Merge pull request #361 from broadinstitute/development

Release 1.34.0

Author: bistline

README.md

@@ -3,7 +3,7 @@
 File Ingest Pipeline for Single Cell Portal
 
 [![Build status](https://img.shields.io/circleci/build/github/broadinstitute/scp-ingest-pipeline.svg)](https://circleci.com/gh/broadinstitute/scp-ingest-pipeline)
-[![Code coverage](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline/branch/master/graph/badge.svg)](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline)
+[![Code coverage](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline/branch/main/graph/badge.svg)](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline)
 
 The SCP Ingest Pipeline is an ETL pipeline for single-cell RNA-seq data.
 
@@ -27,21 +27,21 @@ cd scp-ingest-pipeline
 python3 -m venv env --copies
 source env/bin/activate
 pip install -r requirements.txt
-scripts/setup-mongo-dev.sh <PATH_TO_YOUR_VAULT_TOKEN> # E.g. ~/.github-token
+source scripts/setup-mongo-dev.sh
 ```
 
 ### Docker
 
-With Docker running and Vault active on your local machine, run:
+With Docker running and `gcloud` authenticated on your local machine, run:
 
 ```
-scripts/docker-compose-setup.sh -t <PATH_TO_YOUR_VAULT_TOKEN> # E.g. ~/.github-token
+scripts/docker-compose-setup.sh
 ```
 
 If on Apple silicon Mac (e.g. M1), and performance seems poor, consider generating a docker image using the arm64 base. Example test image: gcr.io/broad-singlecellportal-staging/single-cell-portal:development-2.2.0-arm64, usage:
 
 ```
-scripts/docker-compose-setup.sh -i development-2.2.0-arm64 -t <PATH_TO_YOUR_VAULT_TOKEN>
+scripts/docker-compose-setup.sh -i development-2.2.0-arm64
 ```
 
 To update dependencies when in Docker, you can pip install from within the Docker Bash shell after adjusting your requirements.txt.
@@ -132,10 +132,10 @@ Pro-Tip: For local builds, you can try adding docker build options `--progress=p
 
 ### 2. Set up environment variables
 
-Run the following to pull database-specific secrets out of vault (passing in the path to your vault token):
+Run the following to pull database-specific secrets out of Google Secrets Manager (GSM):
 
 ```
-source scripts/setup-mongo-dev.sh ~/.your-vault-token
+source scripts/setup-mongo-dev.sh
 ```
 
 Now run `env` to make sure you've set the following values:
@@ -152,7 +152,8 @@ DATABASE_HOST=<ip address>
 Run the following to export out your default service account JSON keyfile:
 
 ```
-vault read -format=json secret/kdux/scp/development/$(whoami)/scp_service_account.json | jq .data > /tmp/keyfile.json
+GOOGLE_PROJECT=$(gcloud info --format="value(config.project)")
+gcloud secrets versions access latest --project=$GOOGLE_PROJECT --secret=default-sa-keyfile | jq > /tmp/keyfile.json
 ```
 
 ### 4. Start the Docker container

ingest/anndata_.py

@@ -15,19 +15,19 @@ def _field_template(self, field, precision):
 
 
 try:
-    from ingest_files import IngestFiles
+    from ingest_files import DataArray, IngestFiles
     from expression_files.expression_files import GeneExpression
-    from monitor import log_exception
+    from monitor import log_exception, bypass_mongo_writes
     from validation.validate_metadata import list_duplicates
 except ImportError:
     # Used when importing as external package, e.g. imports in single_cell_portal code
-    from .ingest_files import IngestFiles
+    from .ingest_files import DataArray, IngestFiles
     from .expression_files.expression_files import GeneExpression
-    from .monitor import log_exception
+    from .monitor import log_exception, bypass_mongo_writes
     from .validation.validate_metadata import list_duplicates
 
 
-class AnnDataIngestor(GeneExpression, IngestFiles):
+class AnnDataIngestor(GeneExpression, IngestFiles, DataArray):
     ALLOWED_FILE_TYPES = ['application/x-hdf5']
 
     def __init__(self, file_path, study_file_id, study_id, **kwargs):
@@ -57,6 +57,36 @@ def basic_validation(self):
         except ValueError:
             return False
 
+    def create_cell_data_arrays(self):
+        """Extract cell name DataArray documents for raw data"""
+        adata = self.obtain_adata()
+        cells = list(adata.obs_names)
+        # use filename denoting a raw 'fragment' to allow successful ingest and downstream queries
+        raw_filename = "h5ad_frag.matrix.raw.mtx.gz"
+        data_arrays = []
+        for data_array in GeneExpression.create_data_arrays(
+            name=f"{raw_filename} Cells",
+            array_type="cells",
+            values=cells,
+            linear_data_type="Study",
+            linear_data_id=self.study_file_id,
+            cluster_name=raw_filename,
+            study_file_id=self.study_file_id,
+            study_id=self.study_id
+        ):
+            data_arrays.append(data_array)
+
+        return data_arrays
+
+    def ingest_raw_cells(self):
+        """Insert raw count cells into MongoDB"""
+        arrays = self.create_cell_data_arrays()
+        if not bypass_mongo_writes():
+            self.load(arrays, DataArray.COLLECTION_NAME)
+        else:
+            dev_msg = f"Extracted {len(arrays)} DataArray for {self.study_file_id}:{arrays[0]['name']}"
+            IngestFiles.dev_logger.info(dev_msg)
+
     @staticmethod
     def generate_cluster_header(adata, clustering_name):
         """
@@ -117,7 +147,7 @@ def generate_metadata_file(adata, output_name):
         headers = adata.obs.columns.tolist()
         types = []
         for header in headers:
-            if pd.api.types.is_number(adata.obs[header]):
+            if pd.api.types.is_numeric_dtype(adata.obs[header]):
                 types.append("NUMERIC")
             else:
                 types.append("GROUP")

ingest/expression_files/expression_files.py

@@ -101,6 +101,16 @@ def is_raw_count_file(study_id, study_file_id, client):
         QUERY = {"_id": study_file_id, "study_id": study_id}
 
         study_file_doc = list(client[COLLECTION_NAME].find(QUERY)).pop()
+        # special handling of non-reference AnnData files to always return false
+        # this will allow normal extraction of expression data as raw count cells are already ingested during
+        # the "raw_counts" extract phase
+        if (
+          study_file_doc.get("file_type") == "AnnData" and 
+          "ann_data_file_info" in study_file_doc.keys() and 
+          not study_file_doc["ann_data_file_info"].get("reference_file")
+        ):
+            return False
+
         # Name of embedded document that holds 'is_raw_count_files is named expression_file_info.
         # If study files does not have document expression_file_info
         # field, "is_raw_count_files", will not exist.:

ingest/ingest_pipeline.py

@@ -54,6 +54,9 @@
 # Ingest AnnData - happy path processed expression data only extraction
 python ingest_pipeline.py  --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_anndata --ingest-anndata --anndata-file ../tests/data/anndata/trimmed_compliant_pbmc3K.h5ad  --extract "['processed_expression']"
 
+# Ingest AnnData - happy path raw count cell name only extraction
+python ingest_pipeline.py  --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_anndata --ingest-anndata --anndata-file ../tests/data/anndata/trimmed_compliant_pbmc3K.h5ad  --extract "['raw_counts']"
+
 # Ingest AnnData - happy path cluster and metadata extraction
 python ingest_pipeline.py  --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_anndata --ingest-anndata --anndata-file ../tests/data/anndata/trimmed_compliant_pbmc3K.h5ad  --extract "['cluster', 'metadata']" --obsm-keys "['X_umap','X_tsne']"
 
@@ -537,6 +540,9 @@ def extract_from_anndata(self):
                 "extract"
             ):
                 self.anndata.generate_processed_matrix(self.anndata.adata)
+
+            if self.kwargs.get('extract') and "raw_counts" in self.kwargs.get('extract'):
+                self.anndata.ingest_raw_cells()
             self.report_validation("success")
             return 0
         # scanpy unable to open AnnData file

ingest/monitor.py

@@ -129,13 +129,13 @@ def integrate_sentry():
     See also: links to Sentry resources atop this module
     """
 
-    # Ultimately stored in Vault, passed in as environmen variable to PAPI
+    # Ultimately stored in GSM, passed in as environment variable to PAPI
     sentry_DSN = os.environ.get("SENTRY_DSN")
 
     if sentry_DSN is None:
         # Don't log to Sentry unless its DSN is set.
         # This disables Sentry logging in development and test (i.e.,
-        # environments without a SENTRY_DSN in their scp_config vault secret).
+        # environments without a SENTRY_DSN in their scp-config-json GSM secret).
         return
 
     sentry_logging = LoggingIntegration(

scripts/docker-compose-setup.sh

@@ -10,23 +10,18 @@ usage=$(
 cat <<EOF
 $0 [OPTION]
 -i   Set URL for GCR image; helpful if not using latest development
--t   Set GitHub Vault token (e.g. ~/.github-token)
 -h   print this text
 EOF
 )
 
 GCR_IMAGE=""
 VAULT_TOKEN_PATH=""
-while getopts "i:t:h" OPTION; do
+while getopts "i:h" OPTION; do
 case $OPTION in
   i)
     echo "### SETTING GCR IMAGE ###"
     export GCR_IMAGE="$OPTARG"
     ;;
-  t)
-    echo "### SETTING VAULT TOKEN ###"
-    VAULT_TOKEN_PATH="$OPTARG"
-    ;;
   h)
   	echo "$usage"
   	exit 0
@@ -45,13 +40,8 @@ if [[ $GCR_IMAGE = "" ]]; then
   export GCR_IMAGE="${IMAGE_NAME}:${LATEST_TAG}"
 fi
 
-if [[ $VAULT_TOKEN_PATH = "" ]]; then
-  echo "Did not provide VAULT_TOKEN_PATH"
-  exit 1
-fi
-
 echo "### SETTING UP ENVIRONMENT ###"
-./scripts/ingest-local-setup.sh $VAULT_TOKEN_PATH
+./scripts/ingest-local-setup.sh
 
 docker pull $GCR_IMAGE
 

scripts/ingest-local-setup.sh

@@ -4,25 +4,14 @@
 #
 # Keep "Dev env vars" synced with `setup-mongo-dev.sh`
 
-VAULT_TOKEN_PATH="$1"
-if [[ -z "$VAULT_TOKEN_PATH" ]]
-then
-  echo "You must provide a path to a GitHub token to proceed, e.g. ~/.github-token"
-  exit 1
-fi
-vault login -method=github token=$(cat $VAULT_TOKEN_PATH)
-if [[ $? -ne 0 ]]
-then
-  echo "Unable to authenticate into Vault"
-  exit 1
-fi
+GOOGLE_PROJECT=$(gcloud info --format="value(config.project)")
 
 # Dev env vars
 BROAD_USER=`whoami`
 MONGODB_USERNAME='single_cell'
 DATABASE_NAME='single_cell_portal_development'
-MONGODB_PASSWORD=`vault read secret/kdux/scp/development/$BROAD_USER/mongo/user | grep password | awk '{ print $2 }' `
-DATABASE_HOST=`vault read secret/kdux/scp/development/$BROAD_USER/mongo/hostname | grep ip | awk '{ $2=substr($2,2,length($2)-2); print $2 }' ` 
+MONGODB_PASSWORD=$(gcloud secrets versions access latest --project=$GOOGLE_PROJECT --secret=mongo-user | jq .password)
+DATABASE_HOST=$(gcloud secrets versions access latest --project=$GOOGLE_PROJECT --secret=mongo-hostname| jq -r '.ip[0]')
 BYPASS_MONGO_WRITES='yes'
 BARD_HOST_URL="https://terra-bard-dev.appspot.com"