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Updated implementation
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- Updated implementation of fileObj value
- Review pipeline fully functional with tree view
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@shayanaijaz
shayanaijaz committed Oct 24, 2024
1 parent 81723ef commit 2742ce4
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Showing 19 changed files with 489 additions and 273 deletions.
6 changes: 6 additions & 0 deletions client/src/components/DataFiles/DataFilesProjectFileListing/DataFilesProjectFileListing.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,12 @@ const DataFilesProjectFileListing = ({ system, path }) => {
type: 'PROJECTS_GET_METADATA',
payload: system,
});

dispatch({
type: 'PROJECTS_GET_PUBLICATION_REQUESTS',
payload: system,
})

}, [system]);

useEffect(() => {
Expand Down
10 changes: 5 additions & 5 deletions ...drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ const ReviewProjectStructure = ({ projectTree }) => {

useEffect(() => {
if (projectTree && projectTree.length > 0) {
setExpandedNodes([projectTree[0].uuid]);
setExpandedNodes([projectTree[0].id]);
}
}, [projectTree]);

Expand Down Expand Up @@ -65,7 +65,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
const dataType = node.metadata.data_type;
// reconstruct editFile to mimic SelectedFile object
const editFile = {
id: node.uuid,
id: node.id,
uuid: node.uuid,
metadata: node.metadata,
name: node.metadata.name,
Expand Down Expand Up @@ -122,8 +122,8 @@ const ReviewProjectStructure = ({ projectTree }) => {
>
<div>
<TreeItem
key={node.uuid}
nodeId={node.uuid}
key={node.id}
nodeId={node.id}
label={
<div className={styles['node-name-div']}>
{node.label ?? node.name}
Expand All @@ -139,7 +139,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
}}
onLabelClick={() => handleNodeToggle}
>
{expandedNodes.includes(node.uuid) && node.id !== 'NODE_ROOT' && (
{expandedNodes.includes(node.id) && node.id !== 'NODE_ROOT' && (
<div className={styles['metadata-description-div']}>
{(canEdit || node.metadata.data_type === 'file') && (
<Button
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20 changes: 11 additions & 9 deletions client/src/components/_custom/drp/DataFilesProjectReview/DataFilesProjectReview.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -27,18 +27,20 @@ const DataFilesProjectReview = ({ system }) => {
const { metadata } = useSelector((state) => state.projects);

const fetchTree = useCallback(async () => {
if (projectId) {
try {
const response = await fetchUtil({
url: `api/${portalName.toLowerCase()}/tree`,
params: {
project_id: projectId,
},
});
setTree(response);
const response = await fetchUtil({
url: `api/${portalName.toLowerCase()}/tree`,
params: {
project_id: projectId,
},
});
setTree(response);
} catch (error) {
console.error('Error fetching tree data:', error);
setTree([]);
console.error('Error fetching tree data:', error);
setTree([]);
}
}
}, [portalName, projectId]);

useEffect(() => {
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35 changes: 35 additions & 0 deletions client/src/redux/reducers/projects.reducers.js
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,7 @@ export default function projects(state = initialState, action) {
return {
...state,
metadata: {
...state.metadata,
...action.payload,
loading: false,
error: null,
Expand Down Expand Up @@ -249,6 +250,40 @@ export default function projects(state = initialState, action) {
result: null,
},
};
case 'PROJECTS_GET_PUBLICATION_REQUESTS_STARTED':
return {
...state,
operation: {
name: 'getPublicationRequests',
loading: true,
error: null,
result: null,
},
};
case 'PROJECTS_GET_PUBLICATION_REQUESTS_SUCCESS':
return {
...state,
metadata: {
...state.metadata,
publication_requests: action.payload,
},
operation: {
name: 'getPublicationRequests',
loading: false,
error: null,
result: action.payload,
},
}
case 'PROJECTS_GET_PUBLICATION_REQUESTS_FAILED':
return {
...state,
operation: {
name: 'getPublicationRequests',
loading: false,
error: action.payload,
result: null,
},
};
default:
return state;
}
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27 changes: 27 additions & 0 deletions client/src/redux/sagas/projects.sagas.js
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Expand Up @@ -215,6 +215,32 @@ export function* createPublicationRequest(action) {
}
}

export async function fetchPublicationRequestsUtil(system) {
const result = await fetchUtil({
url: `/api/publications/publication-request/${system}`,
});
return result.response;
}

export function* getPublicationRequests(action) {

yield put({
type: 'PROJECTS_GET_PUBLICATION_REQUESTS_STARTED',
});
try {
const publicationRequests = yield call(fetchPublicationRequestsUtil, action.payload);
yield put({
type: 'PROJECTS_GET_PUBLICATION_REQUESTS_SUCCESS',
payload: publicationRequests,
});
} catch (error) {
yield put({
type: 'PROJECTS_GET_PUBLICATION_REQUESTS_FAILED',
payload: error,
});
}
}

export async function createEntityUtil(entityType, projectId, path, data) {
const result = await fetchUtil({
url: `/api/projects/${projectId}/entities/create`,
Expand Down Expand Up @@ -259,4 +285,5 @@ export function* watchProjects() {
yield takeLatest('PROJECTS_SET_MEMBER', setMember);
yield takeLatest('PROJECTS_SET_TITLE_DESCRIPTION', setTitleDescription);
yield takeLatest('PROJECTS_CREATE_PUBLICATION_REQUEST', createPublicationRequest);
yield takeLatest('PROJECTS_GET_PUBLICATION_REQUESTS', getPublicationRequests);
}
46 changes: 23 additions & 23 deletions server/portal/apps/_custom/drp/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,26 @@ def model_dump(self, *args, **kwargs):
return partial(super().model_dump, by_alias=True, exclude_none=True)(
*args, **kwargs
)

class DrpFileMetadata(DrpMetadataModel):
"""Model for DRP File Metadata"""

model_config = ConfigDict(
extra="forbid",
)

data_type: Literal['file']
name: Optional[str] = None
image_type: Optional[Literal[
'8_bit', '16_bit_signed', '16_bit_unsigned', '32_bit_signed', '32_bit_unsigned', '32_bit_real', '64_bit_real',
'24_bit_rgb', '24_bit_rgb_planar', '24_bit_bgr', '24_bit_integer', '32_bit_argb', '32_bit_abgr', '1_bit_bitmap',
]] = None
height: Optional[int] = None
width: Optional[int] = None
number_of_images: Optional[int] = None
offset_to_first_image: Optional[int] = None
gap_between_images: Optional[int] = None
byte_order: Optional[Literal['big_endian', 'little_endian']] = None

class FileObj(DrpMetadataModel):
"""Model for associated files"""
Expand All @@ -32,6 +52,7 @@ class FileObj(DrpMetadataModel):
length: Optional[int] = None
last_modified: Optional[str] = None
uuid: Optional[str] = None
value: Optional[DrpFileMetadata] = None

class PartialEntityWithFiles(DrpMetadataModel):
"""Model for representing an entity with associated files."""
Expand All @@ -40,7 +61,6 @@ class PartialEntityWithFiles(DrpMetadataModel):

# file_tags: list[FileTag] = []
file_objs: list[FileObj] = []

class DrpProjectRelatedDatasets(DrpMetadataModel):
"""Model for DRP Project Related Datasets"""

Expand Down Expand Up @@ -77,7 +97,6 @@ class DrpProjectRelatedPublications(DrpMetadataModel):
publication_description: Optional[str] = None
publication_link: Optional[str] = None


class DrpProjectMetadata(DrpMetadataModel):
"""Model for DRP Project Metadata"""

Expand All @@ -95,8 +114,9 @@ class DrpProjectMetadata(DrpMetadataModel):
related_software: list[DrpProjectRelatedSoftware] = []
related_publications: list[DrpProjectRelatedPublications] = []
publication_date: Optional[str] = None
authors: list[str] = []
authors: list[dict] = []
file_objs: list[FileObj] = []
is_review_project : Optional[bool] = None

class DrpDatasetMetadata(DrpMetadataModel):
"""Model for Base DRP Dataset Metadata"""
Expand Down Expand Up @@ -192,23 +212,3 @@ class DrpAnalysisDatasetMetadata(DrpDatasetMetadata):
external_uri: Optional[str] = None
sample: str
base_origin_data: Optional[str] = None

class DrpFileMetadata(DrpMetadataModel):
"""Model for DRP File Metadata"""

model_config = ConfigDict(
extra="forbid",
)

data_type: Literal['file']
name: Optional[str] = None
image_type: Optional[Literal[
'8_bit', '16_bit_signed', '16_bit_unsigned', '32_bit_signed', '32_bit_unsigned', '32_bit_real', '64_bit_real',
'24_bit_rgb', '24_bit_rgb_planar', '24_bit_bgr', '24_bit_integer', '32_bit_argb', '32_bit_abgr', '1_bit_bitmap',
]] = None
height: Optional[int] = None
width: Optional[int] = None
number_of_images: Optional[int] = None
offset_to_first_image: Optional[int] = None
gap_between_images: Optional[int] = None
byte_order: Optional[Literal['big_endian', 'little_endian']] = None
31 changes: 17 additions & 14 deletions server/portal/apps/_custom/drp/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from portal.apps.projects.models.project_metadata import ProjectMetadata
from portal.apps._custom.drp import constants
import networkx as nx
from portal.apps.projects.workspace_operations.project_meta_operations import get_ordered_value
class DigitalRocksSampleView(BaseApiView):

def get(self, request):
Expand Down Expand Up @@ -55,8 +56,6 @@ def _get_entity(uuid):

def get(self, request):

metadata_data_types = ['sample', 'origin_data', 'analysis_data', 'file']

project_id = request.GET.get('project_id')
full_project_id = f'{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{project_id}'

Expand All @@ -66,27 +65,31 @@ def get(self, request):

graph = nx.node_link_graph(graph_model.value)

for node in graph.nodes:
node_uuid = graph.nodes[node].get("uuid")
for node_id in graph.nodes:

entity = self._get_entity(node_uuid)
metadata = entity.ordered_value
node = graph.nodes[node_id]

file_objs = entity.value.get('fileObjs', [])
if node.get('value'):
metadata = get_ordered_value(node['name'], node['value'])
file_objs = node['value'].get('fileObjs', [])
else:
node_uuid = node.get("uuid")
entity = self._get_entity(node_uuid)
metadata = get_ordered_value(entity.name, entity.value)
file_objs = entity.value.get('fileObjs', [])

file_objs_dict = []

for file_obj in file_objs:
file_obj_entity = self._get_entity(file_obj.get('uuid'))
file_obj_metadata = file_obj_entity.ordered_value

file_objs_dict.append({
**file_obj,
'metadata': file_obj_metadata
})

graph.nodes[node]['metadata'] = metadata
graph.nodes[node]['fileObjs'] = file_objs_dict
'id': file_obj.get('uuid'),
'metadata': get_ordered_value(constants.FILE, file_obj.get('value'))
})

node['metadata'] = metadata
node['fileObjs'] = file_objs_dict

tree = nx.tree_data(graph, "NODE_ROOT")

Expand Down
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