CLI: Login improvements #1884 to review

opencb · Feb 3, 2022 · e397f69 · e397f69
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diff --git a/docs/data-models/clinicalanalysis.md b/docs/data-models/clinicalanalysis.md
diff --git a/docs/data-models/cohort.md b/docs/data-models/cohort.md
@@ -37,10 +37,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **internal**<br>*[CohortInternal](https://docs.opencga.opencb.org/data-models/cohort#cohortinternal)* <br> | <p>Internal field for manage the object.</p> |
 | **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
-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).
-
-
 ### CohortInternal
 You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/CohortInternal.java).
 
@@ -49,3 +45,7 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/cohort#status)* <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> |
+
+### 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).
+
diff --git a/docs/data-models/family.md b/docs/data-models/family.md
@@ -47,9 +47,19 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |
 | **version**<br>*int* <br> | <p>Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document.</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).
+### Phenotype
+You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java).
 
+| Field | Description |
+| :---  | :--- |
+| **id**<br>*String* <br> | <p>Id to identify the object</p> |
+| **ageOfOnset**<br>*String* <br> | <p>Indicates the age of on set of the phenotype</p> |
+| **status**<br>*Status* <br> | <p>Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN</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> |
 
 ### FamilyInternal
 You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyInternal.java).
@@ -60,40 +70,40 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **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> |
 
-### 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).
+### FamilyQualityControl
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyQualityControl.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> |
+| **relatedness**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/family#relatednessreport"><em>RelatednessReport</em></a>>* <br> | <p>Reports of family relationship.</p> |
+| **files**<br>*List<<em>String</em>>* <br> | <p>File IDs related to the quality control.</p> |
+| **comments**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/family#clinicalcomment"><em>ClinicalComment</em></a>>* <br> | <p>Comments related to the quality control.</p> |
 
-### Phenotype
-You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java).
+### 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> |
-| **ageOfOnset**<br>*String* <br> | <p>Indicates the age of on set of the phenotype</p> |
-| **status**<br>*Status* <br> | <p>Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN</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> |
 
-### FamilyQualityControl
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyQualityControl.java).
+### 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).
+
+
+### 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 |
 | :---  | :--- |
-| **relatedness**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/family#relatednessreport"><em>RelatednessReport</em></a>>* <br> | <p>Reports of family relationship.</p> |
-| **files**<br>*List<<em>String</em>>* <br> | <p>File IDs related to the quality control.</p> |
-| **comments**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/family#clinicalcomment"><em>ClinicalComment</em></a>>* <br> | <p>Comments related to the quality control.</p> |
+| **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> |
 
 ### RelatednessReport
 You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/RelatednessReport.java).
@@ -104,13 +114,3 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop
 | **maf**<br>*String* <br> | <p>Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05</p> |
 | **scores**<br>*List<<em>RelatednessScore</em>>* <br> | <p>Relatedness scores for pair of samples</p> |
 | **files**<br>*List<<em>String</em>>* <br> | <p>List of files of Relatedness Report</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> |
diff --git a/docs/data-models/file.md b/docs/data-models/file.md
@@ -65,16 +65,36 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **internal**<br>*[FileInternal](https://docs.opencga.opencb.org/data-models/file#fileinternal)* <br> | <p>Internal field for manage the object.</p> |
 | **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
+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).
+
+
 ### FileExperiment
 You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileExperiment.java).
 
 
-### URI
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java).
+### Software
+You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Software.java).
+
+| Field | Description |
+| :---  | :--- |
+| **name**<br>*String* <br> | <p>Software name</p> |
+| **version**<br>*String* <br> | <p>Software version</p> |
+| **repository**<br>*String* <br> | <p>Software repository</p> |
+| **commit**<br>*String* <br> | <p>Software commit</p> |
+| **website**<br>*String* <br> | <p>Software website</p> |
+| **params**<br>*Map<String,String>* <br> | <p>Software params</p> |
 
+### FileQualityControl
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileQualityControl.java).
 
-### 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).
+
+### FileRelatedFile
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileRelatedFile.java).
+
+
+### URI
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java).
 
 
 ### FileInternal
@@ -91,28 +111,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **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> |
 
-### FileQualityControl
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileQualityControl.java).
-
-
-### FileRelatedFile
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileRelatedFile.java).
-
-
-### Software
-You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Software.java).
-
-| Field | Description |
-| :---  | :--- |
-| **name**<br>*String* <br> | <p>Software name</p> |
-| **version**<br>*String* <br> | <p>Software version</p> |
-| **repository**<br>*String* <br> | <p>Software repository</p> |
-| **commit**<br>*String* <br> | <p>Software commit</p> |
-| **website**<br>*String* <br> | <p>Software website</p> |
-| **params**<br>*Map<String,String>* <br> | <p>Software params</p> |
-
-### FileInternalVariant
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileInternalVariant.java).
+### FileInternalAlignment
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileInternalAlignment.java).
 
 
 ### MissingSamples
@@ -123,10 +123,10 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
 | **existing**<br>*List<<em>String</em>>* <br> | <p>List of existing samples.</p> |
 | **nonExisting**<br>*List<<em>String</em>>* <br> | <p>List of non existing samples.</p> |
 
-### FileStatus
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileStatus.java).
+### FileInternalVariant
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileInternalVariant.java).
 
 
-### FileInternalAlignment
-You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileInternalAlignment.java).
+### FileStatus
+You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileStatus.java).