From 12ec61e466dd809f334d5993cc65b4acd8240a5f Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:04:10 -0800 Subject: [PATCH 01/44] try not to use time data unless temproally subsetting (#386) * try not to use time data unless temproally subsetting * fix tests --- podaac/subsetter/subset.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index cc4b7179..6a951bf1 100755 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -192,10 +192,21 @@ def subset_with_bbox(dataset: xr.Dataset, # pylint: disable=too-many-branches time_path = None if time_var_name: time_path = file_utils.get_path(time_var_name) - time_data = dataset[time_var_name] - if time_data.ndim == 1 and lon_data.ndim == 2 and temporal_cond is not True: - temporal_cond = mask_utils.align_time_to_lon_dim(time_data, lon_data, temporal_cond) + try: + time_data = dataset[time_var_name] + except KeyError: + time_data = None + + if ( + time_data is not None + and time_data.ndim == 1 + and lon_data.ndim == 2 + and temporal_cond is not True + ): + temporal_cond = mask_utils.align_time_to_lon_dim( + time_data, lon_data, temporal_cond + ) operation = ( oper((lon_data >= lon_bounds[0]), (lon_data <= lon_bounds[1])) & From ee8a340f1f897eb8c1be68d8030710a2bdd6a253 Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:15:30 -0800 Subject: [PATCH 02/44] update readme (#387) --- README.md | 44 +++++++++++++++++++++++++++----------------- 1 file changed, 27 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index dd236c7e..a13a2cc1 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ - # l2ss-py [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=podaac_l2ss-py&metric=coverage)](https://sonarcloud.io/dashboard?id=podaac_l2ss-py) @@ -13,6 +12,7 @@ Harmony service for subsetting L2 data. l2ss-py supports: - GeoJSON subsetting - Temporal subsetting - Variable subsetting +- Vertical subsetting If you would like to contribute to l2ss-py, refer to the [contribution document](CONTRIBUTING.md). @@ -57,11 +57,9 @@ to run this, the l2ss-py package must be installed in your current Python interpreter ``` -$ l2ss-py --help -usage: run_subsetter.py [-h] [--bbox BBOX BBOX BBOX BBOX] - [--variables VARIABLES [VARIABLES ...]] - [--min-time MIN_TIME] [--max-time MAX_TIME] [--cut] - input_file output_file +$ l2ss-py --help +usage: l2ss-py [-h] [--bbox BBOX BBOX BBOX BBOX] [--variables VARIABLES [VARIABLES ...]] [--min-time MIN_TIME] [--max-time MAX_TIME] [--cut] [--shapefile SHAPEFILE] [--pixel_subset] [--vertical-var VERTICAL_VAR] [--vertical-min VERTICAL_MIN] [--vertical-max VERTICAL_MAX] + input_file output_file Run l2ss-py @@ -69,28 +67,40 @@ positional arguments: input_file File to subset output_file Output file -optional arguments: +options: -h, --help show this help message and exit --bbox BBOX BBOX BBOX BBOX - Bounding box in the form min_lon min_lat max_lon - max_lat + Bounding box in the form min_lon min_lat max_lon max_lat --variables VARIABLES [VARIABLES ...] - Variables, only include if variable subset is desired. - Should be a space separated list of variable names - e.g. sst wind_dir sst_error ... - --min-time MIN_TIME Min time. Should be ISO-8601 format. Only include if - temporal subset is desired. - --max-time MAX_TIME Max time. Should be ISO-8601 format. Only include if - temporal subset is desired. + Variables, only include if variable subset is desired. Should be a space separated list of variable names e.g. sst wind_dir sst_error ... + --min-time MIN_TIME Min time. Should be ISO-8601 format. Only include if temporal subset is desired. + --max-time MAX_TIME Max time. Should be ISO-8601 format. Only include if temporal subset is desired. --cut If provided, scanline will be cut --shapefile SHAPEFILE Path to either shapefile or geojson file used to subset the provided input granule + --pixel_subset To pixel cut based the lon lat on the bounding box + --vertical-var VERTICAL_VAR + Name of the vertical variable to subset by (e.g., depth, altitude) + --vertical-min VERTICAL_MIN + Minimum value for vertical subsetting (inclusive) + --vertical-max VERTICAL_MAX + Maximum value for vertical subsetting (inclusive) ``` +#### Additional subsetting options + +The following options are also recorded in the output file's metadata history for provenance and reproducibility: +- `--min-time` and `--max-time` (temporal subsetting) +- `--variables` (variable subsetting) +- `--vertical-var`, `--vertical-min`, `--vertical-max` (vertical subsetting) +- `--cut`, `--pixel_subset`, `--shapefile`, and `--bbox` (spatial subsetting) + +All subsetting parameters used in a run are included in the output file's `history` and `history_json` attributes. + For example: ``` -l2ss-py /path/to/input.nc /path/to/output.nc --bbox -50 -10 50 10 --variables wind_speed wind_dir ice_age time --min-time '2015-07-02T09:00:00' --max-time '2015-07-02T10:00:00' --cut +l2ss-py /path/to/input.nc /path/to/output.nc --bbox -50 -10 50 10 --variables wind_speed wind_dir ice_age time --min-time '2015-07-02T09:00:00' --max-time '2015-07-02T10:00:00' --cut --vertical-var depth --vertical-min 0 --vertical-max 100 ``` An addition to providing a bounding box, spatial subsetting can be achieved by passing in a shapefile or a geojson file. From e8b2eaa136458d89860646fc78be33a71c75b740 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 3 Mar 2026 18:37:34 +0000 Subject: [PATCH 03/44] /version 3.3.0a6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 31a268c0..f06f5be6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.0a5" +version = "3.3.0a6" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From b959d967a43d5f4518698024f0d3dfc2cdfbb353 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 3 Mar 2026 21:27:27 +0000 Subject: [PATCH 04/44] /version 3.4.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4a281634..e655cdfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a0" +version = "3.4.0a1" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 7ebcce7d700e7220868c884c34934e7440efea92 Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Tue, 10 Mar 2026 12:55:24 -0700 Subject: [PATCH 05/44] Feature/fix cygnss collections (#389) * fix the temporal subsettting for cygnss collections check for sample_time and solar_time * update changelog --- CHANGELOG.md | 2 ++ podaac/subsetter/datatree_subset.py | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a7805b13..e602f432 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added +- Updated readme documentation ### Changed +- Changed way Cygnss collection finds time variable ### Deprecated ### Removed ### Fixed diff --git a/podaac/subsetter/datatree_subset.py b/podaac/subsetter/datatree_subset.py index 89f373cb..1b9c36bc 100755 --- a/podaac/subsetter/datatree_subset.py +++ b/podaac/subsetter/datatree_subset.py @@ -690,7 +690,10 @@ def method_6(path, ds): if result: # Normalize /sample_time to /solar_time for this unique case if result == "/sample_time": - return "/solar_time" + # Check if '/solar_time' exists in the dataset + if "/solar_time" in [f"/{v}" for v in ds.variables]: + print('returning solar time') + return "/solar_time" return result return None From 1e651bb775e481f22c08d88b131338e6b1522907 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 10 Mar 2026 20:22:46 +0000 Subject: [PATCH 06/44] /version 3.4.0a2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e655cdfe..0a73559c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a1" +version = "3.4.0a2" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 675ad8d61ca6f19a918d9bb855b30f92e431b7fe Mon Sep 17 00:00:00 2001 From: James Wood <8115931+jamesfwood@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:37:26 -0700 Subject: [PATCH 07/44] Release 3.3.1 --- CHANGELOG.md | 9 + poetry.lock | 575 ++++++++++++++++++++++++++----------------------- pyproject.toml | 2 +- 3 files changed, 312 insertions(+), 274 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e602f432..215ef844 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added +### Changed +### Deprecated +### Removed +### Fixed +### Security + + +## [3.3.1] +### Added - 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Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 10 Mar 2026 20:38:10 +0000 Subject: [PATCH 08/44] /version 3.4.0a0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0a73559c..4a281634 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a2" +version = "3.4.0a0" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 605baf9c723cdbdfb8f0eb75c3c8b3782999dc2a Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 10 Mar 2026 20:59:55 +0000 Subject: [PATCH 09/44] /version 3.3.1rc1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ae2dffba..dffdcdf2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1a0" +version = "3.3.1rc1" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From abf734915821d028ce91d73416e23c417a0560e6 Mon Sep 17 00:00:00 2001 From: thomas loubrieu <60993872+tloubrieu-jpl@users.noreply.github.com> Date: Sat, 14 Mar 2026 12:32:53 -0700 Subject: [PATCH 10/44] Add automatic team/project assignment workflow This workflow automatically, when team label is assigned to an issue: - Set podaac project status to triage - Assign to the team github project when it exists, with a New status. Co-Authored-By: Claude Opus 4.6 --- .github/workflows/team-assignment.yml | 255 ++++++++++++++++++++++++++ 1 file changed, 255 insertions(+) create mode 100644 .github/workflows/team-assignment.yml diff --git a/.github/workflows/team-assignment.yml b/.github/workflows/team-assignment.yml new file mode 100644 index 00000000..3072a20d --- /dev/null +++ b/.github/workflows/team-assignment.yml @@ -0,0 +1,255 @@ +name: Team Assignment + +on: + issues: + types: [labeled] + +jobs: + assign-to-team: + runs-on: ubuntu-latest + steps: + - name: Process team label + uses: actions/github-script@v7 + with: + github-token: ${{ secrets.PROJECTS_PAT }} + script: | + const label = context.payload.label.name; + const issueNumber = context.payload.issue.number; + + // Check if label matches team: pattern + const teamMatch = label.match(/^team:(.+)$/); + if (!teamMatch) { + console.log(`Label "${label}" does not match team: pattern, skipping`); + return; + } + + const teamName = teamMatch[1]; + console.log(`Processing team assignment for team: ${teamName}`); + + const podaacProjectNumber = 75; + const org = 'podaac'; + const repo = context.repo.repo; + + // Define reusable GraphQL mutation for updating project status + const updateStatusMutation = ` + mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $value: String!) { + updateProjectV2ItemFieldValue( + input: { + projectId: $projectId + itemId: $itemId + fieldId: $fieldId + value: { singleSelectOptionId: $value } + } + ) { + projectV2Item { + id + } + } + } + `; + + // ======================================== + // Step 1: Update status to "triaged" in podaac project + // ======================================== + + console.log('Step 1: Updating podaac project status to "triaged"...'); + + // Get the podaac project information + const podaacProjectQuery = ` + query($org: String!, $number: Int!) { + organization(login: $org) { + projectV2(number: $number) { + id + fields(first: 20) { + nodes { + ... on ProjectV2SingleSelectField { + id + name + options { + id + name + } + } + } + } + } + } + } + `; + + const podaacProjectData = await github.graphql(podaacProjectQuery, { + org: org, + number: podaacProjectNumber + }); + + const podaacProject = podaacProjectData.organization.projectV2; + const podaacStatusField = podaacProject.fields.nodes.find(field => field.name === 'Status'); + const triagedOption = podaacStatusField?.options.find(option => option.name === 'triaged'); + + if (!triagedOption) { + core.warning('Could not find "triaged" status option in podaac project'); + } else { + // Get the issue's project item in podaac project + const issueProjectItemQuery = ` + query($org: String!, $repo: String!, $number: Int!) { + repository(owner: $org, name: $repo) { + issue(number: $number) { + projectItems(first: 10) { + nodes { + id + project { + id + number + } + } + } + } + } + } + `; + + const issueData = await github.graphql(issueProjectItemQuery, { + org: org, + repo: repo, + number: issueNumber + }); + + const projectItems = issueData.repository.issue.projectItems.nodes; + const podaacProjectItem = projectItems.find(item => item.project.id === podaacProject.id); + + if (!podaacProjectItem) { + core.warning('Issue is not in podaac project, cannot update status'); + } else { + // Update the status to "triaged" + await github.graphql(updateStatusMutation, { + projectId: podaacProject.id, + itemId: podaacProjectItem.id, + fieldId: podaacStatusField.id, + value: triagedOption.id + }); + + console.log('✅ Successfully updated status to "triaged" in podaac project'); + } + } + + // ======================================== + // Step 2: Add to team project if it exists + // ======================================== + + console.log(`Step 2: Looking for team project named "${teamName}"...`); + + // Search for team project by name + const teamProjectSearchQuery = ` + query($org: String!, $searchQuery: String!) { + organization(login: $org) { + projectsV2(first: 20, query: $searchQuery) { + nodes { + id + number + title + fields(first: 20) { + nodes { + ... on ProjectV2SingleSelectField { + id + name + options { + id + name + } + } + } + } + } + } + } + } + `; + + const teamProjectSearchData = await github.graphql(teamProjectSearchQuery, { + org: org, + searchQuery: teamName + }); + + const teamProjects = teamProjectSearchData.organization.projectsV2.nodes; + const teamProject = teamProjects.find(p => p.title.toLowerCase() === teamName.toLowerCase()); + + if (!teamProject) { + console.log(`⚠️ No project found with name "${teamName}", skipping team project assignment`); + core.notice(`No project found for team "${teamName}". If you want the issue added to a team project, create a project named "${teamName}".`); + return; + } + + console.log(`Found team project: ${teamProject.title} (number: ${teamProject.number})`); + + // Add issue to team project + const addToProjectMutation = ` + mutation($projectId: ID!, $contentId: ID!) { + addProjectV2ItemById(input: { + projectId: $projectId + contentId: $contentId + }) { + item { + id + } + } + } + `; + + const issueNodeIdQuery = ` + query($org: String!, $repo: String!, $number: Int!) { + repository(owner: $org, name: $repo) { + issue(number: $number) { + id + } + } + } + `; + + const issueNodeData = await github.graphql(issueNodeIdQuery, { + org: org, + repo: repo, + number: issueNumber + }); + + const issueNodeId = issueNodeData.repository.issue.id; + + const addResult = await github.graphql(addToProjectMutation, { + projectId: teamProject.id, + contentId: issueNodeId + }); + + const teamProjectItemId = addResult.addProjectV2ItemById.item.id; + console.log(`✅ Successfully added issue to team project "${teamName}"`); + + // ======================================== + // Step 3: Set status to "New" in team project + // ======================================== + + console.log('Step 3: Setting status to "New" in team project...'); + + const teamStatusField = teamProject.fields.nodes.find(field => field.name === 'Status'); + const newStatusOption = teamStatusField?.options.find(option => option.name === '🆕 New'); + + if (!teamStatusField || !newStatusOption) { + core.warning(`Could not find "Status" field or "New" option in team project "${teamName}"`); + console.log(`⚠️ Team project "${teamName}" does not have a Status field with "🆕 New" option`); + } else { + await github.graphql(updateStatusMutation, { + projectId: teamProject.id, + itemId: teamProjectItemId, + fieldId: teamStatusField.id, + value: newStatusOption.id + }); + + console.log('✅ Successfully set status to "🆕 New" in team project'); + } + + // Summary + core.summary + .addHeading(`Team Assignment Complete: ${teamName}`) + .addList([ + `Updated podaac project status to "triaged"`, + `Added issue to team project "${teamName}"`, + `Set status to "🆕 New" in team project` + ]) + .write(); From 5d37721e5e56f2b90994bcfd2d8bf833e199eeac Mon Sep 17 00:00:00 2001 From: thomas loubrieu <60993872+tloubrieu-jpl@users.noreply.github.com> Date: Sat, 14 Mar 2026 13:28:25 -0700 Subject: [PATCH 11/44] Add automatic team/project assignment workflow This workflow automatically, when team label is assigned to an issue: - Set podaac project status to triage - Assign to the team github project when it exists, with a New status. Co-Authored-By: Claude Opus 4.6 --- .github/workflows/team-assignment.yml | 105 ++++++++++++++------------ 1 file changed, 58 insertions(+), 47 deletions(-) diff --git a/.github/workflows/team-assignment.yml b/.github/workflows/team-assignment.yml index 3072a20d..3b0d0343 100644 --- a/.github/workflows/team-assignment.yml +++ b/.github/workflows/team-assignment.yml @@ -86,6 +86,9 @@ jobs: const podaacStatusField = podaacProject.fields.nodes.find(field => field.name === 'Status'); const triagedOption = podaacStatusField?.options.find(option => option.name === 'triaged'); + let podaacProjectItem = null; + let podaacStatusUpdated = false; + if (!triagedOption) { core.warning('Could not find "triaged" status option in podaac project'); } else { @@ -115,7 +118,7 @@ jobs: }); const projectItems = issueData.repository.issue.projectItems.nodes; - const podaacProjectItem = projectItems.find(item => item.project.id === podaacProject.id); + podaacProjectItem = projectItems.find(item => item.project.id === podaacProject.id); if (!podaacProjectItem) { core.warning('Issue is not in podaac project, cannot update status'); @@ -128,6 +131,7 @@ jobs: value: triagedOption.id }); + podaacStatusUpdated = true; console.log('✅ Successfully updated status to "triaged" in podaac project'); } } @@ -181,75 +185,82 @@ jobs: console.log(`Found team project: ${teamProject.title} (number: ${teamProject.number})`); - // Add issue to team project - const addToProjectMutation = ` - mutation($projectId: ID!, $contentId: ID!) { - addProjectV2ItemById(input: { - projectId: $projectId - contentId: $contentId - }) { - item { - id - } - } - } - `; - - const issueNodeIdQuery = ` + // Check if issue is already in the team project + const issueWithProjectsQuery = ` query($org: String!, $repo: String!, $number: Int!) { repository(owner: $org, name: $repo) { issue(number: $number) { id + projectItems(first: 20) { + nodes { + id + project { + id + } + } + } } } } `; - const issueNodeData = await github.graphql(issueNodeIdQuery, { + const issueWithProjects = await github.graphql(issueWithProjectsQuery, { org: org, repo: repo, number: issueNumber }); - const issueNodeId = issueNodeData.repository.issue.id; - - const addResult = await github.graphql(addToProjectMutation, { - projectId: teamProject.id, - contentId: issueNodeId - }); - - const teamProjectItemId = addResult.addProjectV2ItemById.item.id; - console.log(`✅ Successfully added issue to team project "${teamName}"`); - - // ======================================== - // Step 3: Set status to "New" in team project - // ======================================== + const issueNodeId = issueWithProjects.repository.issue.id; + const existingTeamProjectItem = issueWithProjects.repository.issue.projectItems.nodes.find( + item => item.project.id === teamProject.id + ); - console.log('Step 3: Setting status to "New" in team project...'); + let teamProjectItemId; + let wasAlreadyInProject = false; - const teamStatusField = teamProject.fields.nodes.find(field => field.name === 'Status'); - const newStatusOption = teamStatusField?.options.find(option => option.name === '🆕 New'); - - if (!teamStatusField || !newStatusOption) { - core.warning(`Could not find "Status" field or "New" option in team project "${teamName}"`); - console.log(`⚠️ Team project "${teamName}" does not have a Status field with "🆕 New" option`); + if (existingTeamProjectItem) { + // Issue is already in team project + teamProjectItemId = existingTeamProjectItem.id; + wasAlreadyInProject = true; + console.log(`ℹ️ Issue is already in team project "${teamName}"`); } else { - await github.graphql(updateStatusMutation, { + // Add issue to team project + const addToProjectMutation = ` + mutation($projectId: ID!, $contentId: ID!) { + addProjectV2ItemById(input: { + projectId: $projectId + contentId: $contentId + }) { + item { + id + } + } + } + `; + + const addResult = await github.graphql(addToProjectMutation, { projectId: teamProject.id, - itemId: teamProjectItemId, - fieldId: teamStatusField.id, - value: newStatusOption.id + contentId: issueNodeId }); - console.log('✅ Successfully set status to "🆕 New" in team project'); + teamProjectItemId = addResult.addProjectV2ItemById.item.id; + console.log(`✅ Successfully added issue to team project "${teamName}"`); } // Summary + const summaryItems = [`Processed team label: ${teamName}`]; + + if (podaacStatusUpdated) { + summaryItems.push(`Updated podaac project status to "triaged"`); + } + + if (wasAlreadyInProject) { + summaryItems.push(`Issue was already in team project "${teamName}"`); + } else { + summaryItems.push(`Added issue to team project "${teamName}"`); + } + core.summary .addHeading(`Team Assignment Complete: ${teamName}`) - .addList([ - `Updated podaac project status to "triaged"`, - `Added issue to team project "${teamName}"`, - `Set status to "🆕 New" in team project` - ]) + .addList(summaryItems) .write(); From d4f700e90dae975c434564a5b64eb8da781baad1 Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Tue, 17 Mar 2026 09:49:41 -0700 Subject: [PATCH 12/44] remove print and update checking solar time --- podaac/subsetter/datatree_subset.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/podaac/subsetter/datatree_subset.py b/podaac/subsetter/datatree_subset.py index 1b9c36bc..82ccbbaf 100755 --- a/podaac/subsetter/datatree_subset.py +++ b/podaac/subsetter/datatree_subset.py @@ -691,8 +691,7 @@ def method_6(path, ds): # Normalize /sample_time to /solar_time for this unique case if result == "/sample_time": # Check if '/solar_time' exists in the dataset - if "/solar_time" in [f"/{v}" for v in ds.variables]: - print('returning solar time') + if "solar_time" in ds.variables: return "/solar_time" return result return None From 7ec05c08ccbaf4413d24a9874321ea20e2663f6b Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Tue, 17 Mar 2026 10:18:41 -0700 Subject: [PATCH 13/44] poetry update --- poetry.lock | 515 +++++++++++++++++++++++++++------------------------- 1 file changed, 264 insertions(+), 251 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5125bbce..a893d4c0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -72,14 +72,14 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)" [[package]] name = "bokeh" -version = "3.8.2" +version = "3.9.0" description = "Interactive plots and applications in the browser from Python" optional = false python-versions = ">=3.10" groups = ["main"] files = [ - {file = "bokeh-3.8.2-py3-none-any.whl", hash = "sha256:5e2c0d84f75acb25d60efb9e4d2f434a791c4639b47d685534194c4e07bd0111"}, - {file = "bokeh-3.8.2.tar.gz", hash = "sha256:8e7dcacc21d53905581b54328ad2705954f72f2997f99fc332c1de8da53aa3cc"}, + {file = "bokeh-3.9.0-py3-none-any.whl", hash = "sha256:b252bfb16a505f0e0c57d532d0df308ae1667235bafc622aa9441fe9e7c5ce4a"}, + {file = "bokeh-3.9.0.tar.gz", hash = "sha256:775219714a8496973ddbae16b1861606ba19fe670a421e4d43267b41148e07a3"}, ] [package.dependencies] @@ -88,7 +88,6 @@ Jinja2 = ">=2.9" narwhals = ">=1.13" numpy = ">=1.16" packaging = ">=16.8" -pandas = ">=1.2" pillow = ">=7.1.0" PyYAML = ">=3.10" tornado = {version = ">=6.2", markers = "sys_platform != \"emscripten\""} @@ -96,19 +95,19 @@ xyzservices = ">=2021.9.1" [[package]] name = "boto3" -version = "1.42.65" +version = "1.42.69" description = "The AWS SDK for Python" optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "boto3-1.42.65-py3-none-any.whl", hash = "sha256:cc7f2e0aec6c68ee5b10232cf3e01326acf6100bc785a770385b61a0474b31f4"}, - {file = "boto3-1.42.65.tar.gz", hash = "sha256:c740af6bdaebcc1a00f3827a5729050bf6fc820ee148bf7d06f28db11c80e2a1"}, + {file = "boto3-1.42.69-py3-none-any.whl", hash = "sha256:6823a4b59aa578c7d98124280a9b6d83cea04bdb02525cbaa79370e5b6f7f631"}, + {file = "boto3-1.42.69.tar.gz", hash = "sha256:e59846f4ff467b23bae4751948298db554dbdda0d72b09028d2cacbeff27e1ad"}, ] markers = {main = "extra == \"harmony\""} [package.dependencies] -botocore = ">=1.42.65,<1.43.0" +botocore = ">=1.42.69,<1.43.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.16.0,<0.17.0" @@ -117,14 +116,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.42.65" +version = "1.42.69" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "botocore-1.42.65-py3-none-any.whl", hash = "sha256:0283c332ce00cbd1b894e86b7bed89dd624a5ca3a4ee62ec4db3898d16652e98"}, - {file = "botocore-1.42.65.tar.gz", hash = "sha256:7d52c148df07f70c375eeda58f99b439c7c7836c25df74cccfba3bb6e12444d2"}, + {file = "botocore-1.42.69-py3-none-any.whl", hash = "sha256:ef0e3d860a5d7bffc0ccb4911781c4c27d538557ed9a616ba1926c762d72e5f6"}, + {file = "botocore-1.42.69.tar.gz", hash = "sha256:0934f2d90403c5c8c2cba83e754a39d77edcad5885d04a79363edff3e814f55e"}, ] markers = {main = "extra == \"harmony\""} @@ -363,125 +362,141 @@ numpy = ">=1.21.2" [[package]] name = "charset-normalizer" -version = "3.4.5" +version = "3.4.6" description = "The Real First Universal Charset Detector. 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"sha256:0934f2d90403c5c8c2cba83e754a39d77edcad5885d04a79363edff3e814f55e"}, + {file = "botocore-1.42.72-py3-none-any.whl", hash = "sha256:038f34553da68df2ce70edc729f170cc198678daaad43f98649727c59f6404d4"}, + {file = "botocore-1.42.72.tar.gz", hash = "sha256:491b75eb41d46cf99cf8d6cab89f2e2c3602ce8e90d738a1da217a5fb6b2b7ef"}, ] markers = {main = "extra == \"harmony\""} @@ -853,21 +853,21 @@ test-randomorder = ["pytest-randomly"] [[package]] name = "dask" -version = "2026.1.2" +version = "2026.3.0" description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.10" groups = ["main"] files = [ - {file = "dask-2026.1.2-py3-none-any.whl", hash = "sha256:46a0cf3b8d87f78a3d2e6b145aea4418a6d6d606fe6a16c79bd8ca2bb862bc91"}, - {file = "dask-2026.1.2.tar.gz", hash = "sha256:1136683de2750d98ea792670f7434e6c1cfce90cab2cc2f2495a9e60fd25a4fc"}, + {file = "dask-2026.3.0-py3-none-any.whl", hash = "sha256:be614b9242b0b38288060fb2d7696125946469c98a1c30e174883fd199e0428d"}, + {file = "dask-2026.3.0.tar.gz", hash = "sha256:f7d96c8274e8a900d217c1ff6ea8d1bbf0b4c2c21e74a409644498d925eb8f85"}, ] [package.dependencies] bokeh = {version = ">=3.1.0", optional = true, markers = "extra == \"diagnostics\""} click = ">=8.1" cloudpickle = ">=3.0.0" -distributed = {version = ">=2026.1.2,<2026.1.3", optional = true, markers = "extra == \"distributed\""} +distributed = {version = ">=2026.3.0,<2026.3.1", optional = true, markers = "extra == \"distributed\""} fsspec = ">=2021.9.0" jinja2 = {version = ">=2.10.3", optional = true, markers = "extra == \"diagnostics\""} lz4 = {version = ">=4.3.2", optional = true, markers = "extra == \"complete\""} @@ -884,7 +884,7 @@ array = ["numpy (>=1.24)"] complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=16.0)"] dataframe = ["dask[array]", "pandas (>=2.0)", "pyarrow (>=16.0)"] diagnostics = ["bokeh (>=3.1.0)", "jinja2 (>=2.10.3)"] -distributed = ["distributed (>=2026.1.2,<2026.1.3)"] +distributed = ["distributed (>=2026.3.0,<2026.3.1)"] test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"] [[package]] @@ -933,20 +933,20 @@ files = [ [[package]] name = "distributed" -version = "2026.1.2" +version = "2026.3.0" description = "Distributed scheduler for Dask" optional = false python-versions = ">=3.10" groups = ["main"] files = [ - {file = "distributed-2026.1.2-py3-none-any.whl", hash = "sha256:30ccb5587351f50304f6f6e219ea91bc09d88401125779caa8be5253e9d3ecf2"}, - {file = "distributed-2026.1.2.tar.gz", hash = "sha256:8333fa7a34151ed3b4cf1a03136fe1f1799eca706a5e47bdb63022c8795d853b"}, + {file = "distributed-2026.3.0-py3-none-any.whl", hash = "sha256:52518f4b3e6795e87b442e8f57788ba1ddc750c62d0835669c85927280d38f07"}, + {file = "distributed-2026.3.0.tar.gz", hash = "sha256:4a8fc6102fededfbaae45288501276da2297a054d74eb6589f01b087c7f95c26"}, ] [package.dependencies] click = ">=8.0" cloudpickle = ">=3.0.0" -dask = ">=2026.1.2,<2026.1.3" +dask = ">=2026.3.0,<2026.3.1" jinja2 = ">=2.10.3" locket = ">=1.0.0" msgpack = ">=1.0.2" @@ -1346,27 +1346,27 @@ files = [ [[package]] name = "importlib-metadata" -version = "8.7.1" +version = "8.8.0" description = "Read metadata from Python packages" optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" groups = ["main"] files = [ - {file = "importlib_metadata-8.7.1-py3-none-any.whl", hash = "sha256:5a1f80bf1daa489495071efbb095d75a634cf28a8bc299581244063b53176151"}, - {file = "importlib_metadata-8.7.1.tar.gz", hash = "sha256:49fef1ae6440c182052f407c8d34a68f72efc36db9ca90dc0113398f2fdde8bb"}, + {file = "importlib_metadata-8.8.0-py3-none-any.whl", hash = "sha256:f05c37e6b05dc776a1f0bfc39b890634476404ec8449427f7db938e236c4c54e"}, + {file = "importlib_metadata-8.8.0.tar.gz", hash = "sha256:d4ae075d546a9c2db36f0ba957f15f9443c9604e57d0785701621cb7ea2ec5d7"}, ] [package.dependencies] zipp = ">=3.20" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +check = ["pytest-checkdocs (>=2.14)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=3.4)"] perf = ["ipython"] -test = ["flufl.flake8", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] -type = ["mypy (<1.19) ; platform_python_implementation == \"PyPy\"", "pytest-mypy (>=1.0.1)"] +test = ["packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] +type = ["pytest-mypy (>=1.0.1) ; platform_python_implementation != \"PyPy\""] [[package]] name = "iniconfig" @@ -3039,14 +3039,14 @@ six = ">=1.5" [[package]] name = "python-discovery" -version = "1.1.3" +version = "1.2.0" description = "Python interpreter discovery" optional = false python-versions = ">=3.8" groups = ["main"] files = [ - {file = "python_discovery-1.1.3-py3-none-any.whl", hash = "sha256:90e795f0121bc84572e737c9aa9966311b9fde44ffb88a5953b3ec9b31c6945e"}, - {file = "python_discovery-1.1.3.tar.gz", hash = "sha256:7acca36e818cd88e9b2ba03e045ad7e93e1713e29c6bbfba5d90202310b7baa5"}, + {file = "python_discovery-1.2.0-py3-none-any.whl", hash = "sha256:1e108f1bbe2ed0ef089823d28805d5ad32be8e734b86a5f212bf89b71c266e4a"}, + {file = "python_discovery-1.2.0.tar.gz", hash = "sha256:7d33e350704818b09e3da2bd419d37e21e7c30db6e0977bb438916e06b41b5b1"}, ] [package.dependencies] From 62e213a606cc528cf89031bc877ff659d3a02b6c Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Thu, 19 Mar 2026 21:32:41 +0000 Subject: [PATCH 16/44] /version 3.3.1rc3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 204f6813..7a24c432 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc2" +version = "3.3.1rc3" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 9e9ae1d2d55d470a9a2dfa608b9ef9e4be2d8d12 Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Tue, 31 Mar 2026 12:16:50 -0500 Subject: [PATCH 17/44] Fix/hdf handling (#395) Adds capability to recover dimension names for datatree given either GPM DimensionNames attributes or by parsing the ODL StructMetadata.0 present in HDFEOS files. Additionally updates GPM integration test to use correct data. --- CHANGELOG.md | 1 + podaac/subsetter/datatree_subset.py | 3 +- podaac/subsetter/subset.py | 15 +- podaac/subsetter/utils/file_utils.py | 9 +- podaac/subsetter/utils/hdf_utils.py | 241 +++++++++++++++++++++++++++ tests/test_hdf_phony_dims.py | 138 +++++++++++++++ tests/test_subset.py | 139 ++++++++++++++- 7 files changed, 530 insertions(+), 16 deletions(-) create mode 100644 podaac/subsetter/utils/hdf_utils.py create mode 100644 tests/test_hdf_phony_dims.py diff --git a/CHANGELOG.md b/CHANGELOG.md index e602f432..ee141808 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Deprecated ### Removed ### Fixed +- [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Fixes HDF handling with datatree ### Security diff --git a/podaac/subsetter/datatree_subset.py b/podaac/subsetter/datatree_subset.py index 1b9c36bc..da338d21 100755 --- a/podaac/subsetter/datatree_subset.py +++ b/podaac/subsetter/datatree_subset.py @@ -1001,8 +1001,7 @@ def get_ancestor_coords(node: DataTree) -> Set[str]: def update_dataset_with_time(og_ds, time_name="timeMidScan", group_path=None): """ - Update dataset dimensions based on 'DimensionNames' attributes and compute a time variable - if not present, using values from the dataset. + Compute a time variable if not present, using values from the dataset. """ ds = og_ds.copy() diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index 6a951bf1..031340f0 100755 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -40,9 +40,11 @@ from podaac.subsetter.utils import file_utils from podaac.subsetter.utils import variables_utils from podaac.subsetter.vertical_subset import vertical_subset +from podaac.subsetter.utils import hdf_utils SERVICE_NAME = 'l2ss-py' +_HDF_EXTENSIONS: list[str] = ['.hdf5', '.he5', '.h5', '.hdf'] def subset_with_shapefile_multi(dataset: xr.Dataset, lat_var_names: List[str], @@ -329,10 +331,8 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, } with xr.open_datatree(file_to_subset, **args) as dataset: - if '.HDF5' == file_extension: - for group in dataset.groups: - if "ScanTime" in group: - hdf_type = 'GPM' + if file_extension.lower() in _HDF_EXTENSIONS: + hdf_type = file_utils.get_hdf_type(dataset) if min_time or max_time: fill_value_f8 = nc.default_fillvals.get('f8') @@ -398,7 +398,8 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, with xr.open_datatree(file_to_subset, **args) as dataset: - hdf_type = file_utils.get_hdf_type(dataset) + if hdf_type: + dataset = hdf_utils.rename_phony_dims(dataset) lat_var_names, lon_var_names, time_var_names = coordinate_utils.get_coordinate_variable_names( dataset=dataset, @@ -407,7 +408,9 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, time_var_names=time_var_names ) - if '.HDF5' == file_extension: + # note(ocs): I believe this only applies to GPM, but checking + # against general hdf until certain + if hdf_type: new_time_var_names = [] for group in dataset.groups: if "ScanTime" in group: diff --git a/podaac/subsetter/utils/file_utils.py b/podaac/subsetter/utils/file_utils.py index 6808989a..ed5ae44b 100644 --- a/podaac/subsetter/utils/file_utils.py +++ b/podaac/subsetter/utils/file_utils.py @@ -74,14 +74,21 @@ def test_access_sst_dtime_values(nc_dataset): def get_hdf_type(tree: DataTree) -> Optional[str]: """ - Determine the HDF type (OMI or MLS) from a DataTree object. + Determine the HDF type (OMI, MLS, or GPM) from a DataTree object. """ try: + # GPM + for group in tree.groups: + if "ScanTime" in group: + return 'GPM' + + # try to get types from instrument name additional_attrs = tree['/HDFEOS/ADDITIONAL/FILE_ATTRIBUTES'] if additional_attrs is not None and 'InstrumentName' in additional_attrs.attrs: instrument = additional_attrs.attrs['InstrumentName'] if isinstance(instrument, bytes): instrument = instrument.decode("utf-8") + else: return None if 'OMI' in instrument: diff --git a/podaac/subsetter/utils/hdf_utils.py b/podaac/subsetter/utils/hdf_utils.py new file mode 100644 index 00000000..e2b83c9c --- /dev/null +++ b/podaac/subsetter/utils/hdf_utils.py @@ -0,0 +1,241 @@ +import re +from collections import defaultdict +import warnings + +import numpy as np +import xarray as xr +from xarray import DataTree + + +_PHONY_RE = re.compile(r"^phony_dim_(\d+)$") + + +def _is_phony(dim: str) -> bool: + return _PHONY_RE.match(dim) is not None + + +def _phony_index(dim: str) -> int: + m = _PHONY_RE.match(dim) + return int(m.group(1)) if m else -1 + + +def rename_phony_dims(dt: DataTree) -> DataTree: + """ + Return a new DataTree with all phony_dim_N dimensions renamed to + meaningful names. The three strategies are tried in priority order; + the first one that produces a non-empty mapping is used. + + Parameters + ---------- + dt : DataTree + Tree loaded from an HDF/HDF-EOS5 file + + Returns + ------- + DataTree + A new tree with renamed dimensions. + """ + mapping = _mapping_from_dimension_names(dt) + + if not mapping: + mapping = _mapping_from_struct_metadata(dt) + + if not mapping: + return dt + + return _apply_mapping(dt, mapping) + + +def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: + """ + Iterate every variable in every group. If a variable carries a + DimensionNames attribute (comma-separated list of real dim names), + zip those names against the variable's current (phony) dim names to + build the global mapping. + + A variable with dims (phony_dim_0, phony_dim_1) and attribute + DimensionNames = "nTimes,nXtrack" results in {phony_dim_0: nTimes, + phony_dim_1: nXtrack} + """ + mapping: dict[str, str] = {} + + for node in dt.subtree: + ds = node.ds + if ds is None: + continue + for var_name, da in ds.items(): + dim_names_attr = da.attrs.get("DimensionNames") + if dim_names_attr is None: + continue + + real_names = [n.strip() for n in dim_names_attr.split(",")] + + # if attribute shapes mismatch, then continue + if len(real_names) != len(da.dims): + continue + + for phony, real in zip(da.dims, real_names): + if not _is_phony(phony): + continue + existing = mapping.get(phony) + if existing is not None and existing != real: + # if two variables disagree on what this phony dim + # should be called then keep the first assignment and warn. + warnings.warn( + f"Conflicting DimensionNames for {phony!r}: " + f"{existing!r} vs {real!r}. Keeping {existing!r}." + ) + else: + mapping[phony] = real + + return mapping + + +def _mapping_from_struct_metadata(dt: DataTree) -> dict[str, str]: + """ + Locate the StructMetadata.0 variable (typically at /HDFEOS + INFORMATION), parse its ODL (Object Description Language) content + to extract every named dimension and its size, then match those + against the phony dims in the tree by size. + + Returns an empty dict if no StructMetadata.0 is found or parsing + fails. + """ + struct_text = _find_struct_metadata(dt) + if not struct_text: + return {} + + # parse named dimensions: {dim_name: size} + named_dims = _parse_odl_dimensions(struct_text) + if not named_dims: + return {} + + # Build size -> name lookup. If two dims share a size we keep both and + # later rely on positional ordering within each group. + size_to_names: dict[int, list[str]] = defaultdict(list) + for name, size in named_dims.items(): + size_to_names[size].append(name) + + return _match_phony_to_named(dt, size_to_names, named_dims) + + +def _find_struct_metadata(dt: DataTree) -> str | None: + """Return the decoded text of StructMetadata.0 if present anywhere + in the tree. + """ + for node in dt.subtree: + ds = node.ds + if ds is None: + continue + for var_name in ds.data_vars: + if "StructMetadata" in var_name: + raw = ds[var_name].values + # may be bytes, numpy bytes_, or already a string + if isinstance(raw, (bytes, np.bytes_)): + return raw.decode("utf-8", errors="replace") + if hasattr(raw, "item"): + val = raw.item() + if isinstance(val, (bytes, np.bytes_)): + return val.decode("utf-8", errors="replace") + return str(val) + return str(raw) + return None + + +def _parse_odl_dimensions(odl_text: str) -> dict[str, int]: + """ + Extract all ``DimensionName`` / ``Size`` pairs from an ODL + metadata block. + + ODL blocks look like + + OBJECT=Dimension_1 + DimensionName="nTimes" + Size=1496 + END_OBJECT=Dimension_1 + """ + named_dims: dict[str, int] = {} + + # split on END_OBJECT boundaries so we can parse each object block + blocks = re.split(r"END_OBJECT\s*=\s*\w+", odl_text) + for block in blocks: + dim_name_match = re.search(r'DimensionName\s*=\s*"([^"]+)"', block) + size_match = re.search(r"\bSize\s*=\s*(\d+)", block) + if dim_name_match and size_match: + name = dim_name_match.group(1).strip() + size = int(size_match.group(1)) + named_dims[name] = size + + return named_dims + + +def _match_phony_to_named( + dt: DataTree, + size_to_names: dict[int, list[str]], + named_dims: dict[str, int], +) -> dict[str, str]: + """ + For every phony dim in the tree, look up its size in ``size_to_names``. + + - If only one real name has that size, the mapping is unambiguous. + - If multiple real names share the same size, we use the *position* of + the phony dim within its group's sorted dimension list to pick among + the candidates (ordered as they appear in the ODL block). + """ + # ordered list of all named dims so we can use index as a tiebreaker + ordered_named = list(named_dims.keys()) + + mapping: dict[str, str] = {} + + for node in dt.subtree: + ds = node.ds + if ds is None: + continue + + # phony dims in this group sorted by their index (N in + # phony_dim_N) + local_phonies = sorted([d for d in ds.dims if _is_phony(d)], key=_phony_index) + + for phony in local_phonies: + size = ds.dims[phony] + candidates = size_to_names.get(size, []) + if not candidates: + continue + if len(candidates) == 1: + mapping[phony] = candidates[0] + else: + # use the position of this phony dim among same-size dims in + # this group to index into the ordered candidate list. + same_size_in_group = [p for p in local_phonies if ds.dims[p] == size] + pos = same_size_in_group.index(phony) + # sort candidates by their order in the odl block + ordered_candidates = sorted( + candidates, key=lambda n: ordered_named.index(n) + ) + if pos < len(ordered_candidates): + mapping[phony] = ordered_candidates[pos] + + return mapping + + +def _apply_mapping(dt: DataTree, mapping: dict[str, str]) -> DataTree: + """ + Walk the tree, apply rename_dims to every group dataset that contains + any of the phony dims in ``mapping``, then reconstruct the entire tree + from a flat path -> dataset dict using DataTree.from_dict. + + This avoids any direct node copying and is the idiomatic way to rebuild + a modified DataTree. + """ + path_to_ds: dict[str, xr.Dataset] = {} + + for node in dt.subtree: + ds = node.ds if node.ds is not None else xr.Dataset() + + local_mapping = {k: v for k, v in mapping.items() if k in ds.dims} + if local_mapping: + ds = ds.rename_dims(local_mapping) + + path_to_ds[node.path] = ds + + return DataTree.from_dict(path_to_ds) diff --git a/tests/test_hdf_phony_dims.py b/tests/test_hdf_phony_dims.py new file mode 100644 index 00000000..f12257a2 --- /dev/null +++ b/tests/test_hdf_phony_dims.py @@ -0,0 +1,138 @@ +import xarray as xr +from xarray import DataTree + +from podaac.subsetter.utils.hdf_utils import rename_phony_dims + + +def make_tree(groups: dict[str, xr.Dataset]) -> DataTree: + return DataTree.from_dict(groups) + + +def phony(n: int) -> str: + return f"phony_dim_{n}" + + +def test_dimension_names_single_group(): + da = xr.DataArray( + data=[[1, 2], [3, 4], [5, 6]], + dims=[phony(0), phony(1)], + attrs={"DimensionNames": "nTimes,nXtrack"}, + ) + dt = make_tree({"/": xr.Dataset({"var": da})}) + result = rename_phony_dims(dt) + assert "nTimes" in result.ds.dims + assert "nXtrack" in result.ds.dims + + +def test_dimension_names_match_across_groups(): + da_data = xr.DataArray( + [[1.0, 2.0]], + dims=[phony(0), phony(1)], + attrs={"DimensionNames": "nTimes,nXtrack"}, + ) + da_geo = xr.DataArray( + [[3.0, 4.0]], + dims=[phony(2), phony(3)], + attrs={"DimensionNames": "nTimes,nXtrack"}, + ) + dt = make_tree( + { + "/Data Fields": xr.Dataset({"ColumnAmount": da_data}), + "/Geolocation Fields": xr.Dataset({"Latitude": da_geo}), + } + ) + result = rename_phony_dims(dt) + data_dims = result["/Data Fields"].ds["ColumnAmount"].dims + geo_dims = result["/Geolocation Fields"].ds["Latitude"].dims + assert data_dims == geo_dims == ("nTimes", "nXtrack") + + +def test_dimension_names_no_phony_dims_unchanged(): + da = xr.DataArray([[1.0]], dims=["nTimes", "nXtrack"]) + dt = make_tree({"/": xr.Dataset({"var": da})}) + result = rename_phony_dims(dt) + assert list(result.ds.dims) == ["nTimes", "nXtrack"] + + +def test_size_matching_different_sizes_get_different_names(): + da = xr.DataArray( + [[[1.0] * 4] * 60] * 1496, + dims=[phony(0), phony(1), phony(2)], + ) + dt = make_tree({"/HDFEOS/SWATHS/S/Data Fields": xr.Dataset({"a": da})}) + result = rename_phony_dims(dt) + dims = result["/HDFEOS/SWATHS/S/Data Fields"].ds["a"].dims + assert len(set(dims)) == 3 + + +def test_dimension_names_independent_swaths_do_not_share_dims(): + da1 = xr.DataArray( + [[1.0, 2.0]], + dims=[phony(0), phony(1)], + attrs={"DimensionNames": "nTimesA,nXtrackA"}, + ) + da2 = xr.DataArray( + [[3.0, 4.0]], + dims=[phony(2), phony(3)], + attrs={"DimensionNames": "nTimesB,nXtrackB"}, + ) + dt = make_tree( + { + "/HDFEOS/SWATHS/SwathA/Data Fields": xr.Dataset({"a": da1}), + "/HDFEOS/SWATHS/SwathB/Data Fields": xr.Dataset({"b": da2}), + } + ) + result = rename_phony_dims(dt) + dims_a = result["/HDFEOS/SWATHS/SwathA/Data Fields"].ds["a"].dims + dims_b = result["/HDFEOS/SWATHS/SwathB/Data Fields"].ds["b"].dims + assert dims_a == ("nTimesA", "nXtrackA") + assert dims_b == ("nTimesB", "nXtrackB") + assert set(dims_a).isdisjoint(set(dims_b)) + + +def test_struct_metadata_renames_dims(): + odl = ( + "GROUP=SwathStructure\n" + "GROUP=SWATH_1\n" + "GROUP=DimensionMap\n" + "END_GROUP=DimensionMap\n" + "GROUP=Dimension\n" + "OBJECT=Dimension_1\n" + 'DimensionName="nTimes"\n' + "Size=1496\n" + "END_OBJECT=Dimension_1\n" + "OBJECT=Dimension_2\n" + 'DimensionName="nXtrack"\n' + "Size=60\n" + "END_OBJECT=Dimension_2\n" + "END_GROUP=Dimension\n" + "END_GROUP=SWATH_1\n" + "END_GROUP=SwathStructure\n" + ) + struct_da = xr.DataArray(odl) + da = xr.DataArray( + [[1.0] * 60] * 1496, + dims=[phony(0), phony(1)], + ) + dt = make_tree( + { + "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), + "/HDFEOS/SWATHS/MySWATH/Data Fields": xr.Dataset({"ColumnAmount": da}), + } + ) + result = rename_phony_dims(dt) + dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims + assert dims == ("nTimes", "nXtrack") + + +def test_no_phony_dims_returns_unchanged(): + da = xr.DataArray([[1.0]], dims=["x", "y"]) + dt = make_tree({"/": xr.Dataset({"var": da})}) + result = rename_phony_dims(dt) + assert list(result.ds["var"].dims) == ["x", "y"] + + +def test_empty_tree_does_not_raise(): + dt = make_tree({"/": xr.Dataset()}) + result = rename_phony_dims(dt) + assert result is not None diff --git a/tests/test_subset.py b/tests/test_subset.py index 332c7402..299dccb0 100755 --- a/tests/test_subset.py +++ b/tests/test_subset.py @@ -1646,23 +1646,148 @@ def test_get_unique_groups(): assert expected_groups_single == unique_groups_single assert expected_diff_counts_single == diff_counts_single -def test_subset_gpm_compute_new_var_data(data_dir, subset_output_dir, request): +@pytest.fixture(scope="session") +def fake_gpm_file(tmp_path_factory): + """ + Create fake gpm data at run time which mirrors structure and behavior of data pulled from CMR + + Will create data which mirrors how libnetcdf resolves dimension + names with when reading data from CMR. Dimension names are given + phony between groups even if dimension is shared. E.g. all data + variables will share the same dimensions "nTimes,nXtrack", but + will be given phony_dim names as seen below + + Group: + /HDFEOS/SWATHS/GPM_DPR/Data Fields + Dimensions: (phony_dim_0: 10, phony_dim_1: 5) + Dimensions without coordinates: phony_dim_0, phony_dim_1 + Data variables: + precipRateNearSurface (phony_dim_0, phony_dim_1) + Group: /HDFEOS/SWATHS/GPM_DPR/Geolocation Fields + Dimensions: (phony_dim_2: 10, phony_dim_3: 5) + Dimensions without coordinates: phony_dim_2, phony_dim_3 + Data variables: + Latitude (phony_dim_2, phony_dim_3) + Longitude (phony_dim_2, phony_dim_3) + + + """ + filepath = tmp_path_factory.mktemp("data") / "fake_gpm.HDF5" + + with h5py.File(filepath, "w") as f: + + # mirror the real gpm HDFEOS group structure + data_fields = f.require_group("HDFEOS/SWATHS/GPM_DPR/Data Fields") + geo_fields = f.require_group("HDFEOS/SWATHS/GPM_DPR/Geolocation Fields") + scan_time = f.require_group("HDFEOS/SWATHS/GPM_DPR/ScanTime") + + info = f.require_group("HDFEOS INFORMATION") + + n_times = 10 + n_xtrack = 5 + + # write data fields variable with dimensionnames attr as gpm does + precip = data_fields.create_dataset( + "precipRateNearSurface", + data=np.random.rand(n_times, n_xtrack).astype(np.float32), + ) + precip.attrs["DimensionNames"] = "nTimes,nXtrack" + precip.attrs["Units"] = "mm/hr" + precip.attrs["MissingValue"] = -9999.9 + + # geolocation fields variables + lat = geo_fields.create_dataset( + "Latitude", + data=np.linspace(-90, 90, n_times * n_xtrack) + .reshape(n_times, n_xtrack) + .astype(np.float32), + ) + lat.attrs["DimensionNames"] = "nTimes,nXtrack" + lat.attrs["Units"] = "degrees_north" + + lon = geo_fields.create_dataset( + "Longitude", + data=np.linspace(-180, 180, n_times * n_xtrack) + .reshape(n_times, n_xtrack) + .astype(np.float32), + ) + lon.attrs["DimensionNames"] = "nTimes,nXtrack" + lon.attrs["Units"] = "degrees_east" + + # scantime variables + year_data = np.full(n_times, 2021, dtype=np.float32) + month_data = np.full(n_times, 5, dtype=np.float32) + day_data = np.full(n_times, 30, dtype=np.float32) + hour_data = np.full(n_times, 9, dtype=np.float32) + minute_data = np.full(n_times, 57, dtype=np.float32) + second_data = np.full(n_times, 0.0, dtype=np.float32) + milli_data = np.full(n_times, 0.0, dtype=np.float32) + doy_data = np.full(n_times, 150, dtype=np.float32) + sod_data = np.full(n_times, 35820.0, dtype=np.float64) + + for name, data in [ + ("Year", year_data), + ("Month", month_data), + ("DayOfMonth", day_data), + ("Hour", hour_data), + ("Minute", minute_data), + ("Second", second_data), + ("MilliSecond", milli_data), + ("DayOfYear", doy_data), + ("SecondOfDay", sod_data), + ]: + ds = scan_time.create_dataset(name, data=data) + ds.attrs["DimensionNames"] = "nTimes" + + # structmetadata + odl = ( + "GROUP=SwathStructure\n" + "GROUP=SWATH_1\n" + "SwathName=\"GPM_DPR\"\n" + "GROUP=Dimension\n" + "OBJECT=Dimension_1\n" + "DimensionName=\"nTimes\"\n" + f"Size={n_times}\n" + "END_OBJECT=Dimension_1\n" + "OBJECT=Dimension_2\n" + "DimensionName=\"nXtrack\"\n" + f"Size={n_xtrack}\n" + "END_OBJECT=Dimension_2\n" + "END_GROUP=Dimension\n" + "END_GROUP=SWATH_1\n" + "END_GROUP=SwathStructure\n" + ) + info.create_dataset("StructMetadata.0", data=odl) + + return filepath + + +def test_subset_gpm_compute_new_var_data(fake_gpm_file, data_dir, subset_output_dir, request): """Test GPM files that have scantime variable to compute the time for seconds since 1980-01-06""" - - gpm_dir = join(data_dir, 'GPM') - gpm_file = 'GPM_test_file_2.HDF5' # Keep the correct file name + + with xr.open_datatree(fake_gpm_file) as dtree: + for node in dtree.subtree: + ds = node.ds + if isinstance(ds, xr.Dataset): + dims = ds.dims.keys() + + # ensure that test data is being read by netcdf backend with phony dim names + # like we expect from GPM data from CMR + for dim in dims: + assert 'phony' in dim, f"Unexpected non 'phony' dimension found: {dim}" + # Correct bbox with (min_lon, min_lat) and (max_lon, max_lat) bbox = np.array(((-180, 90), (-90, 90))) - output_file = f"gpm_test_{gpm_file}" # Keep the extension + output_file = f"gpm_test_subset.HDF5" # Keep the extension subset_output_file = join(subset_output_dir, output_file) subset.subset( - file_to_subset=join(gpm_dir, gpm_file), + file_to_subset=fake_gpm_file, bbox=bbox, output_file=subset_output_file - ) + ) # Open subsetted file using xarray-datatree dtree = xr.open_datatree(subset_output_file) From eaf39b960002a8525f320b098eadf7576e29d127 Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Tue, 31 Mar 2026 12:48:27 -0500 Subject: [PATCH 18/44] chore(pylint): resolve pylint errors that surfaced on build (#410) --- podaac/subsetter/utils/hdf_utils.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/podaac/subsetter/utils/hdf_utils.py b/podaac/subsetter/utils/hdf_utils.py index e2b83c9c..c5dd4254 100644 --- a/podaac/subsetter/utils/hdf_utils.py +++ b/podaac/subsetter/utils/hdf_utils.py @@ -1,12 +1,19 @@ +""" +=============== +hdf_utils.py +=============== + +Utility functions for handling HDF files, and dimension recovery +""" + import re -from collections import defaultdict import warnings +from collections import defaultdict import numpy as np import xarray as xr from xarray import DataTree - _PHONY_RE = re.compile(r"^phony_dim_(\d+)$") @@ -63,7 +70,7 @@ def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: ds = node.ds if ds is None: continue - for var_name, da in ds.items(): + for _, da in ds.items(): dim_names_attr = da.attrs.get("DimensionNames") if dim_names_attr is None: continue @@ -209,9 +216,7 @@ def _match_phony_to_named( same_size_in_group = [p for p in local_phonies if ds.dims[p] == size] pos = same_size_in_group.index(phony) # sort candidates by their order in the odl block - ordered_candidates = sorted( - candidates, key=lambda n: ordered_named.index(n) - ) + ordered_candidates = sorted(candidates, key=ordered_named.index) if pos < len(ordered_candidates): mapping[phony] = ordered_candidates[pos] From ba46ff683313c22aa3c03319a12a8c61d0d947ce Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Tue, 31 Mar 2026 12:59:02 -0500 Subject: [PATCH 19/44] chore(flake8) (#411) --- podaac/subsetter/subset.py | 1 + 1 file changed, 1 insertion(+) diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index 031340f0..01f24708 100755 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -46,6 +46,7 @@ _HDF_EXTENSIONS: list[str] = ['.hdf5', '.he5', '.h5', '.hdf'] + def subset_with_shapefile_multi(dataset: xr.Dataset, lat_var_names: List[str], lon_var_names: List[str], From 4fe6e17f0422563b8d5c10191fe52b47873510c5 Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Tue, 31 Mar 2026 14:08:34 -0700 Subject: [PATCH 20/44] poetry update (#412) --- poetry.lock | 1058 ++++++++++++++++++++++++++------------------------- 1 file changed, 550 insertions(+), 508 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2f5d7eec..9db47d19 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,14 +14,14 @@ files = [ [[package]] name = "anyio" -version = "4.12.1" +version = "4.13.0" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" groups = ["main"] files = [ - {file = "anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c"}, - {file = "anyio-4.12.1.tar.gz", hash = "sha256:41cfcc3a4c85d3f05c932da7c26d0201ac36f72abd4435ba90d0464a3ffed703"}, + {file = "anyio-4.13.0-py3-none-any.whl", hash = "sha256:08b310f9e24a9594186fd75b4f73f4a4152069e3853f1ed8bfbf58369f4ad708"}, + {file = "anyio-4.13.0.tar.gz", hash = "sha256:334b70e641fd2221c1505b3890c69882fe4a2df910cba14d97019b90b24439dc"}, ] [package.dependencies] @@ -29,7 +29,7 @@ idna = ">=2.8" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -trio = ["trio (>=0.31.0) ; python_version < \"3.10\"", "trio (>=0.32.0) ; python_version >= \"3.10\""] +trio = ["trio (>=0.32.0)"] [[package]] name = "astroid" @@ -45,14 +45,14 @@ files = [ [[package]] name = "attrs" -version = "25.4.0" +version = "26.1.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"}, - {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"}, + {file = "attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309"}, + {file = "attrs-26.1.0.tar.gz", hash = "sha256:d03ceb89cb322a8fd706d4fb91940737b6642aa36998fe130a9bc96c985eff32"}, ] [[package]] @@ -72,14 +72,14 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)" [[package]] name = "bokeh" -version = "3.8.2" +version = "3.9.0" description = "Interactive plots and applications in the browser from Python" optional = false python-versions = ">=3.10" groups = ["main"] files = [ - {file = "bokeh-3.8.2-py3-none-any.whl", hash = "sha256:5e2c0d84f75acb25d60efb9e4d2f434a791c4639b47d685534194c4e07bd0111"}, - {file = "bokeh-3.8.2.tar.gz", hash = "sha256:8e7dcacc21d53905581b54328ad2705954f72f2997f99fc332c1de8da53aa3cc"}, + {file = "bokeh-3.9.0-py3-none-any.whl", hash = "sha256:b252bfb16a505f0e0c57d532d0df308ae1667235bafc622aa9441fe9e7c5ce4a"}, + {file = "bokeh-3.9.0.tar.gz", hash = "sha256:775219714a8496973ddbae16b1861606ba19fe670a421e4d43267b41148e07a3"}, ] [package.dependencies] @@ -88,7 +88,6 @@ Jinja2 = ">=2.9" narwhals = ">=1.13" numpy = ">=1.16" packaging = ">=16.8" -pandas = ">=1.2" pillow = ">=7.1.0" PyYAML = ">=3.10" tornado = {version = ">=6.2", markers = "sys_platform != \"emscripten\""} @@ -96,19 +95,19 @@ xyzservices = ">=2021.9.1" [[package]] name = "boto3" -version = "1.42.56" +version = "1.42.79" description = "The AWS SDK for Python" optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - 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"sha256:fb8c01fe6ab13b9b7cdb46892b99b1d66754e1d7ab8e542e865ec13f526b5351"}, ] [package.dependencies] @@ -4025,14 +4067,14 @@ test = ["pytest", "pytest-cov"] [[package]] name = "xyzservices" -version = "2025.11.0" +version = "2026.3.0" description = "Source of XYZ tiles providers" optional = false python-versions = ">=3.8" groups = ["main"] files = [ - {file = "xyzservices-2025.11.0-py3-none-any.whl", hash = "sha256:de66a7599a8d6dad63980b77defd1d8f5a5a9cb5fc8774ea1c6e89ca7c2a3d2f"}, - {file = "xyzservices-2025.11.0.tar.gz", hash = "sha256:2fc72b49502b25023fd71e8f532fb4beddbbf0aa124d90ea25dba44f545e17ce"}, + {file = "xyzservices-2026.3.0-py3-none-any.whl", hash = "sha256:503183d4b322bfebc3c50cdd21192aa3e81e36c5efbf9133d54ae82143e0576b"}, + {file = "xyzservices-2026.3.0.tar.gz", hash = "sha256:d226866a5d8e9fef337034d8da37a8298f0a1d9d1489b4018e69579eb321fea4"}, ] [[package]] From 868ae014e73ff1bd56856d18cd646dbfa5c70d72 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 31 Mar 2026 21:31:10 +0000 Subject: [PATCH 21/44] /version 3.4.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4a281634..e655cdfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a0" +version = "3.4.0a1" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 44e2e70a00e59573a8a88c92509755ec6cf77d7f Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Tue, 31 Mar 2026 14:38:25 -0700 Subject: [PATCH 22/44] fix develop version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e655cdfe..0a73559c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a1" +version = "3.4.0a2" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From c65855914a97a62628c67531cb1692e2ad1367c5 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 31 Mar 2026 22:00:01 +0000 Subject: [PATCH 23/44] /version 3.4.0a3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0a73559c..4ebf6697 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a2" +version = "3.4.0a3" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 6f94837445ff12b4a33bcaf97fcef9d9c4c3dacf Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 31 Mar 2026 22:37:22 +0000 Subject: [PATCH 24/44] /version 3.3.1rc4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7a24c432..70c242f5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc3" +version = "3.3.1rc4" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 9cd2dc99313b9dd0c5f239846eabc945bacbd28f Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:23:09 -0400 Subject: [PATCH 25/44] Resolve dimension name recovery for multiple swaths with same dim names, but different sizes (#413) Some collections like OMPIXCOR_003 contain multiple swaths with the same dimension names assigned to variables, but with different sizes. This would throw off the current dimension mapping implementation. This updates ODL parser to track multiple dim sizes for a given dimension and parse on a scope basis instead of just assuming single swath group. --- CHANGELOG.md | 1 + podaac/subsetter/utils/hdf_utils.py | 154 +++++++++++++++++++--------- tests/test_hdf_phony_dims.py | 116 ++++++++++++++++++++- 3 files changed, 217 insertions(+), 54 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ee141808..3d0c9959 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed ### Fixed - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Fixes HDF handling with datatree +- [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to handle multi swath/grid collections ### Security diff --git a/podaac/subsetter/utils/hdf_utils.py b/podaac/subsetter/utils/hdf_utils.py index c5dd4254..823175de 100644 --- a/podaac/subsetter/utils/hdf_utils.py +++ b/podaac/subsetter/utils/hdf_utils.py @@ -29,8 +29,10 @@ def _phony_index(dim: str) -> int: def rename_phony_dims(dt: DataTree) -> DataTree: """ Return a new DataTree with all phony_dim_N dimensions renamed to - meaningful names. The three strategies are tried in priority order; - the first one that produces a non-empty mapping is used. + meaningful names. First check if `DimensionNames` is present as + attributes for each variable otherwise check for `StructMeta.0` + and assuming an HDFEOS structure. the first one that produces a + non-empty mapping is used. Parameters ---------- @@ -98,34 +100,6 @@ def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: return mapping -def _mapping_from_struct_metadata(dt: DataTree) -> dict[str, str]: - """ - Locate the StructMetadata.0 variable (typically at /HDFEOS - INFORMATION), parse its ODL (Object Description Language) content - to extract every named dimension and its size, then match those - against the phony dims in the tree by size. - - Returns an empty dict if no StructMetadata.0 is found or parsing - fails. - """ - struct_text = _find_struct_metadata(dt) - if not struct_text: - return {} - - # parse named dimensions: {dim_name: size} - named_dims = _parse_odl_dimensions(struct_text) - if not named_dims: - return {} - - # Build size -> name lookup. If two dims share a size we keep both and - # later rely on positional ordering within each group. - size_to_names: dict[int, list[str]] = defaultdict(list) - for name, size in named_dims.items(): - size_to_names[size].append(name) - - return _match_phony_to_named(dt, size_to_names, named_dims) - - def _find_struct_metadata(dt: DataTree) -> str | None: """Return the decoded text of StructMetadata.0 if present anywhere in the tree. @@ -149,31 +123,109 @@ def _find_struct_metadata(dt: DataTree) -> str | None: return None -def _parse_odl_dimensions(odl_text: str) -> dict[str, int]: +def _find_scope_roots(dt: DataTree) -> list[DataTree]: """ - Extract all ``DimensionName`` / ``Size`` pairs from an ODL - metadata block. + Return the immediate children of /HDFEOS/SWATHS or /HDFEOS/GRIDS. + These represent individual swaths / grids and are the correct scopes + within which phony dims should be unified. + """ + candidates = [] + for node in dt.subtree: + path = node.path.rstrip("/").casefold() + if path in ( + "/hdfeos/swaths", + "/hdfeos/grids", + ): + candidates.extend(node.children.values()) + return candidates + - ODL blocks look like +def _parse_odl_scope_dimensions(odl_text: str) -> dict[str, dict[str, int]]: + """ + Parse the ODL block and return a per-scope dimension mapping: + {scope_name: {dim_name: size}} - OBJECT=Dimension_1 - DimensionName="nTimes" - Size=1496 - END_OBJECT=Dimension_1 + Handles both SwathStructure (SWATH_N / SwathName) and GridStructure + (GRID_N / GridName) blocks. Each scope is parsed independently so that + two scopes sharing a dimension name but with different sizes never + overwrite each other. """ - named_dims: dict[str, int] = {} - - # split on END_OBJECT boundaries so we can parse each object block - blocks = re.split(r"END_OBJECT\s*=\s*\w+", odl_text) - for block in blocks: - dim_name_match = re.search(r'DimensionName\s*=\s*"([^"]+)"', block) - size_match = re.search(r"\bSize\s*=\s*(\d+)", block) - if dim_name_match and size_match: - name = dim_name_match.group(1).strip() - size = int(size_match.group(1)) - named_dims[name] = size - - return named_dims + result: dict[str, dict[str, int]] = {} + + # split on any SWATH_N or GRID_N end-group boundary + scope_blocks = re.split(r"END_GROUP\s*=\s*(?:SWATH|GRID)_\d+", odl_text) + + for block in scope_blocks: + name_match = re.search(r'(?:SwathName|GridName)\s*=\s*"([^"]+)"', block) + if not name_match: + continue + scope_name = name_match.group(1).strip() + + dim_group_match = re.search( + r"GROUP\s*=\s*Dimension(.+?)END_GROUP\s*=\s*Dimension", + block, + re.DOTALL, + ) + if not dim_group_match: + continue + + named_dims: dict[str, int] = {} + for obj_block in re.split( + r"END_OBJECT\s*=\s*Dimension_\d+", dim_group_match.group(1) + ): + dim_name_match = re.search(r'DimensionName\s*=\s*"([^"]+)"', obj_block) + size_match = re.search(r"\bSize\s*=\s*(\d+)", obj_block) + if dim_name_match and size_match: + named_dims[dim_name_match.group(1).strip()] = int(size_match.group(1)) + + if named_dims: + result[scope_name] = named_dims + + return result + + +def _mapping_from_struct_metadata(dt: DataTree) -> dict[str, str]: + """ + Locate the StructMetadata.0 variable (typically at /HDFEOS + INFORMATION), parse its ODL (Object Description Language) content + to extract every named dimension and its size, then match those + against the phony dims in the tree by size. + + Returns an empty dict if no StructMetadata.0 is found or parsing + fails. + """ + struct_text = _find_struct_metadata(dt) + if not struct_text: + return {} + + swath_dims = _parse_odl_scope_dimensions(struct_text) + if not swath_dims: + return {} + + mapping: dict[str, str] = {} + + scope_roots = _find_scope_roots(dt) + if not scope_roots: + scope_roots = [dt] + + for scope_root in scope_roots: + # extract the swath name from the path, e.g. + # "/HDFEOS/SWATHS/OMI Ground Pixel Corners UV-1" -> "OMI Ground Pixel Corners UV-1" + swath_name = scope_root.path.rstrip("/").split("/")[-1] + named_dims = swath_dims.get(swath_name) + + if not named_dims: + # swath name not found in ODL + continue + + size_to_names: dict[int, list[str]] = defaultdict(list) + for name, size in named_dims.items(): + size_to_names[size].append(name) + + scope_mapping = _match_phony_to_named(scope_root, size_to_names, named_dims) + mapping.update(scope_mapping) + + return mapping def _match_phony_to_named( diff --git a/tests/test_hdf_phony_dims.py b/tests/test_hdf_phony_dims.py index f12257a2..fedcdd6a 100644 --- a/tests/test_hdf_phony_dims.py +++ b/tests/test_hdf_phony_dims.py @@ -1,7 +1,6 @@ import xarray as xr -from xarray import DataTree - from podaac.subsetter.utils.hdf_utils import rename_phony_dims +from xarray import DataTree def make_tree(groups: dict[str, xr.Dataset]) -> DataTree: @@ -94,8 +93,44 @@ def test_struct_metadata_renames_dims(): odl = ( "GROUP=SwathStructure\n" "GROUP=SWATH_1\n" + 'SwathName="MySWATH\n"' + "GROUP=Dimension\n" + "OBJECT=Dimension_1\n" + 'DimensionName="nTimes"\n' + "Size=1496\n" + "END_OBJECT=Dimension_1\n" + "OBJECT=Dimension_2\n" + 'DimensionName="nXtrack"\n' + "Size=60\n" + "END_OBJECT=Dimension_2\n" + "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "END_GROUP=SWATH_1\n" + "END_GROUP=SwathStructure\n" + ) + struct_da = xr.DataArray(odl) + da = xr.DataArray( + [[1.0] * 60] * 1496, + dims=[phony(0), phony(1)], + ) + dt = make_tree( + { + "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), + "/HDFEOS/SWATHS/MySWATH/Data Fields": xr.Dataset({"ColumnAmount": da}), + } + ) + result = rename_phony_dims(dt) + dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims + assert dims == ("nTimes", "nXtrack") + + +def test_struct_metadata_renames_dims_multi_swath(): + # note(ocs): this type of multi swatch structure occurs in collections like OMPIXCOR_003 + odl = ( + "GROUP=SwathStructure\n" + "GROUP=SWATH_1\n" + 'SwathName="MySWATH\n"' "GROUP=Dimension\n" "OBJECT=Dimension_1\n" 'DimensionName="nTimes"\n' @@ -106,7 +141,24 @@ def test_struct_metadata_renames_dims(): "Size=60\n" "END_OBJECT=Dimension_2\n" "END_GROUP=Dimension\n" + "GROUP=DimensionMap\n" + "END_GROUP=DimensionMap\n" "END_GROUP=SWATH_1\n" + # start of swath 2 + "GROUP=SWATH_2\n" + 'SwathName="MySWATH2\n"' + "GROUP=Dimension\n" + "OBJECT=Dimension_1\n" + 'DimensionName="nTimes"\n' + "Size=1496\n" + "END_OBJECT=Dimension_1\n" + "OBJECT=Dimension_2\n" + 'DimensionName="nXtrack"\n' + # this nXtrack size is different in swath 2 + "Size=30\n" + "END_OBJECT=Dimension_2\n" + "END_GROUP=Dimension\n" + "END_GROUP=SWATH_2\n" "END_GROUP=SwathStructure\n" ) struct_da = xr.DataArray(odl) @@ -114,14 +166,72 @@ def test_struct_metadata_renames_dims(): [[1.0] * 60] * 1496, dims=[phony(0), phony(1)], ) + + da2 = xr.DataArray( + [[1.0] * 30] * 1496, + dims=[phony(0), phony(1)], + ) dt = make_tree( { "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), "/HDFEOS/SWATHS/MySWATH/Data Fields": xr.Dataset({"ColumnAmount": da}), + "/HDFEOS/SWATHS/MySWATH2/Data Fields": xr.Dataset({"ColumnAmount": da2}), } ) result = rename_phony_dims(dt) - dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims + swath1_dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims + swath2_dims = result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].dims + + # have the names been recovered? + assert swath1_dims == ("nTimes", "nXtrack") + assert swath2_dims == ("nTimes", "nXtrack") + + swath1_dim_shape = ( + result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].shape + ) + swath2_dim_shape = ( + result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].shape + ) + + # are dimensions in differnet swaths, with different sizes but + # same name matched correctly? + assert swath1_dim_shape == (1496, 60) + assert swath2_dim_shape == (1496, 30) + + +def test_struct_grid_metadata_renames_dims(): + odl = ( + "GROUP=GridStructure\n" + "GROUP=GRID_1\n" + 'SwathName="MyGRID\n"' + "GROUP=Dimension\n" + "OBJECT=Dimension_1\n" + 'DimensionName="nTimes"\n' + "Size=1496\n" + "END_OBJECT=Dimension_1\n" + "OBJECT=Dimension_2\n" + 'DimensionName="nXtrack"\n' + "Size=60\n" + "END_OBJECT=Dimension_2\n" + "END_GROUP=Dimension\n" + "GROUP=DimensionMap\n" + "END_GROUP=DimensionMap\n" + "END_GROUP=GRID_1\n" + "END_GROUP=GridStructure\n" + ) + struct_da = xr.DataArray(odl) + da = xr.DataArray( + [[1.0] * 60] * 1496, + dims=[phony(0), phony(1)], + ) + dt = make_tree( + { + "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), + "/HDFEOS/GRIDS/MyGRID/Data Fields": xr.Dataset({"ColumnAmount": da}), + } + ) + result = rename_phony_dims(dt) + dims = result["/HDFEOS/GRIDS/MyGRID/Data Fields"].ds["ColumnAmount"].dims assert dims == ("nTimes", "nXtrack") From 38c3821f5dd496b7a1c1ee77b833788558c95e20 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Thu, 2 Apr 2026 21:59:54 +0000 Subject: [PATCH 26/44] /version 3.4.0a4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4ebf6697..953df0a8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a3" +version = "3.4.0a4" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From d08413cad098c732fc0f62f9a6296c1c19e05d46 Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Fri, 3 Apr 2026 14:19:41 -0400 Subject: [PATCH 27/44] Handle NetCDF with ScanTime swath group (#414) Update checks for ScanTime to occur for all file formats as opposed for only HDF files. If ScanTime is present, compute timeMidScan regardless of format. Added unit test and fake data fixture which mirrors existing structure of GPM V08. --- CHANGELOG.md | 3 +- podaac/subsetter/subset.py | 15 +- podaac/subsetter/utils/file_utils.py | 11 +- tests/test_subset.py | 255 +++++++++++++++++++++++++++ 4 files changed, 274 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d0c9959..a7606e16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,11 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated readme documentation ### Changed - Changed way Cygnss collection finds time variable -### Deprecated +### Deprecated ### Removed ### Fixed - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Fixes HDF handling with datatree - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to handle multi swath/grid collections +- [issue/396] (https://github.com/podaac/l2ss-py/issues/396) Handle new GPM v08 collections with netcdf format, but still containing wonky ScanTime swath group ### Security diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index 01f24708..29c67b91 100755 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -323,7 +323,8 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, file_extension = os.path.splitext(file_to_subset)[1] file_utils.override_decode_cf_datetime() - hdf_type = False + hdf_type = "" + scantime_present = False args = { 'decode_coords': False, @@ -334,6 +335,9 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, with xr.open_datatree(file_to_subset, **args) as dataset: if file_extension.lower() in _HDF_EXTENSIONS: hdf_type = file_utils.get_hdf_type(dataset) + scantime_present = hdf_type == "GPM" + else: + scantime_present = file_utils.has_scantime(dataset) if min_time or max_time: fill_value_f8 = nc.default_fillvals.get('f8') @@ -353,7 +357,8 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, except Exception: # pylint: disable=broad-exception-caught pass - if hdf_type == 'GPM': + # set decode_times to false if scantime present (e.g. GPM) + if scantime_present: args['decode_times'] = False time_encoding = {} @@ -409,9 +414,9 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, time_var_names=time_var_names ) - # note(ocs): I believe this only applies to GPM, but checking - # against general hdf until certain - if hdf_type: + # assumption is that GPM HDFEOS or GPM V08+ NetCDF4 will have + # scantime. + if scantime_present: new_time_var_names = [] for group in dataset.groups: if "ScanTime" in group: diff --git a/podaac/subsetter/utils/file_utils.py b/podaac/subsetter/utils/file_utils.py index ed5ae44b..ef904b18 100644 --- a/podaac/subsetter/utils/file_utils.py +++ b/podaac/subsetter/utils/file_utils.py @@ -77,10 +77,8 @@ def get_hdf_type(tree: DataTree) -> Optional[str]: Determine the HDF type (OMI, MLS, or GPM) from a DataTree object. """ try: - # GPM - for group in tree.groups: - if "ScanTime" in group: - return 'GPM' + if has_scantime(tree): + return 'GPM' # try to get types from instrument name additional_attrs = tree['/HDFEOS/ADDITIONAL/FILE_ATTRIBUTES'] @@ -104,3 +102,8 @@ def get_path(s): """Extracts the path by removing the last part after the final '/'.""" path = s.rsplit('/', 1)[0] if '/' in s else s return path if path.startswith('/') else f'/{path}' + + +def has_scantime(dataset: DataTree) -> bool: + """Check if "ScanTime" group present in dataset""" + return any("ScanTime" in group for group in dataset.groups) diff --git a/tests/test_subset.py b/tests/test_subset.py index 299dccb0..71d17c70 100755 --- a/tests/test_subset.py +++ b/tests/test_subset.py @@ -1806,6 +1806,261 @@ def test_subset_gpm_compute_new_var_data(fake_gpm_file, data_dir, subset_output_ if "ScanTime" in group: assert int(dtree[group].ds.variables["timeMidScan"][:][0]) == 1306403820 + +@pytest.fixture(scope="session") +def fake_gpm_mhs_file(tmp_path_factory): + """ + Creates fake data following structure of GPM_2AGPROFMETOPBMHS_08 + which has a netcdf4 format as opposed to HDF5EOS like previous + iterations of GPM products. + + Specifically based off 2A.METOPB.MHS.GPROFNNv1.20260228-S233156-E011316.069788.V08A.nc + """ + filepath = tmp_path_factory.mktemp("data") / "fake_mhs.nc" + + nscan = 10 + npixel = 5 + nlyrs = 5 + + # root + global attributes + root_dict = { + "attrs": { + "FileHeader": "DOI=10.5067/GPM/MHS/METOPB/GPROF/2A/08;\nAlgorithmID=2AGPROFMHS;", + "InputRecord": "InputFileNames=1C.METOPB.MHS.XCAL2016.nc;", + "NavigationRecord": "LongitudeOnEquator=-44.554371;", + "FileInfo": "DataFormatVersion=8b;", + "GprofInfo": "Satellite=METOPB;Sensor=MHS;", + }, + "dims": {}, + "coords": {}, + "data_vars": {}, + } + xr.Dataset.from_dict(root_dict).to_netcdf(filepath, mode="w", engine="netcdf4") + + # GprofDHeadr group containing the layer heights + headr_dict = { + "attrs": {}, + "dims": {"nlyrs": nlyrs}, + "coords": {}, + "data_vars": { + "hgtTopLayer": { + "dims": ("nlyrs",), + "data": np.arange(nlyrs, dtype=np.float32), + "attrs": {"DimensionNames": "nlyrs", "Units": "km"}, + } + }, + } + xr.Dataset.from_dict(headr_dict).to_netcdf( + filepath, mode="a", group="GprofDHeadr", engine="netcdf4" + ) + + # primary swath variables (but only a few) + s1_dict = { + "attrs": {"SwathHeader": "NumberScansInSet=1;\nNumberPixels=90;"}, + "dims": {"nscan": nscan, "npixel": npixel, "nlyrs": nlyrs}, + "coords": {}, + "data_vars": { + "Latitude": { + "dims": ("nscan", "npixel"), + "data": np.linspace(-90, 90, nscan * npixel) + .reshape(nscan, npixel) + .astype(np.float32), + "attrs": {"DimensionNames": "nscan,npixel", "Units": "degrees"}, + }, + "Longitude": { + "dims": ("nscan", "npixel"), + "data": np.linspace(-180, 180, nscan * npixel) + .reshape(nscan, npixel) + .astype(np.float32), + "attrs": {"DimensionNames": "nscan,npixel", "Units": "degrees"}, + }, + "surfacePrecipitation": { + "dims": ("nscan", "npixel"), + "data": np.linspace(0, 50, nscan * npixel) + .reshape(nscan, npixel) + .astype(np.float32), + "attrs": {"DimensionNames": "nscan,npixel", "Units": "mm/hr"}, + }, + "sunGlintAngle": { + "dims": ("nscan", "npixel"), + "data": np.linspace(0, 180, nscan * npixel) + .reshape(nscan, npixel) + .astype(np.float32), + "attrs": {"DimensionNames": "nscan,npixel", "Units": "degrees"}, + }, + "rainWaterContent": { + "dims": ("nscan", "npixel", "nlyrs"), + "data": np.linspace(0, 10, nscan * npixel * nlyrs) + .reshape(nscan, npixel, nlyrs) + .astype(np.float32), + "attrs": {"DimensionNames": "nscan,npixel,nlyrs", "Units": "g/m3"}, + }, + }, + } + xr.Dataset.from_dict(s1_dict).to_netcdf( + filepath, mode="a", group="S1", engine="netcdf4" + ) + + # scantime subgroup is nested under S1 containing temporal variables + scantime_dict = { + "attrs": {}, + "dims": {"nscan": nscan}, + "coords": {}, + "data_vars": { + "Year": { + "dims": ("nscan",), + "data": np.full(nscan, 2026, dtype=np.int16), + "attrs": { + "DimensionNames": "nscan", + "Units": "years", + "_FillValue": -9999, + "CodeMissingValue": "-9999", + }, + }, + "Month": { + "dims": ("nscan",), + "data": np.full(nscan, 2, dtype=np.int8), + "attrs": { + "DimensionNames": "nscan", + "Units": "months", + "_FillValue": -99, + "CodeMissingValue": "-99", + }, + }, + "DayOfMonth": { + "dims": ("nscan",), + "data": np.full(nscan, 28, dtype=np.int8), + "attrs": { + "DimensionNames": "nscan", + "Units": "days", + "_FillValue": -99, + "CodeMissingValue": "-99", + }, + }, + "Hour": { + "dims": ("nscan",), + "data": np.full(nscan, 23, dtype=np.int8), + "attrs": { + "DimensionNames": "nscan", + "Units": "hours", + "_FillValue": -99, + "CodeMissingValue": "-99", + }, + }, + "Minute": { + "dims": ("nscan",), + "data": np.full(nscan, 31, dtype=np.int8), + "attrs": { + "DimensionNames": "nscan", + "Units": "minutes", + "_FillValue": -99, + "CodeMissingValue": "-99", + }, + }, + "Second": { + "dims": ("nscan",), + "data": np.full(nscan, 56, dtype=np.int8), + "attrs": { + "DimensionNames": "nscan", + "Units": "s", + "_FillValue": -99, + "CodeMissingValue": "-99", + }, + }, + "MilliSecond": { + "dims": ("nscan",), + "data": np.full(nscan, 0, dtype=np.int16), + "attrs": { + "DimensionNames": "nscan", + "Units": "ms", + "_FillValue": -9999, + "CodeMissingValue": "-9999", + }, + }, + "DayOfYear": { + "dims": ("nscan",), + "data": np.full(nscan, 59, dtype=np.int16), + "attrs": { + "DimensionNames": "nscan", + "Units": "days", + "_FillValue": -9999, + "CodeMissingValue": "-9999", + }, + }, + "SecondOfDay": { + "dims": ("nscan",), + "data": np.linspace(84716.0, 84726.0, nscan).astype(np.float64), + "attrs": { + "DimensionNames": "nscan", + "Units": "s", + "_FillValue": -9999.9, + "CodeMissingValue": "-9999.9", + }, + }, + }, + } + xr.Dataset.from_dict(scantime_dict).to_netcdf( + filepath, mode="a", group="S1/ScanTime", engine="netcdf4" + ) + + # SCstatus subgroup nested under S1 + scstatus_dict = { + "attrs": {}, + "dims": {"nscan": nscan}, + "coords": {}, + "data_vars": { + "SCaltitude": { + "dims": ("nscan",), + "data": np.full(nscan, 400.0, dtype=np.float32), + "attrs": {"DimensionNames": "nscan", "Units": "km"}, + } + }, + } + xr.Dataset.from_dict(scstatus_dict).to_netcdf( + filepath, mode="a", group="S1/SCstatus", engine="netcdf4" + ) + + return filepath + + +def test_subset_gpm_mhs_compute_new_var_data(fake_gpm_mhs_file, subset_output_dir): + """ + Tests that a GPM v08 file with NetCDF4 format can run through subset and produce correct variables + """ + + subset_output_file = Path(subset_output_dir) / "mhs_test_subset.nc" + + # perform the subsetting operation on the fake data, make sure to + # keep created timeMidScan var created by l2ss to compare + subset.subset( + file_to_subset=fake_gpm_mhs_file, + bbox=np.array(((-90.1, 90.1), (-45.1, 45.1))), + variables=[ + "S1/surfacePrecipitation", + "S1/ScanTime/timeMidScan", + ], + output_file=subset_output_file, + cut=True, + ) + dtree = xr.open_datatree(subset_output_file) + + # are /only/ the requested variables + neccisary location data present? + assert set(dtree["S1"].variables) == { + "surfacePrecipitation", + "Latitude", + "Longitude", + } + assert "timeMidScan" in dtree["S1/ScanTime"].variables + + # are the requested variables dims the correct size? + assert dtree["S1/Latitude"].shape == (6, 5) + assert dtree["S1/Longitude"].shape == (6, 5) + assert dtree["S1/surfacePrecipitation"].shape == (6, 5) + + # timeMidScan created, and correct? + assert int(dtree["S1/ScanTime"].variables["timeMidScan"][0]) == 1456356716 + + def test_temporal_subset_tempo(data_dir, subset_output_dir, request): tempo_file = "TEMPO_HCHO_L2_V01_20240110T170237Z_S005G08.nc" From bb4d36b1b4e45d2d2d72ddfb5e20173909570173 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Fri, 3 Apr 2026 18:41:24 +0000 Subject: [PATCH 28/44] /version 3.4.0a5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 953df0a8..d2968264 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a4" +version = "3.4.0a5" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 5bac3431940c695dca2d69aa29ea0e95b6895c67 Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Fri, 3 Apr 2026 13:33:08 -0700 Subject: [PATCH 29/44] trigger build From 7d6c8384c04116e35ab631f96d679c34b5bfebb1 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Fri, 3 Apr 2026 20:54:47 +0000 Subject: [PATCH 30/44] /version 3.4.0a6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d2968264..d4aea99e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a5" +version = "3.4.0a6" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 45eb4f485661cc38ff1aca083759eaa50efbe234 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Fri, 3 Apr 2026 21:24:24 +0000 Subject: [PATCH 31/44] /version 3.3.1rc5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 70c242f5..cc2eb2ec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc4" +version = "3.3.1rc5" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 617985c27e6e325d871e617d05665698cd72a28f Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Tue, 7 Apr 2026 09:30:10 -0700 Subject: [PATCH 32/44] trigger build From 139b878b3d7343ec8199030e09eee150aa8c6d68 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 7 Apr 2026 16:52:51 +0000 Subject: [PATCH 33/44] /version 3.3.1rc6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cc2eb2ec..7358c91b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc5" +version = "3.3.1rc6" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From e7cda2389bc710d1fc621b7a1e81b1a1daf00de3 Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Tue, 7 Apr 2026 13:02:12 -0700 Subject: [PATCH 34/44] Issue/400 (#415) * put in fix for MOPITT * removed print * restructure build_temporal_cond * update changelog --- CHANGELOG.md | 1 + podaac/subsetter/subset.py | 2 +- podaac/subsetter/utils/mask_utils.py | 2 +- podaac/subsetter/utils/time_utils.py | 99 ++++++++++++++++++---------- 4 files changed, 69 insertions(+), 35 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a7606e16..03d20e49 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Fixes HDF handling with datatree - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to handle multi swath/grid collections - [issue/396] (https://github.com/podaac/l2ss-py/issues/396) Handle new GPM v08 collections with netcdf format, but still containing wonky ScanTime swath group +- [issue/400] (https://github.com/podaac/l2ss-py/issues/400) Fixed temporal subsetting for MOPITT collections ### Security diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index 29c67b91..1bbfdc1c 100755 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -392,7 +392,7 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, if calendar: time_encoding[group_path][var_name]['calendar'] = calendar if units: - if time != '/solar_time': + if time not in ['/solar_time', '/HDFEOS/SWATHS/MOP02/Geolocation Fields/Time']: time_encoding[group_path][var_name]['units'] = time_utils.check_time_units(units) if dtype and units: time_encoding[group_path][var_name]['dtype'] = dtype diff --git a/podaac/subsetter/utils/mask_utils.py b/podaac/subsetter/utils/mask_utils.py index e1f32ee4..a8a9ddcf 100644 --- a/podaac/subsetter/utils/mask_utils.py +++ b/podaac/subsetter/utils/mask_utils.py @@ -51,7 +51,7 @@ def align_dims_cond_only(dataset: xr.Dataset, cond: xr.Dataset) -> xr.Dataset: # Helper to get dim sizes def get_sizes(obj): if isinstance(obj, xr.Dataset): - return dict(obj.dims) + return dict(obj.sizes) return dict(obj.sizes) dataset_sizes = get_sizes(dataset) diff --git a/podaac/subsetter/utils/time_utils.py b/podaac/subsetter/utils/time_utils.py index 8dee19ce..c8dcfa31 100644 --- a/podaac/subsetter/utils/time_utils.py +++ b/podaac/subsetter/utils/time_utils.py @@ -85,6 +85,68 @@ def _convert_time_from_description(seconds_since, description: str): return result +def _get_time_data(dataset: xr.Dataset, time_var_name: str): + """ + Return the time data array, handling special solar_time encoding. + """ + if time_var_name != '/solar_time': + return dataset[time_var_name] + + reference_date = dataset.attrs.get('time_coverage_start') + ref_ts = pd.to_datetime(reference_date) + if hasattr(ref_ts, 'tzinfo') and ref_ts.tzinfo is not None: + ref_ts = ref_ts.tz_convert(None) + seconds = dataset['solar_time'].values + return ref_ts + pd.to_timedelta(seconds, unit='s') + + +def _coerce_timestamp_for_timedelta(dataset: xr.Dataset, time_var_name: str, timestamp): + """ + Adjust a timestamp when the dataset time is a timedelta from an epoch. + """ + if _is_time_mjd(dataset, time_var_name): + mjd_datetime = _datetime_from_mjd(dataset, time_var_name) + if mjd_datetime is None: + raise ValueError('Unable to get datetime from dataset to calculate time delta') + return timestamp - np.datetime64(mjd_datetime) + epoch_var = _get_time_epoch_var(dataset, time_var_name) + epoch_datetime = dataset[epoch_var].values[0] + return timestamp - epoch_datetime + + +def _convert_time_data_for_floating(dataset: xr.Dataset, time_var_name: str, time_data): + """ + Convert floating time data to datetime64 when possible. + """ + description = time_data.attrs.get('description') or time_data.attrs.get('Units') + long_name = time_data.attrs.get('long_name') + if description: + return _convert_time_from_description(time_data, description) + if long_name == "Approximate observation time for each row": + start_time = dataset.attrs.get('REV_START_TIME') + date_str = start_time.split("T")[0] + start_date = pd.to_datetime(date_str, format="%Y-%j") + return np.datetime64(start_date) + time_data.values.astype('timedelta64[s]') + if time_var_name == '/HDFEOS/SWATHS/MOP02/Geolocation Fields/Time': + start_time = dataset['/HDFEOS/ADDITIONAL/FILE_ATTRIBUTES'].attrs.get('StartDateTime') + date = datetime.datetime.fromisoformat(start_time.replace("Z", "+00:00")).date() + seconds_in_day = dataset['/HDFEOS/SWATHS/MOP02/Geolocation Fields/SecondsinDay'] + start_date = pd.to_datetime(date, format="%Y-%j") + return np.datetime64(start_date) + seconds_in_day.values.astype('timedelta64[s]') + return time_data + + +def _maybe_apply_reference_time_offset(dataset: xr.Dataset, time_data): + """ + Apply the sst reference time offset if present. + """ + if getattr(time_data, 'long_name', None) == "reference time of sst file": + base_time = dataset['time'].astype('datetime64[s]') + offset = dataset['sst_dtime'].astype('timedelta64[s]') + return base_time + offset + return time_data + + def build_temporal_cond(min_time: str, max_time: str, dataset: xr.Dataset, time_var_name: str): """ Build the temporal condition used in the xarray 'where' call which @@ -93,45 +155,16 @@ def build_temporal_cond(min_time: str, max_time: str, dataset: xr.Dataset, time_ def build_cond(str_timestamp, compare): timestamp = pd.to_datetime(_translate_timestamp(str_timestamp)).to_datetime64() - if time_var_name == '/solar_time': - reference_date = dataset.attrs.get('time_coverage_start') # Replace with the correct date - ref_ts = pd.to_datetime(reference_date) - # Remove timezone if present - if hasattr(ref_ts, 'tzinfo') and ref_ts.tzinfo is not None: - ref_ts = ref_ts.tz_convert(None) - seconds = dataset['solar_time'].values - time_data = ref_ts + pd.to_timedelta(seconds, unit='s') - else: - time_data = dataset[time_var_name] + time_data = _get_time_data(dataset, time_var_name) dtype = time_data.dtype if np.issubdtype(dtype, np.datetime64): pass elif np.issubdtype(dtype, np.timedelta64): - if _is_time_mjd(dataset, time_var_name): - mjd_datetime = _datetime_from_mjd(dataset, time_var_name) - if mjd_datetime is None: - raise ValueError('Unable to get datetime from dataset to calculate time delta') - timestamp -= np.datetime64(mjd_datetime) - else: - epoch_var = _get_time_epoch_var(dataset, time_var_name) - epoch_datetime = dataset[epoch_var].values[0] - timestamp -= epoch_datetime + timestamp = _coerce_timestamp_for_timedelta(dataset, time_var_name, timestamp) elif np.issubdtype(dtype, np.floating): - description = time_data.attrs.get('description') or time_data.attrs.get('Units') - long_name = time_data.attrs.get('long_name') - if description: - epoch_datetime = _extract_epoch(description) - time_data = _convert_time_from_description(time_data, description) - elif long_name == "Approximate observation time for each row": - start_time = dataset.attrs.get('REV_START_TIME') - date_str = start_time.split("T")[0] - start_date = pd.to_datetime(date_str, format="%Y-%j") - time_data = np.datetime64(start_date) + time_data.values.astype('timedelta64[s]') - if getattr(time_data, 'long_name', None) == "reference time of sst file": - base_time = dataset['time'].astype('datetime64[s]') - offset = dataset['sst_dtime'].astype('timedelta64[s]') - time_data = base_time + offset + time_data = _convert_time_data_for_floating(dataset, time_var_name, time_data) + time_data = _maybe_apply_reference_time_offset(dataset, time_data) return compare(time_data, timestamp) temporal_conds = [] if min_time: From cd41fc93e77d8dc6d883c794e47b5993a34ef607 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 7 Apr 2026 20:24:09 +0000 Subject: [PATCH 35/44] /version 3.4.0a7 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d4aea99e..6ccd0bd5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a6" +version = "3.4.0a7" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From ef890625b94b88cfebed113a0ed3c67f82ae02dd Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 7 Apr 2026 21:06:32 +0000 Subject: [PATCH 36/44] /version 3.3.1rc7 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7358c91b..f8408fac 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc6" +version = "3.3.1rc7" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 55fefb7000b10c514ef33895044679605e67a4a6 Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Tue, 7 Apr 2026 14:54:45 -0700 Subject: [PATCH 37/44] trigger build From 42a867fc9f1f77867696f49bff2e869c3c2428c8 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Tue, 7 Apr 2026 22:17:02 +0000 Subject: [PATCH 38/44] /version 3.3.1rc8 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f8408fac..8fb07344 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc7" +version = "3.3.1rc8" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 8e5737b80ea079f3e79dd51789778a1a69923932 Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Thu, 9 Apr 2026 12:21:14 -0500 Subject: [PATCH 39/44] rework ODL parser to be fully scope based, not size based (#416) --- CHANGELOG.md | 1 + podaac/subsetter/utils/hdf_utils.py | 221 ++++++++++++---------------- tests/test_hdf_phony_dims.py | 33 ++++- 3 files changed, 125 insertions(+), 130 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03d20e49..94628522 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to handle multi swath/grid collections - [issue/396] (https://github.com/podaac/l2ss-py/issues/396) Handle new GPM v08 collections with netcdf format, but still containing wonky ScanTime swath group - [issue/400] (https://github.com/podaac/l2ss-py/issues/400) Fixed temporal subsetting for MOPITT collections +- [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to apply direct mapping from DataField and GeoField objects ### Security diff --git a/podaac/subsetter/utils/hdf_utils.py b/podaac/subsetter/utils/hdf_utils.py index 823175de..90c012cd 100644 --- a/podaac/subsetter/utils/hdf_utils.py +++ b/podaac/subsetter/utils/hdf_utils.py @@ -8,7 +8,6 @@ import re import warnings -from collections import defaultdict import numpy as np import xarray as xr @@ -21,11 +20,6 @@ def _is_phony(dim: str) -> bool: return _PHONY_RE.match(dim) is not None -def _phony_index(dim: str) -> int: - m = _PHONY_RE.match(dim) - return int(m.group(1)) if m else -1 - - def rename_phony_dims(dt: DataTree) -> DataTree: """ Return a new DataTree with all phony_dim_N dimensions renamed to @@ -45,14 +39,17 @@ def rename_phony_dims(dt: DataTree) -> DataTree: A new tree with renamed dimensions. """ mapping = _mapping_from_dimension_names(dt) + if mapping: + dt = _apply_mapping(dt, mapping) - if not mapping: - mapping = _mapping_from_struct_metadata(dt) - - if not mapping: - return dt + struct_text = _find_struct_metadata(dt) + if struct_text: + scope_field_dimlists = _parse_odl_field_dimlists(struct_text) + if scope_field_dimlists: + dt = _apply_from_field_dimlists(dt, scope_field_dimlists) - return _apply_mapping(dt, mapping) + # null condition + return dt def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: @@ -84,6 +81,8 @@ def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: continue for phony, real in zip(da.dims, real_names): + # guard for incorrectly specified HDFEOS data + # which might not have phony_dims being populated if not _is_phony(phony): continue existing = mapping.get(phony) @@ -111,7 +110,6 @@ def _find_struct_metadata(dt: DataTree) -> str | None: for var_name in ds.data_vars: if "StructMetadata" in var_name: raw = ds[var_name].values - # may be bytes, numpy bytes_, or already a string if isinstance(raw, (bytes, np.bytes_)): return raw.decode("utf-8", errors="replace") if hasattr(raw, "item"): @@ -140,19 +138,18 @@ def _find_scope_roots(dt: DataTree) -> list[DataTree]: return candidates -def _parse_odl_scope_dimensions(odl_text: str) -> dict[str, dict[str, int]]: +def _parse_odl_field_dimlists(odl_text: str) -> dict[str, dict[str, list[str]]]: """ - Parse the ODL block and return a per-scope dimension mapping: - {scope_name: {dim_name: size}} + Parse the ODL block and return a per-scope, per-field dim list: + {scope_name: {field_name: [dim_name, ...]}} Handles both SwathStructure (SWATH_N / SwathName) and GridStructure - (GRID_N / GridName) blocks. Each scope is parsed independently so that - two scopes sharing a dimension name but with different sizes never - overwrite each other. + (GRID_N / GridName) blocks. The DimList order matches the axis + order of the variable as stored in the file, so it can be zipped + directly against the variable's actual (phony) dims. """ - result: dict[str, dict[str, int]] = {} + result: dict[str, dict[str, list[str]]] = {} - # split on any SWATH_N or GRID_N end-group boundary scope_blocks = re.split(r"END_GROUP\s*=\s*(?:SWATH|GRID)_\d+", odl_text) for block in scope_blocks: @@ -160,138 +157,110 @@ def _parse_odl_scope_dimensions(odl_text: str) -> dict[str, dict[str, int]]: if not name_match: continue scope_name = name_match.group(1).strip() + field_dimlists: dict[str, list[str]] = {} + + # GeoField and DataField blocks both use the same OBJECT structure + for field_block in re.split(r"END_OBJECT\s*=\s*(?:Geo|Data)Field_\d+", block): + field_name_match = re.search( + r'(?:GeoFieldName|DataFieldName)\s*=\s*"([^"]+)"', field_block + ) + dimlist_match = re.search(r"DimList\s*=\s*\(([^)]+)\)", field_block) + if not field_name_match or not dimlist_match: + continue - dim_group_match = re.search( - r"GROUP\s*=\s*Dimension(.+?)END_GROUP\s*=\s*Dimension", - block, - re.DOTALL, - ) - if not dim_group_match: - continue - - named_dims: dict[str, int] = {} - for obj_block in re.split( - r"END_OBJECT\s*=\s*Dimension_\d+", dim_group_match.group(1) - ): - dim_name_match = re.search(r'DimensionName\s*=\s*"([^"]+)"', obj_block) - size_match = re.search(r"\bSize\s*=\s*(\d+)", obj_block) - if dim_name_match and size_match: - named_dims[dim_name_match.group(1).strip()] = int(size_match.group(1)) + field_name = field_name_match.group(1).strip() + dim_names = [ + d.strip().strip('"') for d in dimlist_match.group(1).split(",") + ] + field_dimlists[field_name] = dim_names - if named_dims: - result[scope_name] = named_dims + if field_dimlists: + result[scope_name] = field_dimlists return result -def _mapping_from_struct_metadata(dt: DataTree) -> dict[str, str]: +def _apply_mapping(dt: DataTree, mapping: dict[str, str]) -> DataTree: """ - Locate the StructMetadata.0 variable (typically at /HDFEOS - INFORMATION), parse its ODL (Object Description Language) content - to extract every named dimension and its size, then match those - against the phony dims in the tree by size. + Walk the tree, apply rename_dims to every group dataset that contains + any of the phony dims in mapping, then reconstruct the entire tree + from a flat path -> dataset dict using DataTree.from_dict. - Returns an empty dict if no StructMetadata.0 is found or parsing - fails. + This avoids any direct node copying and is the idiomatic way to rebuild + a modified DataTree. """ - struct_text = _find_struct_metadata(dt) - if not struct_text: - return {} - - swath_dims = _parse_odl_scope_dimensions(struct_text) - if not swath_dims: - return {} - - mapping: dict[str, str] = {} - - scope_roots = _find_scope_roots(dt) - if not scope_roots: - scope_roots = [dt] - - for scope_root in scope_roots: - # extract the swath name from the path, e.g. - # "/HDFEOS/SWATHS/OMI Ground Pixel Corners UV-1" -> "OMI Ground Pixel Corners UV-1" - swath_name = scope_root.path.rstrip("/").split("/")[-1] - named_dims = swath_dims.get(swath_name) + path_to_ds: dict[str, xr.Dataset] = {} - if not named_dims: - # swath name not found in ODL - continue + for node in dt.subtree: + ds = node.ds if node.ds is not None else xr.Dataset() - size_to_names: dict[int, list[str]] = defaultdict(list) - for name, size in named_dims.items(): - size_to_names[size].append(name) + local_mapping = {k: v for k, v in mapping.items() if k in ds.dims} + if local_mapping: + ds = ds.rename_dims(local_mapping) - scope_mapping = _match_phony_to_named(scope_root, size_to_names, named_dims) - mapping.update(scope_mapping) + path_to_ds[node.path] = ds - return mapping + return DataTree.from_dict(path_to_ds) -def _match_phony_to_named( - dt: DataTree, - size_to_names: dict[int, list[str]], - named_dims: dict[str, int], -) -> dict[str, str]: +def _find_scope_for_node(node: DataTree, scope_roots: list[DataTree]) -> str | None: """ - For every phony dim in the tree, look up its size in ``size_to_names``. - - - If only one real name has that size, the mapping is unambiguous. - - If multiple real names share the same size, we use the *position* of - the phony dim within its group's sorted dimension list to pick among - the candidates (ordered as they appear in the ODL block). + Return the scope name (last path component of the scope root) that this + node lives under, or None if the node is not under any known scope root. """ - # ordered list of all named dims so we can use index as a tiebreaker - ordered_named = list(named_dims.keys()) - - mapping: dict[str, str] = {} - - for node in dt.subtree: - ds = node.ds - if ds is None: - continue - - # phony dims in this group sorted by their index (N in - # phony_dim_N) - local_phonies = sorted([d for d in ds.dims if _is_phony(d)], key=_phony_index) - - for phony in local_phonies: - size = ds.dims[phony] - candidates = size_to_names.get(size, []) - if not candidates: - continue - if len(candidates) == 1: - mapping[phony] = candidates[0] - else: - # use the position of this phony dim among same-size dims in - # this group to index into the ordered candidate list. - same_size_in_group = [p for p in local_phonies if ds.dims[p] == size] - pos = same_size_in_group.index(phony) - # sort candidates by their order in the odl block - ordered_candidates = sorted(candidates, key=ordered_named.index) - if pos < len(ordered_candidates): - mapping[phony] = ordered_candidates[pos] - - return mapping + for scope_root in scope_roots: + scope_path = scope_root.path.rstrip("/") + if node.path == scope_path or node.path.startswith(scope_path + "/"): + return scope_path.split("/")[-1] + return None -def _apply_mapping(dt: DataTree, mapping: dict[str, str]) -> DataTree: +def _apply_from_field_dimlists( + dt: DataTree, + scope_field_dimlists: dict[str, dict[str, list[str]]], +) -> DataTree: """ - Walk the tree, apply rename_dims to every group dataset that contains - any of the phony dims in ``mapping``, then reconstruct the entire tree - from a flat path -> dataset dict using DataTree.from_dict. + Walk every node in the tree. For each variable in the node, look up its + real dim names by scope name + variable name directly from the ODL field + dimlists, then rename only that variable's dims within that node. - This avoids any direct node copying and is the idiomatic way to rebuild - a modified DataTree. + This never builds a global phony to real mapping, so two variables with the + same name in different scopes are always resolved against their own scope's + DimList entries independently. """ + scope_roots = _find_scope_roots(dt) path_to_ds: dict[str, xr.Dataset] = {} for node in dt.subtree: ds = node.ds if node.ds is not None else xr.Dataset() - local_mapping = {k: v for k, v in mapping.items() if k in ds.dims} - if local_mapping: - ds = ds.rename_dims(local_mapping) + scope_name = _find_scope_for_node(node, scope_roots) + field_dimlists = scope_field_dimlists.get(scope_name, {}) if scope_name else {} + + if field_dimlists: + local_mapping: dict[str, str] = {} + + for var_name, da in ds.items(): + odl_dims = field_dimlists.get(var_name) + if odl_dims is None or len(odl_dims) != len(da.dims): + continue + for current_dim, real_name in zip(da.dims, odl_dims): + # guard for incorrectly specified HDFEOS data + # which might not have phony_dims being populated + if not _is_phony(current_dim): + continue + existing = local_mapping.get(current_dim) + if existing is not None and existing != real_name: + warnings.warn( + f"Conflicting ODL DimList for {current_dim!r} in " + f"{node.path!r}: {existing!r} vs {real_name!r}. " + f"Keeping {existing!r}." + ) + else: + local_mapping[current_dim] = real_name + + if local_mapping: + ds = ds.rename_dims(local_mapping) path_to_ds[node.path] = ds diff --git a/tests/test_hdf_phony_dims.py b/tests/test_hdf_phony_dims.py index fedcdd6a..492ca1e8 100644 --- a/tests/test_hdf_phony_dims.py +++ b/tests/test_hdf_phony_dims.py @@ -106,9 +106,16 @@ def test_struct_metadata_renames_dims(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_1\n" "END_GROUP=SwathStructure\n" ) + struct_da = xr.DataArray(odl) da = xr.DataArray( [[1.0] * 60] * 1496, @@ -143,6 +150,12 @@ def test_struct_metadata_renames_dims_multi_swath(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_1\n" # start of swath 2 "GROUP=SWATH_2\n" @@ -158,6 +171,12 @@ def test_struct_metadata_renames_dims_multi_swath(): "Size=30\n" "END_OBJECT=Dimension_2\n" "END_GROUP=Dimension\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount2"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_2\n" "END_GROUP=SwathStructure\n" ) @@ -169,18 +188,18 @@ def test_struct_metadata_renames_dims_multi_swath(): da2 = xr.DataArray( [[1.0] * 30] * 1496, - dims=[phony(0), phony(1)], + dims=[phony(2), phony(3)], ) dt = make_tree( { "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), "/HDFEOS/SWATHS/MySWATH/Data Fields": xr.Dataset({"ColumnAmount": da}), - "/HDFEOS/SWATHS/MySWATH2/Data Fields": xr.Dataset({"ColumnAmount": da2}), + "/HDFEOS/SWATHS/MySWATH2/Data Fields": xr.Dataset({"ColumnAmount2": da2}), } ) result = rename_phony_dims(dt) swath1_dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims - swath2_dims = result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].dims + swath2_dims = result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount2"].dims # have the names been recovered? assert swath1_dims == ("nTimes", "nXtrack") @@ -190,7 +209,7 @@ def test_struct_metadata_renames_dims_multi_swath(): result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].shape ) swath2_dim_shape = ( - result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].shape + result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount2"].shape ) # are dimensions in differnet swaths, with different sizes but @@ -216,6 +235,12 @@ def test_struct_grid_metadata_renames_dims(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=GRID_1\n" "END_GROUP=GridStructure\n" ) From 81a83a86735861772010c136a87ea84411b7ba93 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Thu, 9 Apr 2026 17:41:44 +0000 Subject: [PATCH 40/44] /version 3.4.0a8 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6ccd0bd5..070c4041 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.4.0a7" +version = "3.4.0a8" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From a86460852487dfaec060cd07726c755f0f6d663c Mon Sep 17 00:00:00 2001 From: Owen Smith <55674113+ocsmit@users.noreply.github.com> Date: Thu, 9 Apr 2026 12:21:14 -0500 Subject: [PATCH 41/44] rework ODL parser to be fully scope based, not size based (#416) --- CHANGELOG.md | 1 + podaac/subsetter/utils/hdf_utils.py | 221 ++++++++++++---------------- tests/test_hdf_phony_dims.py | 33 ++++- 3 files changed, 125 insertions(+), 130 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 607e7422..74a5af49 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to handle multi swath/grid collections - [issue/396] (https://github.com/podaac/l2ss-py/issues/396) Handle new GPM v08 collections with netcdf format, but still containing wonky ScanTime swath group - [issue/400] (https://github.com/podaac/l2ss-py/issues/400) Fixed temporal subsetting for MOPITT collections +- [issue/394] (https://github.com/podaac/l2ss-py/issues/394) Update ODL parser to apply direct mapping from DataField and GeoField objects ### Security diff --git a/podaac/subsetter/utils/hdf_utils.py b/podaac/subsetter/utils/hdf_utils.py index 823175de..90c012cd 100644 --- a/podaac/subsetter/utils/hdf_utils.py +++ b/podaac/subsetter/utils/hdf_utils.py @@ -8,7 +8,6 @@ import re import warnings -from collections import defaultdict import numpy as np import xarray as xr @@ -21,11 +20,6 @@ def _is_phony(dim: str) -> bool: return _PHONY_RE.match(dim) is not None -def _phony_index(dim: str) -> int: - m = _PHONY_RE.match(dim) - return int(m.group(1)) if m else -1 - - def rename_phony_dims(dt: DataTree) -> DataTree: """ Return a new DataTree with all phony_dim_N dimensions renamed to @@ -45,14 +39,17 @@ def rename_phony_dims(dt: DataTree) -> DataTree: A new tree with renamed dimensions. """ mapping = _mapping_from_dimension_names(dt) + if mapping: + dt = _apply_mapping(dt, mapping) - if not mapping: - mapping = _mapping_from_struct_metadata(dt) - - if not mapping: - return dt + struct_text = _find_struct_metadata(dt) + if struct_text: + scope_field_dimlists = _parse_odl_field_dimlists(struct_text) + if scope_field_dimlists: + dt = _apply_from_field_dimlists(dt, scope_field_dimlists) - return _apply_mapping(dt, mapping) + # null condition + return dt def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: @@ -84,6 +81,8 @@ def _mapping_from_dimension_names(dt: DataTree) -> dict[str, str]: continue for phony, real in zip(da.dims, real_names): + # guard for incorrectly specified HDFEOS data + # which might not have phony_dims being populated if not _is_phony(phony): continue existing = mapping.get(phony) @@ -111,7 +110,6 @@ def _find_struct_metadata(dt: DataTree) -> str | None: for var_name in ds.data_vars: if "StructMetadata" in var_name: raw = ds[var_name].values - # may be bytes, numpy bytes_, or already a string if isinstance(raw, (bytes, np.bytes_)): return raw.decode("utf-8", errors="replace") if hasattr(raw, "item"): @@ -140,19 +138,18 @@ def _find_scope_roots(dt: DataTree) -> list[DataTree]: return candidates -def _parse_odl_scope_dimensions(odl_text: str) -> dict[str, dict[str, int]]: +def _parse_odl_field_dimlists(odl_text: str) -> dict[str, dict[str, list[str]]]: """ - Parse the ODL block and return a per-scope dimension mapping: - {scope_name: {dim_name: size}} + Parse the ODL block and return a per-scope, per-field dim list: + {scope_name: {field_name: [dim_name, ...]}} Handles both SwathStructure (SWATH_N / SwathName) and GridStructure - (GRID_N / GridName) blocks. Each scope is parsed independently so that - two scopes sharing a dimension name but with different sizes never - overwrite each other. + (GRID_N / GridName) blocks. The DimList order matches the axis + order of the variable as stored in the file, so it can be zipped + directly against the variable's actual (phony) dims. """ - result: dict[str, dict[str, int]] = {} + result: dict[str, dict[str, list[str]]] = {} - # split on any SWATH_N or GRID_N end-group boundary scope_blocks = re.split(r"END_GROUP\s*=\s*(?:SWATH|GRID)_\d+", odl_text) for block in scope_blocks: @@ -160,138 +157,110 @@ def _parse_odl_scope_dimensions(odl_text: str) -> dict[str, dict[str, int]]: if not name_match: continue scope_name = name_match.group(1).strip() + field_dimlists: dict[str, list[str]] = {} + + # GeoField and DataField blocks both use the same OBJECT structure + for field_block in re.split(r"END_OBJECT\s*=\s*(?:Geo|Data)Field_\d+", block): + field_name_match = re.search( + r'(?:GeoFieldName|DataFieldName)\s*=\s*"([^"]+)"', field_block + ) + dimlist_match = re.search(r"DimList\s*=\s*\(([^)]+)\)", field_block) + if not field_name_match or not dimlist_match: + continue - dim_group_match = re.search( - r"GROUP\s*=\s*Dimension(.+?)END_GROUP\s*=\s*Dimension", - block, - re.DOTALL, - ) - if not dim_group_match: - continue - - named_dims: dict[str, int] = {} - for obj_block in re.split( - r"END_OBJECT\s*=\s*Dimension_\d+", dim_group_match.group(1) - ): - dim_name_match = re.search(r'DimensionName\s*=\s*"([^"]+)"', obj_block) - size_match = re.search(r"\bSize\s*=\s*(\d+)", obj_block) - if dim_name_match and size_match: - named_dims[dim_name_match.group(1).strip()] = int(size_match.group(1)) + field_name = field_name_match.group(1).strip() + dim_names = [ + d.strip().strip('"') for d in dimlist_match.group(1).split(",") + ] + field_dimlists[field_name] = dim_names - if named_dims: - result[scope_name] = named_dims + if field_dimlists: + result[scope_name] = field_dimlists return result -def _mapping_from_struct_metadata(dt: DataTree) -> dict[str, str]: +def _apply_mapping(dt: DataTree, mapping: dict[str, str]) -> DataTree: """ - Locate the StructMetadata.0 variable (typically at /HDFEOS - INFORMATION), parse its ODL (Object Description Language) content - to extract every named dimension and its size, then match those - against the phony dims in the tree by size. + Walk the tree, apply rename_dims to every group dataset that contains + any of the phony dims in mapping, then reconstruct the entire tree + from a flat path -> dataset dict using DataTree.from_dict. - Returns an empty dict if no StructMetadata.0 is found or parsing - fails. + This avoids any direct node copying and is the idiomatic way to rebuild + a modified DataTree. """ - struct_text = _find_struct_metadata(dt) - if not struct_text: - return {} - - swath_dims = _parse_odl_scope_dimensions(struct_text) - if not swath_dims: - return {} - - mapping: dict[str, str] = {} - - scope_roots = _find_scope_roots(dt) - if not scope_roots: - scope_roots = [dt] - - for scope_root in scope_roots: - # extract the swath name from the path, e.g. - # "/HDFEOS/SWATHS/OMI Ground Pixel Corners UV-1" -> "OMI Ground Pixel Corners UV-1" - swath_name = scope_root.path.rstrip("/").split("/")[-1] - named_dims = swath_dims.get(swath_name) + path_to_ds: dict[str, xr.Dataset] = {} - if not named_dims: - # swath name not found in ODL - continue + for node in dt.subtree: + ds = node.ds if node.ds is not None else xr.Dataset() - size_to_names: dict[int, list[str]] = defaultdict(list) - for name, size in named_dims.items(): - size_to_names[size].append(name) + local_mapping = {k: v for k, v in mapping.items() if k in ds.dims} + if local_mapping: + ds = ds.rename_dims(local_mapping) - scope_mapping = _match_phony_to_named(scope_root, size_to_names, named_dims) - mapping.update(scope_mapping) + path_to_ds[node.path] = ds - return mapping + return DataTree.from_dict(path_to_ds) -def _match_phony_to_named( - dt: DataTree, - size_to_names: dict[int, list[str]], - named_dims: dict[str, int], -) -> dict[str, str]: +def _find_scope_for_node(node: DataTree, scope_roots: list[DataTree]) -> str | None: """ - For every phony dim in the tree, look up its size in ``size_to_names``. - - - If only one real name has that size, the mapping is unambiguous. - - If multiple real names share the same size, we use the *position* of - the phony dim within its group's sorted dimension list to pick among - the candidates (ordered as they appear in the ODL block). + Return the scope name (last path component of the scope root) that this + node lives under, or None if the node is not under any known scope root. """ - # ordered list of all named dims so we can use index as a tiebreaker - ordered_named = list(named_dims.keys()) - - mapping: dict[str, str] = {} - - for node in dt.subtree: - ds = node.ds - if ds is None: - continue - - # phony dims in this group sorted by their index (N in - # phony_dim_N) - local_phonies = sorted([d for d in ds.dims if _is_phony(d)], key=_phony_index) - - for phony in local_phonies: - size = ds.dims[phony] - candidates = size_to_names.get(size, []) - if not candidates: - continue - if len(candidates) == 1: - mapping[phony] = candidates[0] - else: - # use the position of this phony dim among same-size dims in - # this group to index into the ordered candidate list. - same_size_in_group = [p for p in local_phonies if ds.dims[p] == size] - pos = same_size_in_group.index(phony) - # sort candidates by their order in the odl block - ordered_candidates = sorted(candidates, key=ordered_named.index) - if pos < len(ordered_candidates): - mapping[phony] = ordered_candidates[pos] - - return mapping + for scope_root in scope_roots: + scope_path = scope_root.path.rstrip("/") + if node.path == scope_path or node.path.startswith(scope_path + "/"): + return scope_path.split("/")[-1] + return None -def _apply_mapping(dt: DataTree, mapping: dict[str, str]) -> DataTree: +def _apply_from_field_dimlists( + dt: DataTree, + scope_field_dimlists: dict[str, dict[str, list[str]]], +) -> DataTree: """ - Walk the tree, apply rename_dims to every group dataset that contains - any of the phony dims in ``mapping``, then reconstruct the entire tree - from a flat path -> dataset dict using DataTree.from_dict. + Walk every node in the tree. For each variable in the node, look up its + real dim names by scope name + variable name directly from the ODL field + dimlists, then rename only that variable's dims within that node. - This avoids any direct node copying and is the idiomatic way to rebuild - a modified DataTree. + This never builds a global phony to real mapping, so two variables with the + same name in different scopes are always resolved against their own scope's + DimList entries independently. """ + scope_roots = _find_scope_roots(dt) path_to_ds: dict[str, xr.Dataset] = {} for node in dt.subtree: ds = node.ds if node.ds is not None else xr.Dataset() - local_mapping = {k: v for k, v in mapping.items() if k in ds.dims} - if local_mapping: - ds = ds.rename_dims(local_mapping) + scope_name = _find_scope_for_node(node, scope_roots) + field_dimlists = scope_field_dimlists.get(scope_name, {}) if scope_name else {} + + if field_dimlists: + local_mapping: dict[str, str] = {} + + for var_name, da in ds.items(): + odl_dims = field_dimlists.get(var_name) + if odl_dims is None or len(odl_dims) != len(da.dims): + continue + for current_dim, real_name in zip(da.dims, odl_dims): + # guard for incorrectly specified HDFEOS data + # which might not have phony_dims being populated + if not _is_phony(current_dim): + continue + existing = local_mapping.get(current_dim) + if existing is not None and existing != real_name: + warnings.warn( + f"Conflicting ODL DimList for {current_dim!r} in " + f"{node.path!r}: {existing!r} vs {real_name!r}. " + f"Keeping {existing!r}." + ) + else: + local_mapping[current_dim] = real_name + + if local_mapping: + ds = ds.rename_dims(local_mapping) path_to_ds[node.path] = ds diff --git a/tests/test_hdf_phony_dims.py b/tests/test_hdf_phony_dims.py index fedcdd6a..492ca1e8 100644 --- a/tests/test_hdf_phony_dims.py +++ b/tests/test_hdf_phony_dims.py @@ -106,9 +106,16 @@ def test_struct_metadata_renames_dims(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_1\n" "END_GROUP=SwathStructure\n" ) + struct_da = xr.DataArray(odl) da = xr.DataArray( [[1.0] * 60] * 1496, @@ -143,6 +150,12 @@ def test_struct_metadata_renames_dims_multi_swath(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_1\n" # start of swath 2 "GROUP=SWATH_2\n" @@ -158,6 +171,12 @@ def test_struct_metadata_renames_dims_multi_swath(): "Size=30\n" "END_OBJECT=Dimension_2\n" "END_GROUP=Dimension\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount2"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=SWATH_2\n" "END_GROUP=SwathStructure\n" ) @@ -169,18 +188,18 @@ def test_struct_metadata_renames_dims_multi_swath(): da2 = xr.DataArray( [[1.0] * 30] * 1496, - dims=[phony(0), phony(1)], + dims=[phony(2), phony(3)], ) dt = make_tree( { "/HDFEOS INFORMATION": xr.Dataset({"StructMetadata.0": struct_da}), "/HDFEOS/SWATHS/MySWATH/Data Fields": xr.Dataset({"ColumnAmount": da}), - "/HDFEOS/SWATHS/MySWATH2/Data Fields": xr.Dataset({"ColumnAmount": da2}), + "/HDFEOS/SWATHS/MySWATH2/Data Fields": xr.Dataset({"ColumnAmount2": da2}), } ) result = rename_phony_dims(dt) swath1_dims = result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].dims - swath2_dims = result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].dims + swath2_dims = result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount2"].dims # have the names been recovered? assert swath1_dims == ("nTimes", "nXtrack") @@ -190,7 +209,7 @@ def test_struct_metadata_renames_dims_multi_swath(): result["/HDFEOS/SWATHS/MySWATH/Data Fields"].ds["ColumnAmount"].shape ) swath2_dim_shape = ( - result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount"].shape + result["/HDFEOS/SWATHS/MySWATH2/Data Fields"].ds["ColumnAmount2"].shape ) # are dimensions in differnet swaths, with different sizes but @@ -216,6 +235,12 @@ def test_struct_grid_metadata_renames_dims(): "END_GROUP=Dimension\n" "GROUP=DimensionMap\n" "END_GROUP=DimensionMap\n" + "GROUP=DataField\n" + "OBJECT=DataField_1\n" + 'DataFieldName="ColumnAmount"\n' + 'DimList=("nTimes","nXtrack")\n' + "END_OBJECT=DataField_1\n" + "END_GROUP=DataField\n" "END_GROUP=GRID_1\n" "END_GROUP=GridStructure\n" ) From 0d7335fd7ef50ced55b00698037baf96599c6d50 Mon Sep 17 00:00:00 2001 From: l2ss-py bot Date: Thu, 9 Apr 2026 20:01:20 +0000 Subject: [PATCH 42/44] /version 3.3.1rc9 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 8fb07344..94f5fc14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ [tool.poetry] name = "l2ss-py" -version = "3.3.1rc8" +version = "3.3.1rc9" description = "L2 Subsetter Service" authors = ["podaac-tva "] license = "Apache-2.0" From 0383843da02bfd07a34811d01b3ed6b1cf362265 Mon Sep 17 00:00:00 2001 From: Simon Liu Date: Thu, 9 Apr 2026 13:12:26 -0700 Subject: [PATCH 43/44] poetry update --- poetry.lock | 790 ++++++++++++++++++++++++++-------------------------- 1 file changed, 395 insertions(+), 395 deletions(-) diff --git a/poetry.lock b/poetry.lock index 62066197..ed9596c3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -95,19 +95,19 @@ xyzservices = ">=2021.9.1" [[package]] name = "boto3" -version = "1.42.80" +version = "1.42.86" description = "The AWS SDK for Python" optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "boto3-1.42.80-py3-none-any.whl", hash = "sha256:293cbdeaec7eda2a0b08e6a9c2bf1a51c54453863137d45a6431058a9280fdda"}, - {file = "boto3-1.42.80.tar.gz", hash = "sha256:797cec65f8a36dde38d2397119a114ab0d807cf92c43fb44b72b0522558acc0a"}, + {file = "boto3-1.42.86-py3-none-any.whl", hash = "sha256:492c3c7cbbe9842882680064902f50cf711b5ab770d26525549872339ed95d5b"}, + {file = "boto3-1.42.86.tar.gz", hash = "sha256:c87d2a750b1a8cad0384d1a83d3bad6aedf924ae9a14aaba814bcb3297b39c01"}, ] markers = {main = "extra == \"harmony\""} [package.dependencies] -botocore = ">=1.42.80,<1.43.0" +botocore = ">=1.42.86,<1.43.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.16.0,<0.17.0" @@ -116,14 +116,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.42.80" +version = "1.42.86" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "botocore-1.42.80-py3-none-any.whl", hash = "sha256:7291632b2ede71b7c69e6e366480bb6e2a5d2fae8f7d2d2eb49215e32b7c7a12"}, - {file = "botocore-1.42.80.tar.gz", hash = "sha256:fe32af53dc87f5f4d61879bc231e2ca2cc0719b19b8f6d268e82a34f713a8a09"}, + {file = "botocore-1.42.86-py3-none-any.whl", hash = "sha256:443387337864e069f7e4e885ccdc81592725b5598ca966514af3e9776bce0bfe"}, + {file = "botocore-1.42.86.tar.gz", hash = "sha256:baa49e93b4c92d63e0c8288026ee1ef8de83f182743127cc9175504440a48e49"}, ] markers = {main = "extra == \"harmony\""} @@ -362,141 +362,141 @@ numpy = ">=1.21.2" [[package]] name = "charset-normalizer" -version = "3.4.6" +version = "3.4.7" description = "The Real First Universal Charset Detector. 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