilters.curationFilters.has("chemphen")} type="checkbox" label="Chemically induced phenotype"
199195
onChange={() => dispatch(togglePaperListFilter("chemphen", "curation"))}/>
200196
<Form.Check checked={paperListFilters.curationFilters.has("envpheno")} type="checkbox" label="Environmental induced phenotype"

‎src/frontend/curator_dashboard/src/pages/paper_viewer/OtherYesNoDataTypesTab.js‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -44,9 +44,6 @@ const OtherYesNoDataTypesTab = () => {
4444
<FlaggedInfoRow title="Time of action data" afpChecked={queryRes.data.data.afp_timeaction_checked}
4545
afpDetails={queryRes.data.data.afp_timeaction_details}
4646
/>
47-
<FlaggedInfoRow title="RNAseq data" afpChecked={queryRes.data.data.afp_rnaseq_checked}
48-
afpDetails={queryRes.data.data.afp_rnaseq_details}
49-
/>
5047
<FlaggedInfoRow title="Chemically induced phenotype" afpChecked={queryRes.data.data.afp_chemphen_checked}
5148
afpDetails={queryRes.data.data.afp_chemphen_details}
5249
/>

‎src/frontend/submission_form/src/components/SaveAllChangesButton.js‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -66,8 +66,7 @@ const SaveCurrentWidgetButton = () => {
6666
return (currentWidgetData.anatomicExpression.checked ||
6767
currentWidgetData.siteOfAction.checked ||
6868
currentWidgetData.timeOfAction.checked ||
69-
currentWidgetData.rnaseq.checked ||
70-
(currentWidgetData.additionalExpr && currentWidgetData.additionalExpr.trim() !== ''));
69+
currentWidgetData.additionalExpr.checked);
7170
case 5: // Interactions
7271
return (currentWidgetData.geneticInteractions.checked ||
7372
currentWidgetData.physicalInteractions.checked ||

‎src/frontend/submission_form/src/redux/actions/expressionActions.js‎

Lines changed: 6 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -4,9 +4,8 @@ export const SET_SITE_OF_ACTION = "SET_SITE_OF_ACTION";
44
export const TOGGLE_SITE_OF_ACTION = "TOGGLE_SITE_OF_ACTION";
55
export const SET_TIME_OF_ACTION = "SET_TIME_OF_ACTION";
66
export const TOGGLE_TIME_OF_ACTION = "TOGGLE_TIME_OF_ACTION";
7-
export const SET_RNASEQ = "SET_RNASEQ";
8-
export const TOGGLE_RNASEQ = "TOGGLE_RNASEQ";
97
export const SET_ADDITIONAL_EXPR = "SET_ADDITIONAL_EXPR";
8+
export const TOGGLE_ADDITIONAL_EXPR = "TOGGLE_ADDITIONAL_EXPR";
109
export const SET_IS_EXPRESSION_SAVED_TO_DB = "SET_IS_EXPRESSION_SAVED_TO_DB";
1110

1211

@@ -49,26 +48,20 @@ export const toggleTimeOfAction = () => ({
4948
payload: {}
5049
});
5150

52-
export const setRnaseq = (checked, details) => ({
53-
type: SET_RNASEQ,
51+
52+
export const setAdditionalExpr = (checked, details) => ({
53+
type: SET_ADDITIONAL_EXPR,
5454
payload: {
5555
checked: checked,
5656
details: details
5757
}
5858
});
5959

60-
export const toggleRnaseq = () => ({
61-
type: TOGGLE_RNASEQ,
60+
export const toggleAdditionalExpr = () => ({
61+
type: TOGGLE_ADDITIONAL_EXPR,
6262
payload: {}
6363
});
6464

65-
export const setAdditionalExpr = details => ({
66-
type: SET_ADDITIONAL_EXPR,
67-
payload: {
68-
details
69-
}
70-
});
71-
7265
export const setIsExpressionSavedToDB = () => ({
7366
type: SET_IS_EXPRESSION_SAVED_TO_DB,
7467
payload: {}

‎src/frontend/submission_form/src/redux/actions/paperActions.js‎

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,6 @@ import {
2828
setAdditionalExpr,
2929
setExpression,
3030
setIsExpressionSavedToDB,
31-
setRnaseq,
3231
setSiteOfAction,
3332
setTimeOfAction
3433
} from "./expressionActions";
@@ -135,12 +134,10 @@ export const fetchPaperData = (paper_id, paper_passwd) => {
135134
dispatch(setSiteOfAction(siteOfAction.isChecked(), siteOfAction.details()));
136135
let timeOfAction = getCheckbxOrSingleFieldFromWBAPIData(result.data.timeaction, undefined);
137136
dispatch(setTimeOfAction(timeOfAction.isChecked(), timeOfAction.details()));
138-
let rnaSeq = getCheckbxOrSingleFieldFromWBAPIData(result.data.rnaseq, result.data.rnaseq);
139-
dispatch(setRnaseq(rnaSeq.isChecked(), rnaSeq.details()));
140137
let additionalExpr = getCheckbxOrSingleFieldFromWBAPIData(result.data.additionalexpr, undefined);
141-
dispatch(setAdditionalExpr(additionalExpr.details()));
138+
dispatch(setAdditionalExpr(additionalExpr.isChecked(), additionalExpr.details()));
142139
if (expression.prevSaved() && siteOfAction.prevSaved() && timeOfAction.prevSaved() &&
143-
rnaSeq.prevSaved() && additionalExpr.prevSaved()) {
140+
additionalExpr.prevSaved()) {
144141
dispatch(setIsExpressionSavedToDB());
145142
}
146143

‎src/frontend/submission_form/src/redux/reducers/expressionReducer.js‎

Lines changed: 8 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -5,9 +5,9 @@ import {
55
TOGGLE_SITE_OF_ACTION,
66
SET_TIME_OF_ACTION,
77
TOGGLE_TIME_OF_ACTION,
8-
SET_RNASEQ,
9-
TOGGLE_RNASEQ,
10-
SET_ADDITIONAL_EXPR, SET_IS_EXPRESSION_SAVED_TO_DB
8+
SET_ADDITIONAL_EXPR,
9+
TOGGLE_ADDITIONAL_EXPR,
10+
SET_IS_EXPRESSION_SAVED_TO_DB
1111
} from "../actions/expressionActions";
1212

1313

@@ -24,11 +24,10 @@ const initialState = {
2424
checked: false,
2525
details: ''
2626
},
27-
rnaseq: {
27+
additionalExpr: {
2828
checked: false,
2929
details: ''
3030
},
31-
additionalExpr: "",
3231
isSavedToDB: false
3332
};
3433

@@ -40,7 +39,6 @@ export default function(state = initialState, action) {
4039
expression: action.payload,
4140
siteOfAction: state.siteOfAction,
4241
timeOfAction: state.timeOfAction,
43-
rnaseq: state.rnaseq,
4442
additionalExpr: state.additionalExpr,
4543
isSavedToDB: false
4644
};
@@ -51,7 +49,6 @@ export default function(state = initialState, action) {
5149
expression: {checked: !state.expression.checked, details: ''},
5250
siteOfAction: state.siteOfAction,
5351
timeOfAction: state.timeOfAction,
54-
rnaseq: state.rnaseq,
5552
additionalExpr: state.additionalExpr,
5653
isSavedToDB: false
5754
};
@@ -62,7 +59,6 @@ export default function(state = initialState, action) {
6259
expression: state.expression,
6360
siteOfAction: action.payload,
6461
timeOfAction: state.timeOfAction,
65-
rnaseq: state.rnaseq,
6662
additionalExpr: state.additionalExpr,
6763
isSavedToDB: false
6864
};
@@ -73,7 +69,6 @@ export default function(state = initialState, action) {
7369
expression: state.expression,
7470
siteOfAction: {checked: !state.siteOfAction.checked, details: ''},
7571
timeOfAction: state.timeOfAction,
76-
rnaseq: state.rnaseq,
7772
additionalExpr: state.additionalExpr,
7873
isSavedToDB: false
7974
};
@@ -84,7 +79,6 @@ export default function(state = initialState, action) {
8479
expression: state.expression,
8580
siteOfAction: state.siteOfAction,
8681
timeOfAction: action.payload,
87-
rnaseq: state.rnaseq,
8882
additionalExpr: state.additionalExpr,
8983
isSavedToDB: false
9084
};
@@ -95,41 +89,27 @@ export default function(state = initialState, action) {
9589
expression: state.expression,
9690
siteOfAction: state.siteOfAction,
9791
timeOfAction: {checked: !state.timeOfAction.checked, details: ''},
98-
rnaseq: state.rnaseq,
9992
additionalExpr: state.additionalExpr,
10093
isSavedToDB: false
10194
};
10295
}
103-
case SET_RNASEQ: {
104-
return {
105-
...state,
106-
expression: state.expression,
107-
siteOfAction: state.siteOfAction,
108-
timeOfAction: state.timeOfAction,
109-
rnaseq: action.payload,
110-
additionalExpr: state.additionalExpr,
111-
isSavedToDB: false
112-
};
113-
}
114-
case TOGGLE_RNASEQ: {
96+
case SET_ADDITIONAL_EXPR: {
11597
return {
11698
...state,
11799
expression: state.expression,
118100
siteOfAction: state.siteOfAction,
119101
timeOfAction: state.timeOfAction,
120-
rnaseq: {checked: !state.rnaseq.checked, details: ''},
121-
additionalExpr: state.additionalExpr,
102+
additionalExpr: action.payload,
122103
isSavedToDB: false
123104
};
124105
}
125-
case SET_ADDITIONAL_EXPR: {
106+
case TOGGLE_ADDITIONAL_EXPR: {
126107
return {
127108
...state,
128109
expression: state.expression,
129110
siteOfAction: state.siteOfAction,
130111
timeOfAction: state.timeOfAction,
131-
rnaseq: state.rnaseq,
132-
additionalExpr: action.payload.details,
112+
additionalExpr: {checked: !state.additionalExpr.checked, details: ''},
133113
isSavedToDB: false
134114
};
135115
}
@@ -139,7 +119,6 @@ export default function(state = initialState, action) {
139119
expression: state.expression,
140120
siteOfAction: state.siteOfAction,
141121
timeOfAction: state.timeOfAction,
142-
rnaseq: state.rnaseq,
143122
additionalExpr: state.additionalExpr,
144123
isSavedToDB: true
145124
};

‎src/frontend/submission_form/src/redux/selectors/expressionSelectors.js‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,6 @@ export const getTimeOfAction = store => getExpressionState(store) ? getExpressio
88

99
export const getRnaseq = store => getExpressionState(store) ? getExpressionState(store).rnaseq : {checked: false, details: ''};
1010

11-
export const getAdditionalExpr = store => getExpressionState(store) ? getExpressionState(store).additionalExpr : '';
11+
export const getAdditionalExpr = store => getExpressionState(store) ? getExpressionState(store).additionalExpr : {checked: false, details: ''};
1212

1313
export const isExpressionSavedToDB = store => getExpressionState(store) ? getExpressionState(store).isSavedToDB : false;

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