diff options
| author | Peter Amstutz | 2020-07-17 14:55:19 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-17 14:55:19 -0400 |
| commit | b34f5f42b9bd7a522b9d9b22d736998c4815d9e7 (patch) | |
| tree | 5fed256bb0e90f7aeb54d9d0cf76bfb1e2ba82b6 /bh20seqanalyzer | |
| parent | abdf121de73e4fdc8144c988f724ad7c04fe235c (diff) | |
| download | bh20-seq-resource-b34f5f42b9bd7a522b9d9b22d736998c4815d9e7.tar.gz bh20-seq-resource-b34f5f42b9bd7a522b9d9b22d736998c4815d9e7.tar.lz bh20-seq-resource-b34f5f42b9bd7a522b9d9b22d736998c4815d9e7.zip | |
Make sure move_fastq_to_fasta_results gets everything
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 37 |
1 files changed, 20 insertions, 17 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index b3a439d..ad3c3d7 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -211,9 +211,10 @@ class SeqAnalyzer: self.run_workflow(self.pangenome_analysis_project, self.pangenome_workflow_uuid, "Pangenome analysis", inputobj) - def get_workflow_output_from_project(self, uuid): + def get_workflow_output_from_project(self, uuid, named): cr = self.api.container_requests().list(filters=[['owner_uuid', '=', uuid], - ["requesting_container_uuid", "=", None]]).execute() + ["requesting_container_uuid", "=", None], + ["name", "=", named]]).execute() if cr["items"] and cr["items"][0]["output_uuid"]: container = self.api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute() if container["state"] == "Complete" and container["exit_code"] == 0: @@ -225,24 +226,26 @@ class SeqAnalyzer: most_recent_analysis = self.api.groups().list(filters=[['owner_uuid', '=', self.pangenome_analysis_project]], order="created_at desc").execute() for m in most_recent_analysis["items"]: - wf = self.get_workflow_output_from_project(m["uuid"]) - if wf: - src = self.api.collections().get(uuid=wf["output_uuid"]).execute() - dst = self.api.collections().get(uuid=self.latest_result_uuid).execute() - if src["portable_data_hash"] != dst["portable_data_hash"]: - logging.info("Copying latest result from '%s' to %s", m["name"], self.latest_result_uuid) - self.api.collections().update(uuid=self.latest_result_uuid, - body={"manifest_text": src["manifest_text"], - "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() - break + wf = self.get_workflow_output_from_project(m["uuid"], "pangenome-generate.cwl") + if wf is None: + continue + src = self.api.collections().get(uuid=wf["output_uuid"]).execute() + dst = self.api.collections().get(uuid=self.latest_result_uuid).execute() + if src["portable_data_hash"] != dst["portable_data_hash"]: + logging.info("Copying latest result from '%s' to %s", m["name"], self.latest_result_uuid) + self.api.collections().update(uuid=self.latest_result_uuid, + body={"manifest_text": src["manifest_text"], + "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() + break def move_fastq_to_fasta_results(self): - projects = self.api.groups().list(filters=[['owner_uuid', '=', self.fastq_project], - ["properties.moved_output", "!=", True]], - order="created_at asc",).execute() - for p in projects["items"]: - wf = self.get_workflow_output_from_project(p["uuid"]) + projects = arvados.util.list_all(self.api.groups().list, + filters=[['owner_uuid', '=', self.fastq_project], + ["properties.moved_output", "!=", True]], + order="created_at asc") + for p in projects: + wf = self.get_workflow_output_from_project(p["uuid"], "fastq2fasta.cwl") if not wf: continue |