From 1b6b620c35985be11fd2a86ed2736a9ce0d86437 Mon Sep 17 00:00:00 2001 From: natalyatodorova Date: Tue, 21 Oct 2025 15:54:59 +0100 Subject: [PATCH 1/5] ODM-12813: spec for omics/cells/expression/data endpoint --- openapi/v1/integrationCurator.yaml | 223 ++++++++++++++++++++++++++++- openapi/v1/integrationUser.yaml | 223 ++++++++++++++++++++++++++++- 2 files changed, 444 insertions(+), 2 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index c072f3ff..8dbe057b 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -4545,10 +4545,231 @@ paths: summary: Retrieve Cell objects by searching across multiple data types tags: - Omics queries as Curator + /api/v1/as-curator/omics/cells/expression/data: + get: + description: |- + Retrieve cell expression objects by searching across multiple metadata types. + + ## Conditions + It is possible to supply conditions for: + 1. Parent studies (full-text or metadata key-value pair) + 2. Samples (full-text or metadata key-value pair) + 3. Libraries (full-text or metadata key-value pair) + 4. Preparations (full-text or metadata key-value pair) + + ## Metadata full-text queries + Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`). + + ## Metadata filters + Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). + + ## Data queries + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + + ## Combinations + Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. + + ## Paging + For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. + operationId: omicsSearchCellsExpressionDataAsCurator + parameters: + - description: | + Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress` + in: query + name: studyFilter + schema: + type: string + - description: Search for objects via a full-text query over all study metadata + fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary + terms are automatically expanded to include synonyms. + in: query + name: studyQuery + schema: + type: string + - description: | + Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"` + in: query + name: sampleFilter + schema: + type: string + - description: Search for objects via a full-text query over all sample metadata + fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically + expanded to include synonyms. + in: query + name: sampleQuery + schema: + type: string + - description: Filter by library metadata (key-value metadata pair(s)). E.g. + `"Library Type"=RNA-Seq-1` + in: query + name: libraryFilter + schema: + type: string + - description: Search for library objects via a full-text query over all library + metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary + terms are automatically expanded to include synonyms. + in: query + name: libraryQuery + schema: + type: string + - description: Filter by preparation metadata (key-value metadata pair(s)). + E.g. `Digestion=Trypsin` + in: query + name: preparationFilter + schema: + type: string + - description: Search for preparation objects via a full-text query over all + preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`. + Queries matching dictionary terms are automatically expanded to include + synonyms. + in: query + name: preparationQuery + schema: + type: string + - description: |- + Search for cells by their metadata attributes. The following attributes are supported: + 1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes. + 2. Integers: `nCounts` + 3. Floats: `percentMito` + 4. Float coordinates: `UMAP`, `PCA`. + 5. All other attributes are considered to be custom and stored as string data type. + + To use filters for cell metadata objects use the following query types: + 1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type. + 2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`. + 3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`. + 4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`. + 5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: + * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search. + * `batch=BatchA && percentMito<0.8` or `batch=BatchA AND percentMito<8`: select all objects with BatchA and percentMito less than 0.8. + * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2. + * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000. + * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query. + in: query + name: cellQuery + schema: + type: string + - description: "Search for objects linked to expression data and originally\ + \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\ + \ value>=1.50`\n For the case when the original data is represented by multiple\ + \ attributes per feature scenarios, extended filtering syntax is as follows:\ + \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\ + \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\ + \ single words can be supplied as is; otherwise, use speech marks (`\"`)\ + \ to quote queries that include whitespace. \n2. It is possible to specify\ + \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\ + \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\ + \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\ + \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\ + \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\ + \ all rows where the feature attribute Name_2 values are greater than or\ + \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\ + \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\ + \ Use substring search to get the records where the attribute field contains\ + \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\ + \ first column for each original data file is identified as feature accession\ + \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\ + \ by such feature accession would significantly outperform more complex\ + \ queries by combining the other feature attributes. To enable such a search,\ + \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\ + \ \nThe `value` keyword can be used to select rows where the sample (library\ + \ or preparation) measurements has values from a certain range. Examples:\ + \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\ + \ multiple measurements for a single item, such as a sample (library or\ + \ preparation), use the measurement name to specify the exact column type,\ + \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\ + \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\ + \ rows where the measurement attribute intensity is not equal 2 and is not\ + \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\ + \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\ + \ Selects all rows where the measurement attribute 'FC' values lie within\ + \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\ + \ been deprecated and should be replaced with the aforementioned comparisons.\n\ + \ \nCombine multiple filters for different feature attributes and measurements\ + \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\ + * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\ + \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\ + \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\ + \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\ + \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\ + \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\ + \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\ + \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\ + \ B or minimal possible measurement value is 1.0." + in: query + name: exQuery + schema: + type: string + - description: "Filter by expression metadata (key-value metadata pair(s)).\ + \ E.g. `\"Genome Version\"=hg19-BROAD`." + in: query + name: exFilter + schema: + type: string + - description: |- + If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. + + For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results. + + The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary. + + If the full query term is not present in a dictionary then this parameter has no effect. + in: query + name: searchSpecificTerms + schema: + type: boolean + - description: |- + Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: + + \* or `v` or ``:`v` or ``:`` + in: query + name: useVersions + schema: + type: string + - description: The page tag to resume results from (see paging above). + in: query + name: cursor + schema: + type: string + - description: "This parameter determines the number of results to retrieve\ + \ per page, with the default set at 2000." + in: query + name: pageLimit + schema: + format: int32 + type: integer + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/OmicsResponse" + description: Omics query result. + "400": + content: { } + description: Invalid data in request. See error message for details. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] + summary: Retrieve cell expression objects by searching across multiple metadata types + tags: + - Omics queries as Curator /api/v1/as-curator/omics/expression/data: get: description: "Retrieve any data objects whose linked data matches all supplied\ - \ conditions. \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\ + \ conditions.This endpoint does not support search by expression linked to Cell\ + \ group. Use /omics/cells/expression/data endpoint for search by Cell expression.\ + \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\ It is possible to supply conditions for:\n\n1. Samples (full-text or metadata\ \ key-value pair)\n2. Parent studies (full-text or metadata key-value pair)\n\ 3. Linked variant objects (list of data key-value pairs)\n4. Linked flow cytometry\ diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index 033ae61f..a391b406 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -2992,10 +2992,231 @@ paths: summary: Retrieve Cell objects by searching across multiple data types tags: - Omics queries as User + /api/v1/as-user/omics/cells/expression/data: + get: + description: |- + Retrieve cell expression objects by searching across multiple metadata types. + + ## Conditions + It is possible to supply conditions for: + 1. Parent studies (full-text or metadata key-value pair) + 2. Samples (full-text or metadata key-value pair) + 3. Libraries (full-text or metadata key-value pair) + 4. Preparations (full-text or metadata key-value pair) + + ## Metadata full-text queries + Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`). + + ## Metadata filters + Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). + + ## Data queries + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + + ## Combinations + Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. + + ## Paging + For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. + operationId: omicsSearchCellsExpressionDataAsUser + parameters: + - description: | + Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress` + in: query + name: studyFilter + schema: + type: string + - description: Search for objects via a full-text query over all study metadata + fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary + terms are automatically expanded to include synonyms. + in: query + name: studyQuery + schema: + type: string + - description: | + Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"` + in: query + name: sampleFilter + schema: + type: string + - description: Search for objects via a full-text query over all sample metadata + fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically + expanded to include synonyms. + in: query + name: sampleQuery + schema: + type: string + - description: Filter by library metadata (key-value metadata pair(s)). E.g. + `"Library Type"=RNA-Seq-1` + in: query + name: libraryFilter + schema: + type: string + - description: Search for library objects via a full-text query over all library + metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary + terms are automatically expanded to include synonyms. + in: query + name: libraryQuery + schema: + type: string + - description: Filter by preparation metadata (key-value metadata pair(s)). + E.g. `Digestion=Trypsin` + in: query + name: preparationFilter + schema: + type: string + - description: Search for preparation objects via a full-text query over all + preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`. + Queries matching dictionary terms are automatically expanded to include + synonyms. + in: query + name: preparationQuery + schema: + type: string + - description: |- + Search for cells by their metadata attributes. The following attributes are supported: + 1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes. + 2. Integers: `nCounts` + 3. Floats: `percentMito` + 4. Float coordinates: `UMAP`, `PCA`. + 5. All other attributes are considered to be custom and stored as string data type. + + To use filters for cell metadata objects use the following query types: + 1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type. + 2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`. + 3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP or PCA values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, e.g. `umap.1 > 0.5`. + 4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`. + 5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: + * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search. + * `batch=BatchA && percentMito<0.8` or `batch=BatchA AND percentMito<8`: select all objects with BatchA and percentMito less than 0.8. + * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2. + * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000. + * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query. + in: query + name: cellQuery + schema: + type: string + - description: "Search for objects linked to expression data and originally\ + \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\ + \ value>=1.50`\n For the case when the original data is represented by multiple\ + \ attributes per feature scenarios, extended filtering syntax is as follows:\ + \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\ + \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\ + \ single words can be supplied as is; otherwise, use speech marks (`\"`)\ + \ to quote queries that include whitespace. \n2. It is possible to specify\ + \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\ + \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\ + \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\ + \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\ + \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\ + \ all rows where the feature attribute Name_2 values are greater than or\ + \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\ + \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\ + \ Use substring search to get the records where the attribute field contains\ + \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\ + \ first column for each original data file is identified as feature accession\ + \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\ + \ by such feature accession would significantly outperform more complex\ + \ queries by combining the other feature attributes. To enable such a search,\ + \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\ + \ \nThe `value` keyword can be used to select rows where the sample (library\ + \ or preparation) measurements has values from a certain range. Examples:\ + \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\ + \ multiple measurements for a single item, such as a sample (library or\ + \ preparation), use the measurement name to specify the exact column type,\ + \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\ + \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\ + \ rows where the measurement attribute intensity is not equal 2 and is not\ + \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\ + \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\ + \ Selects all rows where the measurement attribute 'FC' values lie within\ + \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\ + \ been deprecated and should be replaced with the aforementioned comparisons.\n\ + \ \nCombine multiple filters for different feature attributes and measurements\ + \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\ + * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\ + \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\ + \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\ + \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\ + \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\ + \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\ + \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\ + \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\ + \ B or minimal possible measurement value is 1.0." + in: query + name: exQuery + schema: + type: string + - description: "Filter by expression metadata (key-value metadata pair(s)).\ + \ E.g. `\"Genome Version\"=hg19-BROAD`." + in: query + name: exFilter + schema: + type: string + - description: |- + If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. + + For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results. + + The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary. + + If the full query term is not present in a dictionary then this parameter has no effect. + in: query + name: searchSpecificTerms + schema: + type: boolean + - description: |- + Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: + + \* or `v` or ``:`v` or ``:`` + in: query + name: useVersions + schema: + type: string + - description: The page tag to resume results from (see paging above). + in: query + name: cursor + schema: + type: string + - description: "This parameter determines the number of results to retrieve\ + \ per page, with the default set at 2000." + in: query + name: pageLimit + schema: + format: int32 + type: integer + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/OmicsResponse" + description: Omics query result. + "400": + content: { } + description: Invalid data in request. See error message for details. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] + summary: Retrieve cell expression objects by searching across multiple metadata types + tags: + - Omics queries as User /api/v1/as-user/omics/expression/data: get: description: "Retrieve any data objects whose linked data matches all supplied\ - \ conditions. \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\ + \ conditions.This endpoint does not support search by expression linked to Cell\ + \ group. Use /omics/cells/expression/data endpoint for search by Cell expression.\ + \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\ It is possible to supply conditions for:\n\n1. Samples (full-text or metadata\ \ key-value pair)\n2. Parent studies (full-text or metadata key-value pair)\n\ 3. Linked variant objects (list of data key-value pairs)\n4. Linked flow cytometry\ From 9fc68f41630c29cced093e1f3767d7b8ef1f5a8e Mon Sep 17 00:00:00 2001 From: natalyatodorova Date: Tue, 21 Oct 2025 16:07:36 +0100 Subject: [PATCH 2/5] !!tmp buid fix --- Earthfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Earthfile b/Earthfile index 1f382234..391f812c 100644 --- a/Earthfile +++ b/Earthfile @@ -83,7 +83,7 @@ r-api-client: # Gcc and other stuff for R source packages building RUN \ apt update && \ - apt install -y libssl-dev libcurl4-gnutls-dev curl && \ + apt install -y libssl-dev libcurl4-gnutls-dev curl && libcurl4t64:amd64=8.16.0-4 --allow-downgrades && \ Rscript requirements.R COPY +build/generated generated From 7a5963e00b88cca9c718cf7cce2600a9b5064a3c Mon Sep 17 00:00:00 2001 From: natalyatodorova Date: Tue, 21 Oct 2025 16:21:46 +0100 Subject: [PATCH 3/5] !!tmp buid fix --- Earthfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Earthfile b/Earthfile index 391f812c..fd0e7e92 100644 --- a/Earthfile +++ b/Earthfile @@ -83,7 +83,7 @@ r-api-client: # Gcc and other stuff for R source packages building RUN \ apt update && \ - apt install -y libssl-dev libcurl4-gnutls-dev curl && libcurl4t64:amd64=8.16.0-4 --allow-downgrades && \ + apt install -y libssl-dev libcurl4-gnutls-dev curl libcurl4t64:amd64=8.16.0-4 --allow-downgrades && \ Rscript requirements.R COPY +build/generated generated From c642e0690db077a1b1e98978a979aaa7a31cd934 Mon Sep 17 00:00:00 2001 From: natalyatodorova Date: Mon, 27 Oct 2025 14:34:35 +0000 Subject: [PATCH 4/5] remove useVersions param --- openapi/v1/integrationCurator.yaml | 8 -------- openapi/v1/integrationUser.yaml | 8 -------- 2 files changed, 16 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 8dbe057b..402abab3 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -4718,14 +4718,6 @@ paths: name: searchSpecificTerms schema: type: boolean - - description: |- - Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: - - \* or `v` or ``:`v` or ``:`` - in: query - name: useVersions - schema: - type: string - description: The page tag to resume results from (see paging above). in: query name: cursor diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index a391b406..a2a21f62 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -3165,14 +3165,6 @@ paths: name: searchSpecificTerms schema: type: boolean - - description: |- - Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: - - \* or `v` or ``:`v` or ``:`` - in: query - name: useVersions - schema: - type: string - description: The page tag to resume results from (see paging above). in: query name: cursor From 4d8be1072ba2e19b15395432ebd3669b8d5ba5d0 Mon Sep 17 00:00:00 2001 From: natalyatodorova Date: Tue, 28 Oct 2025 13:03:34 +0000 Subject: [PATCH 5/5] fix cr review comments --- openapi/v1/integrationCurator.yaml | 33 +++++++++++++++--------------- openapi/v1/integrationUser.yaml | 33 +++++++++++++++--------------- 2 files changed, 32 insertions(+), 34 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 402abab3..593ed793 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -1693,7 +1693,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -2491,7 +2491,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -2785,7 +2785,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -2915,7 +2915,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3125,7 +3125,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3255,7 +3255,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3386,7 +3386,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4416,7 +4416,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4564,7 +4564,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4780,8 +4780,7 @@ paths: \ in the query parameter summary. The values can be simple non-whitespace\ \ strings, or strings enclosed by speech marks (`\"`). Depending on the key,\ \ the value may be be a comma-delimited list of string values. Others require\ - \ numerical values. Ranges can be supplied with `(0:1)` syntax, OR values\ - \ with `|`.\n\n## Combinations\nMetadata queries/filters for the same parameter\ + \ numerical values.\n\n## Combinations\nMetadata queries/filters for the same parameter\ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\ \ to separate out the terms and operators. Parentheses `( )` can be used for\ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\ @@ -5053,7 +5052,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -5501,7 +5500,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -5770,7 +5769,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -6038,7 +6037,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -6309,7 +6308,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -6577,7 +6576,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index a2a21f62..d6617f00 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -922,7 +922,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -1388,7 +1388,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -1518,7 +1518,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -1648,7 +1648,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -1858,7 +1858,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -1988,7 +1988,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -2119,7 +2119,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -2863,7 +2863,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3011,7 +3011,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with (`0:1`) syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3227,8 +3227,7 @@ paths: \ in the query parameter summary. The values can be simple non-whitespace\ \ strings, or strings enclosed by speech marks (`\"`). Depending on the key,\ \ the value may be be a comma-delimited list of string values. Others require\ - \ numerical values. Ranges can be supplied with `(0:1)` syntax, OR values\ - \ with `|`.\n\n## Combinations\nMetadata queries/filters for the same parameter\ + \ numerical values.\n\n## Combinations\nMetadata queries/filters for the same parameter\ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\ \ to separate out the terms and operators. Parentheses `( )` can be used for\ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\ @@ -3500,7 +3499,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -3952,7 +3951,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4221,7 +4220,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4489,7 +4488,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -4760,7 +4759,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions. @@ -5028,7 +5027,7 @@ paths: Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`). ## Data queries - Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`. + Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## Combinations Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.