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Port Patch version 1.4.0.1
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@juanfeSanahuja
juanfeSanahuja committed Jan 23, 2023
2 parents d71f95b + a98cc7b commit 3c06f5a
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4 changes: 0 additions & 4 deletions README.md
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Expand Up @@ -171,11 +171,7 @@ Remember that **_develop_** branch dependencies are not ensured to be deployed a
├── conf
├── libs
├── LICENSE
<<<<<<< HEAD
├── opencga-2.0.0-rc3.war
=======
├── opencga-2.0.0.war
>>>>>>> release-2.0.0
├── README.md
├── misc
└── test
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243 changes: 3 additions & 240 deletions docs/data-models/clinicalanalysis.md
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Expand Up @@ -36,15 +36,7 @@ ClinicalAnalysis data model hosts information about any analysis.
## Data Model

### ClinicalAnalysis
<<<<<<< HEAD
<<<<<<< HEAD
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysis.java).
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysis.java).
>>>>>>> release-2.2.x
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysis.java).
>>>>>>> release-2.2.x

| Field | Description |
| :--- | :--- |
Expand Down Expand Up @@ -77,120 +69,9 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15
| **attributes**<br>*Map<String,Object>* <br> | <p>You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.</p> |
| **status**<br>*Status* <br> | <p>Object status.</p> |

<<<<<<< HEAD
<<<<<<< HEAD
### Panel
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).

| Field | Description |
| :--- | :--- |
| **uuid**<br>*String* <br> | <p>Unique 32-character identifier assigned automatically by OpenCGA.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |
| **version**<br>*int* <br> | <p>OpenCGA version of this panel, this is incremented when the panel is updated.</p> |
| **~~author~~**<br>*String* <br><br>_Deprecated_ | <p>Author of the panel.</p> |
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/clinicalanalysis#status)* <br> | <p>Panel status can have the values READY or DELETED.</p> |
| **internal**<br>*[PanelInternal](https://docs.opencga.opencb.org/data-models/clinicalanalysis#panelinternal)* <br><br>_since_: 2.3.0 | <p>Internal field to manage the object.</p> |
| **studyUid**<br>*long* <br> | <p>Panel reference to study.</p> |
| **uid**<br>*long* <br> | <p>Panel reference to study.</p> |

### ClinicalAnalysisInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisInternal.java).

| Field | Description |
| :--- | :--- |
| **status**<br>*[InternalStatus](https://docs.opencga.opencb.org/data-models/clinicalanalysis#internalstatus)* <br> | <p>Status of the internal object.</p> |
| **registrationDate**<br>*String* <br> | <p>Registration date of the internal object.</p> |
| **lastModified**<br>*String* <br> | <p>Date of the last modification of the internal object.</p> |

### ClinicalAudit
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java).
=======
### ClinicalAnalyst
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java).
>>>>>>> release-2.2.x
| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Id to identify the object</p> |
| **name**<br>*String* <br> | <p>Object name</p> |
| **email**<br>*String* <br> | <p>Email of the analyst</p> |
| **assignedBy**<br>*String* <br> | <p>Assigned by field</p> |
| **date**<br>*String* <br> | <p>Date of the clinical analyst</p> |

<<<<<<< HEAD
### ClinicalConsentAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java).

| Field | Description |
| :--- | :--- |
| **consents**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalconsentparam"><em>ClinicalConsentParam</em></a>>* <br> | <p>List of ClinicalConsentParam.</p> |
| **date**<br>*String* <br> | <p>Date of the ClinicalConsentAnnotation.</p> |

### ClinicalPriorityAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java).

| Field | Description |
| :--- | :--- |
=======
### ClinicalPriorityAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java).

| Field | Description |
| :--- | :--- |
>>>>>>> release-2.2.x
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **rank**<br>*int* <br> | <p>ClinicalPriorityAnnotation rank.</p> |
| **date**<br>*String* <br> | <p>ClinicalPriorityAnnotation date.</p> |
<<<<<<< HEAD

### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).
=======

### ClinicalConsentAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java).

| Field | Description |
| :--- | :--- |
| **consents**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalconsentparam"><em>ClinicalConsentParam</em></a>>* <br> | <p>List of ClinicalConsentParam.</p> |
| **date**<br>*String* <br> | <p>Date of the ClinicalConsentAnnotation.</p> |

### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).
>>>>>>> release-2.2.x
| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **date**<br>*String* <br> | <p>FlagAnnotation date.</p> |

<<<<<<< HEAD
### Interpretation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/Interpretation.java).

| Field | Description |
| :--- | :--- |
| **studyUid**<br>*long* <br> | <p>Study identifier.</p> |
| **uid**<br>*long* <br> | <p>Interpretation identifier.</p> |
| **panels**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#panel"><em>Panel</em></a>>* <br> | <p>Interpretation panel list.</p> |
| **internal**<br>*[InterpretationInternal](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationinternal)* <br> | <p>Internal field to manage the object.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |
=======
=======
>>>>>>> release-2.2.x
### ClinicalAnalysisQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java).

| Field | Description |
| :--- | :--- |
| **summary**<br>*QualityControlSummary* <br> | <p>ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.</p> |
| **comments**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalcomment"><em>ClinicalComment</em></a>>* <br> | <p>List of ClinicalAnalysisQualityControl comments.</p> |
| **comments**<br>*List<<em>String</em>>* <br> | <p>List of ClinicalAnalysisQualityControl files.</p> |
>>>>>>> release-2.2.x
<<<<<<< HEAD
### ClinicalComment
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java).

Expand All @@ -201,7 +82,6 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop
| **tags**<br>*List<<em>String</em>>* <br> | <p>List of tags for the clinical comment</p> |
| **date**<br>*String* <br> | <p>Date of the clinical comment</p> |

<<<<<<< HEAD
### ClinicalAnalysisQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java).

Expand All @@ -223,30 +103,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52
| **signedBy**<br>*String* <br> | <p>Indicates who has signed the report.</p> |
| **signature**<br>*String* <br> | <p>Report signature.</p> |
| **date**<br>*String* <br> | <p>Report date.</p> |
=======
=======
>>>>>>> release-2.2.x
### Interpretation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/Interpretation.java).

| Field | Description |
| :--- | :--- |
| **studyUid**<br>*long* <br> | <p>Study identifier.</p> |
| **uid**<br>*long* <br> | <p>Interpretation identifier.</p> |
| **panels**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#panel"><em>Panel</em></a>>* <br> | <p>Interpretation panel list.</p> |
| **internal**<br>*[InterpretationInternal](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationinternal)* <br> | <p>Internal field for manage the object.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |

### ClinicalAudit
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java).

| Field | Description |
| :--- | :--- |
| **author**<br>*String* <br> | <p>Audit author</p> |
| **action**<br>*Action* <br> | <p>Enum action that can have the values CREATE_CLINICAL_ANALYSIS, CREATE_INTERPRETATION, UPDATE_CLINICAL_ANALYSIS, DELETE_CLINICAL_ANALYSIS, UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and DELETE_INTERPRETATION</p> |
| **message**<br>*String* <br> | <p>Audit message</p> |
| **date**<br>*String* <br> | <p>Date of the audit</p> |
>>>>>>> release-2.2.x

### ClinicalAnalysisInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisInternal.java).
Expand All @@ -270,17 +126,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15
| **signature**<br>*String* <br> | <p>Report signature.</p> |
| **date**<br>*String* <br> | <p>Report date.</p> |

<<<<<<< HEAD
### ClinicalAnalyst
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java).
=======
### Panel
<<<<<<< HEAD
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).
>>>>>>> release-2.2.x
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).
>>>>>>> release-2.2.x

| Field | Description |
| :--- | :--- |
Expand All @@ -290,7 +137,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15
| **assignedBy**<br>*String* <br> | <p>Assigned by field</p> |
| **date**<br>*String* <br> | <p>Date of the clinical analyst</p> |

<<<<<<< HEAD
### ClinicalConsentParam
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentParam.java).

Expand All @@ -300,8 +146,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52
| **name**<br>*String* <br> | <p>Name of the .</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **value**<br>*Value* <br> | <p>Value of the param that can have the values YES, NO and UNKNOWN.</p> |

<<<<<<< HEAD
### Status
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java).

Expand All @@ -311,90 +155,16 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52

| Field | Description |
| :--- | :--- |
=======
=======
### ClinicalPriorityAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **rank**<br>*int* <br> | <p>ClinicalPriorityAnnotation rank.</p> |
| **date**<br>*String* <br> | <p>ClinicalPriorityAnnotation date.</p> |

### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **date**<br>*String* <br> | <p>FlagAnnotation date.</p> |

### ClinicalComment
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java).

| Field | Description |
| :--- | :--- |
| **author**<br>*String* <br> | <p>Clinical comment author</p> |
| **message**<br>*String* <br> | <p>Clinical comment message</p> |
| **tags**<br>*List<<em>String</em>>* <br> | <p>List of tags for the clinical comment</p> |
| **date**<br>*String* <br> | <p>Date of the clinical comment</p> |

>>>>>>> release-2.2.x
### Disorder
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Disorder.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Id to identify the object</p> |
| **name**<br>*String* <br> | <p>Object name</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **source**<br>*String* <br> | <p>Ontology source</p> |
| **url**<br>*String* <br> | <p>Ontology url</p> |
| **attributes**<br>*Map<String,String>* <br> | <p>Dictionary that can be customised by users to store any additional information users may require..</p> |

### ClinicalAnalyst
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Id to identify the object</p> |
| **name**<br>*String* <br> | <p>Object name</p> |
| **email**<br>*String* <br> | <p>Email of the analyst</p> |
| **assignedBy**<br>*String* <br> | <p>Assigned by field</p> |
| **date**<br>*String* <br> | <p>Date of the clinical analyst</p> |

### ClinicalConsentAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java).

| Field | Description |
| :--- | :--- |
| **consents**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalconsentparam"><em>ClinicalConsentParam</em></a>>* <br> | <p>List of ClinicalConsentParam.</p> |
| **date**<br>*String* <br> | <p>Date of the ClinicalConsentAnnotation.</p> |

### Status
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java).


### InterpretationInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java).

| Field | Description |
| :--- | :--- |
| **status**<br>*[InterpretationStatus](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationstatus)* <br> | <p>State of the interpretation that can have the values READY, DELETED, NOT_REVIEWED, UNDER_REVIEW, REVIEWED and REJECTED.</p> |
>>>>>>> release-2.2.x
| **status**<br>*[InternalStatus](https://docs.opencga.opencb.org/data-models/clinicalanalysis#internalstatus)* <br> | <p>Status of the internal object.</p> |
| **registrationDate**<br>*String* <br> | <p>Registration date of the internal object.</p> |
| **lastModified**<br>*String* <br> | <p>Date of the last modification of the internal object.</p> |

<<<<<<< HEAD

### InternalStatus
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java).


<<<<<<< HEAD

### InterpretationInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java).

Expand All @@ -407,9 +177,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52

### InterpretationStatus
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java).
=======
=======
>>>>>>> release-2.2.x
### ClinicalConsentParam
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentParam.java).

Expand All @@ -425,10 +192,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15


### InterpretationStatus
<<<<<<< HEAD
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java).
>>>>>>> release-2.2.x
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java).
>>>>>>> release-2.2.x


9 changes: 1 addition & 8 deletions docs/data-models/family.md
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Expand Up @@ -25,15 +25,8 @@ Family data model hosts information about any family.
## Data Model

### Family
<<<<<<< HEAD
<<<<<<< HEAD
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java).
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java).
>>>>>>> release-2.2.x
=======
You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java).
>>>>>>> release-2.2.x


| Field | Description |
| :--- | :--- |
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