Remove pandas from gsaid api

cg/cli/upload/fohm.py

@@ -79,7 +79,7 @@ def preprocess_all(
     upload_cases = []
     for case_id in cases:
         try:
-            gisaid_api.upload(case_id=case_id)
+            gisaid_api.upload_to_gisaid(case_id)
             fohm_api.update_upload_started_at(case_id=case_id)
             LOG.info(f"Upload of case {case_id} to GISAID was successful")
             upload_cases.append(case_id)

cg/cli/upload/gisaid.py

@@ -1,4 +1,4 @@
-"""Code for uploading genotype data via CLI"""
+"""Code for uploading genotype data via CLI."""
 
 import logging
 
@@ -18,7 +18,7 @@ def upload_to_gisaid(context: CGConfig, case_id: str):
 
     LOG.info("----------------- GISAID UPLOAD -------------------")
 
-    gisaid_api = GisaidAPI(config=context)
+    gisaid_api = GisaidAPI(context)
 
-    gisaid_api.upload(case_id=case_id)
+    gisaid_api.upload_to_gisaid(case_id)
     LOG.info("Upload to GISAID successful")

cg/constants/constants.py

@@ -201,6 +201,7 @@ class FileExtensions(StrEnum):
     CONFIG: str = ".config"
     CRAM: str = ".cram"
     CSV: str = ".csv"
+    FASTA: str = ".fasta"
     FASTQ: str = ".fastq"
     FASTQ_GZ: str = ".fastq.gz"
     GPG: str = ".gpg"

cg/constants/housekeeper_tags.py

@@ -250,3 +250,10 @@ class JanusTags:
 class FohmTag(StrEnum):
     COMPLEMENTARY = "komplettering"
     PANGOLIN_TYPING = "pangolin-typing-fohm"
+
+
+class GisaidTag(StrEnum):
+    FASTA = "gisaid-fasta"
+    CONSENSUS_SAMPLE = "consensus-sample"
+    CSV = "gisaid-csv"
+    LOG = "gisaid-log"

cg/meta/upload/gisaid/models.py

@@ -45,26 +45,26 @@ class GisaidSample(BaseModel):
     model_config = ConfigDict(coerce_numbers_to_str=True)
     case_id: str
     cg_lims_id: str
-    submitter: str
-    region: str
-    region_code: str
-    fn: str
+    covv_authors: str | None = " ,".join(AUTHORS)
     covv_collection_date: str
-    covv_subm_sample_id: str
-    covv_virus_name: str | None = None
+    covv_gender: str | None = "unknown"
+    covv_host: str | None = "Human"
+    covv_location: str | None = None
     covv_orig_lab: str | None = None
-    covv_type: str | None = "betacoronavirus"
+    covv_orig_lab_addr: str | None = None
     covv_passage: str | None = "Original"
-    covv_location: str | None = None
-    covv_host: str | None = "Human"
-    covv_gender: str | None = "unknown"
     covv_patient_age: str | None = "unknown"
     covv_patient_status: str | None = "unknown"
     covv_seq_technology: str | None = "Illumina NovaSeq"
-    covv_orig_lab_addr: str | None = None
     covv_subm_lab: str | None = "Karolinska University Hospital"
     covv_subm_lab_addr: str | None = "171 76 Stockholm, Sweden"
-    covv_authors: str | None = " ,".join(AUTHORS)
+    covv_subm_sample_id: str
+    covv_type: str | None = "betacoronavirus"
+    covv_virus_name: str | None = None
+    fn: str
+    region: str
+    region_code: str
+    submitter: str
 
     @model_validator(mode="before")
     @classmethod

cg/models/gisaid/reports.py

@@ -0,0 +1,11 @@
+"""GISAID report models."""
+
+from pydantic import BaseModel, Field
+
+
+class GisaidComplementaryReport(BaseModel):
+    """Model for validating a GSAID complementary reports."""
+
+    gisaid_accession: str = Field(None, alias="GISAID_accession")
+    sample_number: str = Field(str, alias="provnummer")
+    selection_criteria: str = Field(str, alias="urvalskriterium")

pyproject.toml

@@ -57,7 +57,6 @@ marshmallow = "*"
 MarkupSafe = "*"
 openpyxl = "*"
 packaging = "*"
-pandas = "*"
 paramiko = "*"
 petname = "*"
 psutil = "*"

tests/conftest.py

@@ -28,7 +28,13 @@
 from cg.apps.slurm.slurm_api import SlurmAPI
 from cg.apps.tb.dto.summary_response import AnalysisSummary, StatusSummary
 from cg.constants import FileExtensions, SequencingFileTag, Workflow
-from cg.constants.constants import CaseActions, CustomerId, FileFormat, GenomeVersion, Strandedness
+from cg.constants.constants import (
+    CaseActions,
+    CustomerId,
+    FileFormat,
+    GenomeVersion,
+    Strandedness,
+)
 from cg.constants.gene_panel import GenePanelMasterList
 from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
 from cg.constants.priority import SlurmQos
@@ -49,16 +55,24 @@
 from cg.models import CompressionData
 from cg.models.cg_config import CGConfig, PDCArchivingDirectory
 from cg.models.downsample.downsample_data import DownsampleData
-from cg.models.raredisease.raredisease import RarediseaseParameters, RarediseaseSampleSheetHeaders
+from cg.models.raredisease.raredisease import (
+    RarediseaseParameters,
+    RarediseaseSampleSheetHeaders,
+)
 from cg.models.rnafusion.rnafusion import RnafusionParameters, RnafusionSampleSheetEntry
 from cg.models.run_devices.illumina_run_directory_data import IlluminaRunDirectoryData
-from cg.models.taxprofiler.taxprofiler import TaxprofilerParameters, TaxprofilerSampleSheetEntry
+from cg.models.taxprofiler.taxprofiler import (
+    TaxprofilerParameters,
+    TaxprofilerSampleSheetEntry,
+)
 from cg.models.tomte.tomte import TomteParameters, TomteSampleSheetHeaders
 from cg.services.deliver_files.delivery_rsync_service.delivery_rsync_service import (
     DeliveryRsyncService,
 )
 from cg.services.illumina.backup.encrypt_service import IlluminaRunEncryptionService
-from cg.services.illumina.data_transfer.data_transfer_service import IlluminaDataTransferService
+from cg.services.illumina.data_transfer.data_transfer_service import (
+    IlluminaDataTransferService,
+)
 from cg.store.database import create_all_tables, drop_all_tables, initialize_database
 from cg.store.models import (
     Application,
@@ -110,22 +124,25 @@
     "tests.fixture_plugins.device_fixtures",
     "tests.fixture_plugins.encryption_fixtures.encryption_fixtures",
     "tests.fixture_plugins.fohm.fohm_fixtures",
-    "tests.fixture_plugins.io.csv_fixtures",
+    "tests.fixture_plugins.gisaid_fixtures.gisaid_fixtures",
     "tests.fixture_plugins.illumina_clean_fixtures.clean_fixtures",
+    "tests.fixture_plugins.io.csv_fixtures",
+    "tests.fixture_plugins.io.csv_fixtures",
     "tests.fixture_plugins.loqusdb_fixtures.loqusdb_api_fixtures",
     "tests.fixture_plugins.loqusdb_fixtures.loqusdb_output_fixtures",
     "tests.fixture_plugins.observations_fixtures.observations_api_fixtures",
     "tests.fixture_plugins.observations_fixtures.observations_input_files_fixtures",
+    "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
+    "tests.fixture_plugins.orders_fixtures.order_store_service_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.context_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.metrics_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.name_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.path_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.service_fixtures",
     "tests.fixture_plugins.quality_controller_fixtures.sequencing_qc_check_scenario",
     "tests.fixture_plugins.quality_controller_fixtures.sequencing_qc_fixtures",
+    "tests.fixture_plugins.sample.sample_fixtures",
     "tests.fixture_plugins.timestamp_fixtures",
-    "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
-    "tests.fixture_plugins.orders_fixtures.order_store_service_fixtures",
 ]