lamindb 0.76.6__py3-none-any.whl → 0.76.8__py3-none-any.whl

lamindb/core/datasets/_core.py

@@ -1,571 +1,571 @@
-from __future__ import annotations
-
-from pathlib import Path
-from typing import TYPE_CHECKING
-from urllib.request import urlretrieve
-
-import anndata as ad
-import numpy as np
-import pandas as pd
-from lnschema_core import ids
-from upath import UPath
-
-from lamindb.core._settings import settings
-
-if TYPE_CHECKING:
-    from mudata import MuData
-
-
-def file_fcs() -> Path:
-    """Example FCS artifact."""
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/example.fcs", "example.fcs"
-    )
-    return Path(filepath)
-
-
-def file_fcs_alpert19(populate_registries: bool = False) -> Path:  # pragma: no cover
-    """FCS file from Alpert19.
-
-    Args:
-        populate_registries: pre-populate metadata records to simulate existing registries  # noqa
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/Alpert19-070314-Mike-Study+15-2013-plate+1-15-004-1-13_cells_found.fcs",
-        "Alpert19.fcs",
-    )
-    if populate_registries:
-        import bionty as bt
-        import readfcs
-
-        import lamindb as ln
-
-        verbosity = ln.settings.verbosity
-        ln.settings.verbosity = "error"
-        adata = readfcs.read(filepath)
-        std = bt.CellMarker.public().standardize(adata.var.index)
-        ln.save(
-            bt.CellMarker.from_values(
-                bt.CellMarker.public().inspect(std, "name").validated, "name"
-            )
-        )
-        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
-        ln.Feature(name="organism", dtype=[bt.Organism]).save()
-        ln.settings.verbosity = verbosity
-    return Path(filepath)
-
-
-def file_jpg_paradisi05() -> Path:
-    """Return jpg file example.
-
-    Originally from: https://upload.wikimedia.org/wikipedia/commons/2/28/Laminopathic_nuclei.jpg
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/Laminopathic_nuclei.jpg",
-        "paradisi05_laminopathic_nuclei.jpg",
-    )
-    return Path(filepath)
-
-
-def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
-    populate_registries: bool = False,
-) -> Path:  # pragma: no cover
-    """Gene counts table from nf-core RNA-seq pipeline.
-
-    Output of: https://nf-co.re/rnaseq
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/salmon.merged.gene_counts.tsv",
-        "salmon.merged.gene_counts.tsv",
-    )
-    if populate_registries:
-        import bionty as bt
-
-        import lamindb as ln
-
-        verbosity = ln.settings.verbosity
-        ln.settings.verbosity = "error"
-        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
-        ln.Feature(name="organism", dtype=[bt.Organism]).save()
-        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008896").save()
-        ln.settings.verbosity = verbosity
-
-    return Path(filepath)
-
-
-def file_fastq(in_storage_root=False) -> Path:
-    """Mini mock fastq artifact."""
-    basedir = Path() if not in_storage_root else settings.storage.root
-    filepath = basedir / "input.fastq.gz"
-    with open(filepath, "w") as f:
-        f.write("Mock fastq artifact.")
-    return filepath
-
-
-def file_bam(in_storage_root=False) -> Path:  # pragma: no cover
-    """Mini mock bam artifact."""
-    basedir = Path() if not in_storage_root else settings.storage.root
-    filepath = basedir / "output.bam"
-    with open(filepath, "w") as f:
-        f.write("Mock bam artifact.")
-    return filepath
-
-
-def file_mini_csv(in_storage_root=False) -> Path:
-    """Mini csv artifact."""
-    basedir = Path() if not in_storage_root else settings.storage.root
-    filepath = basedir / "mini.csv"
-    df = pd.DataFrame([1, 2, 3], columns=["test"])
-    df.to_csv(filepath, index=False)
-    return filepath
-
-
-def file_tiff_suo22() -> Path:  # pragma: no cover
-    """Image file from Suo22.
-
-    Pair with anndata_suo22_Visium10X
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/F121_LP1_4LIV.tiff",
-        "F121_LP1_4LIV.tiff",
-    )
-    Path("suo22/").mkdir(exist_ok=True)
-    filepath = Path(filepath).rename("suo22/F121_LP1_4LIV.tiff")  # type: ignore
-    return Path(filepath)
-
-
-def dir_iris_images() -> UPath:  # pragma: no cover
-    """Directory with 3 studies of the Iris flower: 405 images & metadata.
-
-    Based on: https://github.com/laminlabs/lamindb-dev-datasets/pull/2
-    """
-    return UPath("s3://lamindata/iris_studies")
-
-
-def anndata_mouse_sc_lymph_node(
-    populate_registries: bool = False,
-) -> ad.AnnData:  # pragma: no cover
-    """Mouse lymph node scRNA-seq collection from EBI.
-
-    Subsampled to 10k genes.
-
-    From: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8414/
-
-    Args:
-        populate_registries: pre-populate metadata records to simulate existing registries  # noqa
-    """
-    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/E-MTAB-8414.h5ad")
-    adata = ad.read_h5ad(filepath)
-
-    # The column names are a bit lengthy, let's abbreviate them:
-    adata.obs.columns = (
-        adata.obs.columns.str.replace("Sample Characteristic", "")
-        .str.replace("Factor Value ", "Factor Value:", regex=True)
-        .str.replace("Factor Value\\[", "Factor Value:", regex=True)
-        .str.replace(" Ontology Term\\[", "ontology_id:", regex=True)
-        .str.strip("[]")
-        .str.replace("organism part", "tissue")
-        .str.replace("organism", "organism")
-        .str.replace("developmental stage", "developmental_stage")
-        .str.replace("cell type", "cell_type")
-        # the last one could be interesting, too
-        # .str.replace("Factor Value:Ontology Term[inferred cell_type - authors labels", "cell_type_authors")
-    )
-    # subset columns to only the ones with names
-    columns = [
-        col
-        for col in adata.obs.columns
-        if not col.startswith("ontology_id")
-        and not col.startswith("Factor Value")
-        and col != "strain"
-    ]
-    adata.obs = adata.obs[columns]
-
-    # pre-populate registries
-    if populate_registries:
-        import bionty as bt
-
-        import lamindb as ln
-
-        verbosity = ln.settings.verbosity
-        ln.settings.verbosity = "error"
-        # strain
-        bt.ExperimentalFactor.from_source(ontology_id="EFO:0004472").save()
-        # developmental stage
-        bt.ExperimentalFactor.from_source(ontology_id="EFO:0001272").save()
-        # tissue
-        bt.Tissue.from_source(ontology_id="UBERON:0001542").save()
-        # cell types
-        ln.save(bt.CellType.from_values(["CL:0000115", "CL:0000738"], "ontology_id"))
-        # assays
-        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
-        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
-        # genes
-        validated = bt.Gene.public(organism="mouse").validate(
-            adata.var.index, field="ensembl_gene_id"
-        )
-        ln.save(
-            bt.Gene.from_values(
-                adata.var.index[validated][:-19],
-                field="ensembl_gene_id",
-                organism="mouse",
-            )
-        )
-        # labels
-        labels = []
-        for col in ["sex", "age", "genotype", "immunophenotype"]:
-            labels += [ln.ULabel(name=name) for name in adata.obs[col]]
-        ln.save(labels)
-        ln.settings.verbosity = verbosity
-
-    return adata
-
-
-def anndata_pbmc68k_reduced() -> ad.AnnData:
-    """Modified from scanpy.collections.pbmc68k_reduced().
-
-    This code was run::
-
-        pbmc68k = sc.collections.pbmc68k_reduced()
-        pbmc68k.obs.rename(columns={"bulk_labels": "cell_type"}, inplace=True)
-        pbmc68k.obs["cell_type"] = pbmc68k.obs["cell_type"].cat.rename_categories(
-            {"Dendritic": "Dendritic cells", "CD14+ Monocyte": "CD14+ Monocytes"}
-        )
-        del pbmc68k.obs["G2M_score"]
-        del pbmc68k.obs["S_score"]
-        del pbmc68k.obs["phase"]
-        del pbmc68k.obs["n_counts"]
-        del pbmc68k.var["dispersions"]
-        del pbmc68k.var["dispersions_norm"]
-        del pbmc68k.var["means"]
-        del pbmc68k.uns["rank_genes_groups"]
-        del pbmc68k.uns["bulk_labels_colors"]
-        sc.pp.subsample(pbmc68k, fraction=0.1, random_state=123)
-        pbmc68k.write("scrnaseq_pbmc68k_tiny.h5ad")
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-dev-datasets.s3.amazonaws.com/scrnaseq_pbmc68k_tiny.h5ad"
-    )
-    return ad.read_h5ad(filepath)
-
-
-def anndata_file_pbmc68k_test() -> Path:
-    """Modified from scanpy.collections.pbmc68k_reduced().
-
-    Additional slots were added for testing purposes. Returns the filepath.
-
-    To reproduce::
-
-        pbmc68k = ln.core.datasets.anndata_pbmc68k_reduced()
-        pbmc68k_test = pbmc68k[:30, :200].copy()
-        pbmc68k_test.raw = pbmc68k_test[:, :100]
-        pbmc68k_test.obsp["test"] = sparse.eye(pbmc68k_test.shape[0], format="csr")
-        pbmc68k_test.varp["test"] = sparse.eye(pbmc68k_test.shape[1], format="csr")
-        pbmc68k_test.layers["test"] = sparse.csr_matrix(pbmc68k_test.shape)
-        pbmc68k_test.layers["test"][0] = 1.
-        pbmc68k_test.write("pbmc68k_test.h5ad")
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/pbmc68k_test.h5ad", "pbmc68k_test.h5ad"
-    )
-    return Path(filepath)
-
-
-def anndata_pbmc3k_processed() -> ad.AnnData:  # pragma: no cover
-    """Modified from scanpy.pbmc3k_processed()."""
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/scrnaseq_scanpy_pbmc3k_processed.h5ad"
-    )
-    pbmc3k = ad.read_h5ad(filepath)
-    pbmc3k.obs.rename(columns={"louvain": "cell_type"}, inplace=True)
-    return pbmc3k
-
-
-def anndata_human_immune_cells(
-    populate_registries: bool = False,
-) -> ad.AnnData:  # pragma: no cover
-    """Cross-tissue immune cell analysis reveals tissue-specific features in humans.
-
-    From: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3
-    Collection: Global
-
-    To reproduce the subsample::
-        >>> adata = sc.read('Global.h5ad')
-        >>> adata.obs = adata.obs[['donor_id', 'tissue', 'cell_type', 'assay', 'tissue_ontology_term_id', 'cell_type_ontology_term_id', 'assay_ontology_term_id']].copy()
-        >>> sc.pp.subsample(adata, fraction=0.005)
-        >>> del adata.uns["development_cache_ontology_term_id_colors"]
-        >>> del adata.uns["sex_ontology_term_id_colors"]
-        >>> adata.write('human_immune.h5ad')
-    """
-    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/human_immune.h5ad")
-    adata = ad.read_h5ad(filepath)
-    adata.var.drop(columns=["gene_symbols", "feature_name"], inplace=True)
-    adata.uns.pop("cell_type_ontology_term_id_colors")
-    adata.uns.pop("title")
-    adata.uns.pop("schema_version")
-    adata.obs.columns = adata.obs.columns.str.replace("donor_id", "donor")
-    columns = [col for col in adata.obs.columns if "ontology_term" not in col]
-    adata.obs = adata.obs[columns]
-    if populate_registries:
-        import bionty as bt
-
-        import lamindb as ln
-
-        verbosity = ln.settings.verbosity
-        ln.settings.verbosity = "error"
-        ln.save(
-            bt.Gene.from_values(
-                adata.var.index, field="ensembl_gene_id", organism="human"
-            )
-        )
-        ln.save(bt.CellType.from_values(adata.obs.cell_type, field="name"))
-        ln.save(bt.ExperimentalFactor.from_values(adata.obs.assay, field="name"))
-        ln.save(bt.Tissue.from_values(adata.obs.tissue, field="name"))
-        ln.Feature(name="cell_type", dtype=[bt.CellType]).save()
-        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
-        ln.Feature(name="tissue", dtype=[bt.Tissue]).save()
-        ln.Feature(name="organism", dtype=[bt.Organism]).save()
-        ln.Feature(name="donor", dtype=[ln.ULabel]).save()
-        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
-        ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
-        ln.settings.verbosity = verbosity
-    return adata
-
-
-def anndata_with_obs() -> ad.AnnData:
-    """Create a mini anndata with cell_type, disease and tissue."""
-    import anndata as ad
-    import bionty.base as bionty_base
-
-    celltypes = ["T cell", "hematopoietic stem cell", "hepatocyte", "my new cell type"]
-    celltype_ids = ["CL:0000084", "CL:0000037", "CL:0000182", ""]
-    diseases = [
-        "chronic kidney disease",
-        "liver lymphoma",
-        "cardiac ventricle disorder",
-        "Alzheimer disease",
-    ]
-    tissues = ["kidney", "liver", "heart", "brain"]
-    df = pd.DataFrame()
-    df["cell_type"] = celltypes * 10
-    df["cell_type_id"] = celltype_ids * 10
-    df["tissue"] = tissues * 10
-    df["disease"] = diseases * 10
-    df.index = "obs" + df.index.astype(str)
-
-    adata = ad.AnnData(X=np.zeros(shape=(40, 100), dtype=np.float32), obs=df)
-    adata.var.index = bionty_base.Gene().df().head(100)["ensembl_gene_id"].values
-
-    return adata
-
-
-def anndata_suo22_Visium10X():  # pragma: no cover
-    """AnnData from Suo22 generated by 10x Visium."""
-    import anndata as ad
-
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/suo22_Visium10X_data_LI_subset.h5ad",
-        "Visium10X_data_LI_subset.h5ad",
-    )
-    Path("suo22/").mkdir(exist_ok=True)
-    filepath = Path(filepath).rename("suo22/Visium10X_data_LI_subset.h5ad")
-    return ad.read_h5ad(filepath)
-
-
-def mudata_papalexi21_subset() -> MuData:  # pragma: no cover
-    """A subsetted mudata from papalexi21.
-
-    To reproduce the subsetting:
-        >>> !wget https://figshare.com/ndownloader/files/36509460
-        >>> import mudata as md
-        >>> import scanpy as sc
-        >>> mdata = md.read_h5mu("36509460")
-        >>> mdata = sc.pp.subsample(mdata, n_obs=200, copy=True)[0]
-        >>> mdata[:, -300:].copy().write("papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu")
-    """
-    import mudata as md
-
-    md.set_options(pull_on_update=False)
-
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu",
-        "papalexi21_subset.h5mu",
-    )
-
-    mdata = md.read_h5mu(filepath)
-
-    mdata.pull_obs()
-
-    # The MuData object is malformed with duplicated information
-    # Drop all columns for the modalities and add them again correspondingly
-    for mod in ["rna", "adt", "hto", "gdo"]:
-        mdata[mod].obs.drop(mdata[mod].obs.columns, axis=1, inplace=True)
-    for col in mdata.obs.columns:
-        for mod in ["rna", "adt", "hto", "gdo"]:
-            if col.endswith(f"_{mod.upper()}"):
-                new_col = col.replace(f"{mod}:", "")
-                if new_col != col:
-                    mdata[mod].obs[new_col] = mdata.obs.pop(col)
-            else:
-                new_col = col.replace(f"{mod}:", "")
-                if new_col not in mdata.obs.columns and col in mdata.obs.columns:
-                    mdata.obs[new_col] = mdata.obs.pop(col)
-
-    for col in mdata.obs.columns:
-        for mod in ["rna", "adt", "hto", "gdo"]:
-            if col.endswith(f"_{mod.upper()}"):
-                del mdata.obs[col]
-
-    for col in [
-        "orig.ident",
-        "MULTI_ID",
-        "NT",
-        "S.Score",
-        "G2M.Score",
-        "Phase",
-        "gene_target",
-        "guide_ID",
-        "HTO_classification",
-    ]:
-        del mdata.obs[col]
-
-    mdata.push_obs(["percent.mito"], mods=["rna"], drop=True)
-    mdata["hto"].obs["technique"] = "cell hashing"
-    mdata["hto"].obs["technique"] = mdata["hto"].obs["technique"].astype("category")
-    mdata.pull_obs(["technique"], mods="hto")
-
-    return mdata
-
-
-def df_iris() -> pd.DataFrame:
-    """The iris collection as in sklearn.
-
-    Original code::
-
-        sklearn.collections.load_iris(as_frame=True).frame
-    """
-    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/iris.parquet")
-    return pd.read_parquet(filepath)
-
-
-def df_iris_in_meter() -> pd.DataFrame:
-    """The iris collection with lengths in meter."""
-    df = df_iris()
-    # rename columns
-    df.rename(
-        columns={
-            "sepal length (cm)": "sepal_length",
-            "sepal width (cm)": "sepal_width",
-            "petal length (cm)": "petal_length",
-            "petal width (cm)": "petal_width",
-        },
-        inplace=True,
-    )
-    df[["sepal_length", "sepal_width", "petal_length", "petal_width"]] /= 100
-    df["iris_organism_name"] = df["target"].map(
-        {0: "setosa", 1: "versicolor", 2: "virginica"}
-    )
-    del df["target"]
-    return df
-
-
-def df_iris_in_meter_study1() -> pd.DataFrame:
-    """The iris collection with lengths in meter."""
-    df_iris = df_iris_in_meter()
-    return df_iris.iloc[: len(df_iris) // 2]
-
-
-def df_iris_in_meter_study2() -> pd.DataFrame:
-    """The iris collection with lengths in meter."""
-    df_iris = df_iris_in_meter()
-    return df_iris.iloc[len(df_iris) // 2 :]
-
-
-def dir_scrnaseq_cellranger(
-    sample_name: str, basedir: str | Path = "./", output_only: bool = True
-):  # pragma: no cover
-    """Generate mock cell ranger outputs.
-
-    Args:
-        sample_name: name of the sample
-        basedir: run directory
-        output_only: only generate output files
-    """
-    basedir = Path(basedir)
-
-    if not output_only:  # pragma: no cover
-        fastqdir = basedir / "fastq"
-        fastqdir.mkdir(parents=True, exist_ok=True)
-        fastqfile1 = fastqdir / f"{sample_name}_R1_001.fastq.gz"
-        with open(fastqfile1, "w") as f:
-            f.write(f"{ids.base62(n_char=6)}")
-        fastqfile2 = fastqdir / f"{sample_name}_R2_001.fastq.gz"
-        fastqfile2.touch(exist_ok=True)
-        with open(fastqfile2, "w") as f:
-            f.write(f"{ids.base62(n_char=6)}")
-
-    sampledir = basedir / f"{sample_name}"
-    for folder in ["raw_feature_bc_matrix", "filtered_feature_bc_matrix", "analysis"]:
-        filedir = sampledir / folder
-        filedir.mkdir(parents=True, exist_ok=True)
-
-    for filename in [
-        "web_summary.html",
-        "metrics_summary.csv",
-        "possorted_genome_bam.bam",
-        "possorted_genome_bam.bam.bai",
-        "molecule_info.h5",
-        "cloupe.cloupe",
-        "raw_feature_bc_matrix.h5",
-        "raw_feature_bc_matrix/barcodes.tsv.gz",
-        "raw_feature_bc_matrix/features.tsv.gz",
-        "raw_feature_bc_matrix/matrix.mtx.gz",
-        "filtered_feature_bc_matrix.h5",
-        "filtered_feature_bc_matrix/barcodes.tsv.gz",
-        "filtered_feature_bc_matrix/features.tsv.gz",
-        "filtered_feature_bc_matrix/matrix.mtx.gz",
-        "analysis/analysis.csv",
-    ]:
-        file = sampledir / filename
-        with open(file, "w") as f:
-            f.write(f"{ids.base62(n_char=6)}")
-
-    return sampledir
-
-
-def schmidt22_crispra_gws_IFNG(basedir=".") -> Path:  # pragma: no cover
-    """CRISPRi screen collection of Schmidt22.
-
-    Originally from: https://zenodo.org/record/5784651
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/schmidt22-crispra-gws-IFNG.csv",
-        "schmidt22-crispra-gws-IFNG.csv",
-    )
-    return Path(filepath).rename(Path(basedir) / filepath)
-
-
-def schmidt22_perturbseq(basedir=".") -> Path:  # pragma: no cover
-    """Perturb-seq collection of Schmidt22.
-
-    Subsampled and converted to h5ad from R file: https://zenodo.org/record/5784651
-
-    To reproduce the subsample:
-    >>> adata = sc.read('HuTcellsCRISPRaPerturbSeq_Re-stimulated.h5ad')
-    >>> adata.obs = adata.obs[['cluster_name']]
-    >>> del adata.obsp
-    >>> del adata.var['features']
-    >>> del adata.obsm['X_pca']
-    >>> del adata.uns
-    >>> del adata.raw
-    >>> del adata.varm
-    >>> adata.obs = adata.obs.reset_index()
-    >>> del adata.obs['index']
-    >>> sc.pp.subsample(adata, 0.03)
-    >>> adata.write('schmidt22_perturbseq.h5ad')
-    """
-    filepath, _ = urlretrieve(
-        "https://lamindb-test.s3.amazonaws.com/schmidt22_perturbseq.h5ad",
-        "schmidt22_perturbseq.h5ad",
-    )
-    return Path(filepath).rename(Path(basedir) / filepath)
+from __future__ import annotations
+
+from pathlib import Path
+from typing import TYPE_CHECKING
+from urllib.request import urlretrieve
+
+import anndata as ad
+import numpy as np
+import pandas as pd
+from lnschema_core import ids
+from upath import UPath
+
+from lamindb.core._settings import settings
+
+if TYPE_CHECKING:
+    from mudata import MuData
+
+
+def file_fcs() -> Path:
+    """Example FCS artifact."""
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/example.fcs", "example.fcs"
+    )
+    return Path(filepath)
+
+
+def file_fcs_alpert19(populate_registries: bool = False) -> Path:  # pragma: no cover
+    """FCS file from Alpert19.
+
+    Args:
+        populate_registries: pre-populate metadata records to simulate existing registries  # noqa
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/Alpert19-070314-Mike-Study+15-2013-plate+1-15-004-1-13_cells_found.fcs",
+        "Alpert19.fcs",
+    )
+    if populate_registries:
+        import bionty as bt
+        import readfcs
+
+        import lamindb as ln
+
+        verbosity = ln.settings.verbosity
+        ln.settings.verbosity = "error"
+        adata = readfcs.read(filepath)
+        std = bt.CellMarker.public().standardize(adata.var.index)
+        ln.save(
+            bt.CellMarker.from_values(
+                bt.CellMarker.public().inspect(std, "name").validated, "name"
+            )
+        )
+        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
+        ln.Feature(name="organism", dtype=[bt.Organism]).save()
+        ln.settings.verbosity = verbosity
+    return Path(filepath)
+
+
+def file_jpg_paradisi05() -> Path:
+    """Return jpg file example.
+
+    Originally from: https://upload.wikimedia.org/wikipedia/commons/2/28/Laminopathic_nuclei.jpg
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/Laminopathic_nuclei.jpg",
+        "paradisi05_laminopathic_nuclei.jpg",
+    )
+    return Path(filepath)
+
+
+def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
+    populate_registries: bool = False,
+) -> Path:  # pragma: no cover
+    """Gene counts table from nf-core RNA-seq pipeline.
+
+    Output of: https://nf-co.re/rnaseq
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/salmon.merged.gene_counts.tsv",
+        "salmon.merged.gene_counts.tsv",
+    )
+    if populate_registries:
+        import bionty as bt
+
+        import lamindb as ln
+
+        verbosity = ln.settings.verbosity
+        ln.settings.verbosity = "error"
+        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
+        ln.Feature(name="organism", dtype=[bt.Organism]).save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008896").save()
+        ln.settings.verbosity = verbosity
+
+    return Path(filepath)
+
+
+def file_fastq(in_storage_root=False) -> Path:
+    """Mini mock fastq artifact."""
+    basedir = Path() if not in_storage_root else settings.storage.root
+    filepath = basedir / "input.fastq.gz"
+    with open(filepath, "w") as f:
+        f.write("Mock fastq artifact.")
+    return filepath
+
+
+def file_bam(in_storage_root=False) -> Path:  # pragma: no cover
+    """Mini mock bam artifact."""
+    basedir = Path() if not in_storage_root else settings.storage.root
+    filepath = basedir / "output.bam"
+    with open(filepath, "w") as f:
+        f.write("Mock bam artifact.")
+    return filepath
+
+
+def file_mini_csv(in_storage_root=False) -> Path:
+    """Mini csv artifact."""
+    basedir = Path() if not in_storage_root else settings.storage.root
+    filepath = basedir / "mini.csv"
+    df = pd.DataFrame([1, 2, 3], columns=["test"])
+    df.to_csv(filepath, index=False)
+    return filepath
+
+
+def file_tiff_suo22() -> Path:  # pragma: no cover
+    """Image file from Suo22.
+
+    Pair with anndata_suo22_Visium10X
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/F121_LP1_4LIV.tiff",
+        "F121_LP1_4LIV.tiff",
+    )
+    Path("suo22/").mkdir(exist_ok=True)
+    filepath = Path(filepath).rename("suo22/F121_LP1_4LIV.tiff")  # type: ignore
+    return Path(filepath)
+
+
+def dir_iris_images() -> UPath:  # pragma: no cover
+    """Directory with 3 studies of the Iris flower: 405 images & metadata.
+
+    Based on: https://github.com/laminlabs/lamindb-dev-datasets/pull/2
+    """
+    return UPath("s3://lamindata/iris_studies")
+
+
+def anndata_mouse_sc_lymph_node(
+    populate_registries: bool = False,
+) -> ad.AnnData:  # pragma: no cover
+    """Mouse lymph node scRNA-seq collection from EBI.
+
+    Subsampled to 10k genes.
+
+    From: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8414/
+
+    Args:
+        populate_registries: pre-populate metadata records to simulate existing registries  # noqa
+    """
+    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/E-MTAB-8414.h5ad")
+    adata = ad.read_h5ad(filepath)
+
+    # The column names are a bit lengthy, let's abbreviate them:
+    adata.obs.columns = (
+        adata.obs.columns.str.replace("Sample Characteristic", "")
+        .str.replace("Factor Value ", "Factor Value:", regex=True)
+        .str.replace("Factor Value\\[", "Factor Value:", regex=True)
+        .str.replace(" Ontology Term\\[", "ontology_id:", regex=True)
+        .str.strip("[]")
+        .str.replace("organism part", "tissue")
+        .str.replace("organism", "organism")
+        .str.replace("developmental stage", "developmental_stage")
+        .str.replace("cell type", "cell_type")
+        # the last one could be interesting, too
+        # .str.replace("Factor Value:Ontology Term[inferred cell_type - authors labels", "cell_type_authors")
+    )
+    # subset columns to only the ones with names
+    columns = [
+        col
+        for col in adata.obs.columns
+        if not col.startswith("ontology_id")
+        and not col.startswith("Factor Value")
+        and col != "strain"
+    ]
+    adata.obs = adata.obs[columns]
+
+    # pre-populate registries
+    if populate_registries:
+        import bionty as bt
+
+        import lamindb as ln
+
+        verbosity = ln.settings.verbosity
+        ln.settings.verbosity = "error"
+        # strain
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0004472").save()
+        # developmental stage
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0001272").save()
+        # tissue
+        bt.Tissue.from_source(ontology_id="UBERON:0001542").save()
+        # cell types
+        ln.save(bt.CellType.from_values(["CL:0000115", "CL:0000738"], "ontology_id"))
+        # assays
+        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
+        # genes
+        validated = bt.Gene.public(organism="mouse").validate(
+            adata.var.index, field="ensembl_gene_id"
+        )
+        ln.save(
+            bt.Gene.from_values(
+                adata.var.index[validated][:-19],
+                field="ensembl_gene_id",
+                organism="mouse",
+            )
+        )
+        # labels
+        labels = []
+        for col in ["sex", "age", "genotype", "immunophenotype"]:
+            labels += [ln.ULabel(name=name) for name in adata.obs[col]]
+        ln.save(labels)
+        ln.settings.verbosity = verbosity
+
+    return adata
+
+
+def anndata_pbmc68k_reduced() -> ad.AnnData:
+    """Modified from scanpy.collections.pbmc68k_reduced().
+
+    This code was run::
+
+        pbmc68k = sc.collections.pbmc68k_reduced()
+        pbmc68k.obs.rename(columns={"bulk_labels": "cell_type"}, inplace=True)
+        pbmc68k.obs["cell_type"] = pbmc68k.obs["cell_type"].cat.rename_categories(
+            {"Dendritic": "Dendritic cells", "CD14+ Monocyte": "CD14+ Monocytes"}
+        )
+        del pbmc68k.obs["G2M_score"]
+        del pbmc68k.obs["S_score"]
+        del pbmc68k.obs["phase"]
+        del pbmc68k.obs["n_counts"]
+        del pbmc68k.var["dispersions"]
+        del pbmc68k.var["dispersions_norm"]
+        del pbmc68k.var["means"]
+        del pbmc68k.uns["rank_genes_groups"]
+        del pbmc68k.uns["bulk_labels_colors"]
+        sc.pp.subsample(pbmc68k, fraction=0.1, random_state=123)
+        pbmc68k.write("scrnaseq_pbmc68k_tiny.h5ad")
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-dev-datasets.s3.amazonaws.com/scrnaseq_pbmc68k_tiny.h5ad"
+    )
+    return ad.read_h5ad(filepath)
+
+
+def anndata_file_pbmc68k_test() -> Path:
+    """Modified from scanpy.collections.pbmc68k_reduced().
+
+    Additional slots were added for testing purposes. Returns the filepath.
+
+    To reproduce::
+
+        pbmc68k = ln.core.datasets.anndata_pbmc68k_reduced()
+        pbmc68k_test = pbmc68k[:30, :200].copy()
+        pbmc68k_test.raw = pbmc68k_test[:, :100]
+        pbmc68k_test.obsp["test"] = sparse.eye(pbmc68k_test.shape[0], format="csr")
+        pbmc68k_test.varp["test"] = sparse.eye(pbmc68k_test.shape[1], format="csr")
+        pbmc68k_test.layers["test"] = sparse.csr_matrix(pbmc68k_test.shape)
+        pbmc68k_test.layers["test"][0] = 1.
+        pbmc68k_test.write("pbmc68k_test.h5ad")
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/pbmc68k_test.h5ad", "pbmc68k_test.h5ad"
+    )
+    return Path(filepath)
+
+
+def anndata_pbmc3k_processed() -> ad.AnnData:  # pragma: no cover
+    """Modified from scanpy.pbmc3k_processed()."""
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/scrnaseq_scanpy_pbmc3k_processed.h5ad"
+    )
+    pbmc3k = ad.read_h5ad(filepath)
+    pbmc3k.obs.rename(columns={"louvain": "cell_type"}, inplace=True)
+    return pbmc3k
+
+
+def anndata_human_immune_cells(
+    populate_registries: bool = False,
+) -> ad.AnnData:  # pragma: no cover
+    """Cross-tissue immune cell analysis reveals tissue-specific features in humans.
+
+    From: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3
+    Collection: Global
+
+    To reproduce the subsample::
+        >>> adata = sc.read('Global.h5ad')
+        >>> adata.obs = adata.obs[['donor_id', 'tissue', 'cell_type', 'assay', 'tissue_ontology_term_id', 'cell_type_ontology_term_id', 'assay_ontology_term_id']].copy()
+        >>> sc.pp.subsample(adata, fraction=0.005)
+        >>> del adata.uns["development_cache_ontology_term_id_colors"]
+        >>> del adata.uns["sex_ontology_term_id_colors"]
+        >>> adata.write('human_immune.h5ad')
+    """
+    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/human_immune.h5ad")
+    adata = ad.read_h5ad(filepath)
+    adata.var.drop(columns=["gene_symbols", "feature_name"], inplace=True)
+    adata.uns.pop("cell_type_ontology_term_id_colors")
+    adata.uns.pop("title")
+    adata.uns.pop("schema_version")
+    adata.obs.columns = adata.obs.columns.str.replace("donor_id", "donor")
+    columns = [col for col in adata.obs.columns if "ontology_term" not in col]
+    adata.obs = adata.obs[columns]
+    if populate_registries:
+        import bionty as bt
+
+        import lamindb as ln
+
+        verbosity = ln.settings.verbosity
+        ln.settings.verbosity = "error"
+        ln.save(
+            bt.Gene.from_values(
+                adata.var.index, field="ensembl_gene_id", organism="human"
+            )
+        )
+        ln.save(bt.CellType.from_values(adata.obs.cell_type, field="name"))
+        ln.save(bt.ExperimentalFactor.from_values(adata.obs.assay, field="name"))
+        ln.save(bt.Tissue.from_values(adata.obs.tissue, field="name"))
+        ln.Feature(name="cell_type", dtype=[bt.CellType]).save()
+        ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
+        ln.Feature(name="tissue", dtype=[bt.Tissue]).save()
+        ln.Feature(name="organism", dtype=[bt.Organism]).save()
+        ln.Feature(name="donor", dtype=[ln.ULabel]).save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
+        ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
+        ln.settings.verbosity = verbosity
+    return adata
+
+
+def anndata_with_obs() -> ad.AnnData:
+    """Create a mini anndata with cell_type, disease and tissue."""
+    import anndata as ad
+    import bionty.base as bionty_base
+
+    celltypes = ["T cell", "hematopoietic stem cell", "hepatocyte", "my new cell type"]
+    celltype_ids = ["CL:0000084", "CL:0000037", "CL:0000182", ""]
+    diseases = [
+        "chronic kidney disease",
+        "liver lymphoma",
+        "cardiac ventricle disorder",
+        "Alzheimer disease",
+    ]
+    tissues = ["kidney", "liver", "heart", "brain"]
+    df = pd.DataFrame()
+    df["cell_type"] = celltypes * 10
+    df["cell_type_id"] = celltype_ids * 10
+    df["tissue"] = tissues * 10
+    df["disease"] = diseases * 10
+    df.index = "obs" + df.index.astype(str)
+
+    adata = ad.AnnData(X=np.zeros(shape=(40, 100), dtype=np.float32), obs=df)
+    adata.var.index = bionty_base.Gene().df().head(100)["ensembl_gene_id"].values
+
+    return adata
+
+
+def anndata_suo22_Visium10X():  # pragma: no cover
+    """AnnData from Suo22 generated by 10x Visium."""
+    import anndata as ad
+
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/suo22_Visium10X_data_LI_subset.h5ad",
+        "Visium10X_data_LI_subset.h5ad",
+    )
+    Path("suo22/").mkdir(exist_ok=True)
+    filepath = Path(filepath).rename("suo22/Visium10X_data_LI_subset.h5ad")
+    return ad.read_h5ad(filepath)
+
+
+def mudata_papalexi21_subset() -> MuData:  # pragma: no cover
+    """A subsetted mudata from papalexi21.
+
+    To reproduce the subsetting:
+        >>> !wget https://figshare.com/ndownloader/files/36509460
+        >>> import mudata as md
+        >>> import scanpy as sc
+        >>> mdata = md.read_h5mu("36509460")
+        >>> mdata = sc.pp.subsample(mdata, n_obs=200, copy=True)[0]
+        >>> mdata[:, -300:].copy().write("papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu")
+    """
+    import mudata as md
+
+    md.set_options(pull_on_update=False)
+
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/papalexi21_subset_200x300_lamindb_demo_2023-07-25.h5mu",
+        "papalexi21_subset.h5mu",
+    )
+
+    mdata = md.read_h5mu(filepath)
+
+    mdata.pull_obs()
+
+    # The MuData object is malformed with duplicated information
+    # Drop all columns for the modalities and add them again correspondingly
+    for mod in ["rna", "adt", "hto", "gdo"]:
+        mdata[mod].obs.drop(mdata[mod].obs.columns, axis=1, inplace=True)
+    for col in mdata.obs.columns:
+        for mod in ["rna", "adt", "hto", "gdo"]:
+            if col.endswith(f"_{mod.upper()}"):
+                new_col = col.replace(f"{mod}:", "")
+                if new_col != col:
+                    mdata[mod].obs[new_col] = mdata.obs.pop(col)
+            else:
+                new_col = col.replace(f"{mod}:", "")
+                if new_col not in mdata.obs.columns and col in mdata.obs.columns:
+                    mdata.obs[new_col] = mdata.obs.pop(col)
+
+    for col in mdata.obs.columns:
+        for mod in ["rna", "adt", "hto", "gdo"]:
+            if col.endswith(f"_{mod.upper()}"):
+                del mdata.obs[col]
+
+    for col in [
+        "orig.ident",
+        "MULTI_ID",
+        "NT",
+        "S.Score",
+        "G2M.Score",
+        "Phase",
+        "gene_target",
+        "guide_ID",
+        "HTO_classification",
+    ]:
+        del mdata.obs[col]
+
+    mdata.push_obs(["percent.mito"], mods=["rna"], drop=True)
+    mdata["hto"].obs["technique"] = "cell hashing"
+    mdata["hto"].obs["technique"] = mdata["hto"].obs["technique"].astype("category")
+    mdata.pull_obs(["technique"], mods="hto")
+
+    return mdata
+
+
+def df_iris() -> pd.DataFrame:
+    """The iris collection as in sklearn.
+
+    Original code::
+
+        sklearn.collections.load_iris(as_frame=True).frame
+    """
+    filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/iris.parquet")
+    return pd.read_parquet(filepath)
+
+
+def df_iris_in_meter() -> pd.DataFrame:
+    """The iris collection with lengths in meter."""
+    df = df_iris()
+    # rename columns
+    df.rename(
+        columns={
+            "sepal length (cm)": "sepal_length",
+            "sepal width (cm)": "sepal_width",
+            "petal length (cm)": "petal_length",
+            "petal width (cm)": "petal_width",
+        },
+        inplace=True,
+    )
+    df[["sepal_length", "sepal_width", "petal_length", "petal_width"]] /= 100
+    df["iris_organism_name"] = df["target"].map(
+        {0: "setosa", 1: "versicolor", 2: "virginica"}
+    )
+    del df["target"]
+    return df
+
+
+def df_iris_in_meter_study1() -> pd.DataFrame:
+    """The iris collection with lengths in meter."""
+    df_iris = df_iris_in_meter()
+    return df_iris.iloc[: len(df_iris) // 2]
+
+
+def df_iris_in_meter_study2() -> pd.DataFrame:
+    """The iris collection with lengths in meter."""
+    df_iris = df_iris_in_meter()
+    return df_iris.iloc[len(df_iris) // 2 :]
+
+
+def dir_scrnaseq_cellranger(
+    sample_name: str, basedir: str | Path = "./", output_only: bool = True
+):  # pragma: no cover
+    """Generate mock cell ranger outputs.
+
+    Args:
+        sample_name: name of the sample
+        basedir: run directory
+        output_only: only generate output files
+    """
+    basedir = Path(basedir)
+
+    if not output_only:  # pragma: no cover
+        fastqdir = basedir / "fastq"
+        fastqdir.mkdir(parents=True, exist_ok=True)
+        fastqfile1 = fastqdir / f"{sample_name}_R1_001.fastq.gz"
+        with open(fastqfile1, "w") as f:
+            f.write(f"{ids.base62(n_char=6)}")
+        fastqfile2 = fastqdir / f"{sample_name}_R2_001.fastq.gz"
+        fastqfile2.touch(exist_ok=True)
+        with open(fastqfile2, "w") as f:
+            f.write(f"{ids.base62(n_char=6)}")
+
+    sampledir = basedir / f"{sample_name}"
+    for folder in ["raw_feature_bc_matrix", "filtered_feature_bc_matrix", "analysis"]:
+        filedir = sampledir / folder
+        filedir.mkdir(parents=True, exist_ok=True)
+
+    for filename in [
+        "web_summary.html",
+        "metrics_summary.csv",
+        "possorted_genome_bam.bam",
+        "possorted_genome_bam.bam.bai",
+        "molecule_info.h5",
+        "cloupe.cloupe",
+        "raw_feature_bc_matrix.h5",
+        "raw_feature_bc_matrix/barcodes.tsv.gz",
+        "raw_feature_bc_matrix/features.tsv.gz",
+        "raw_feature_bc_matrix/matrix.mtx.gz",
+        "filtered_feature_bc_matrix.h5",
+        "filtered_feature_bc_matrix/barcodes.tsv.gz",
+        "filtered_feature_bc_matrix/features.tsv.gz",
+        "filtered_feature_bc_matrix/matrix.mtx.gz",
+        "analysis/analysis.csv",
+    ]:
+        file = sampledir / filename
+        with open(file, "w") as f:
+            f.write(f"{ids.base62(n_char=6)}")
+
+    return sampledir
+
+
+def schmidt22_crispra_gws_IFNG(basedir=".") -> Path:  # pragma: no cover
+    """CRISPRi screen collection of Schmidt22.
+
+    Originally from: https://zenodo.org/record/5784651
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/schmidt22-crispra-gws-IFNG.csv",
+        "schmidt22-crispra-gws-IFNG.csv",
+    )
+    return Path(filepath).rename(Path(basedir) / filepath)
+
+
+def schmidt22_perturbseq(basedir=".") -> Path:  # pragma: no cover
+    """Perturb-seq collection of Schmidt22.
+
+    Subsampled and converted to h5ad from R file: https://zenodo.org/record/5784651
+
+    To reproduce the subsample:
+    >>> adata = sc.read('HuTcellsCRISPRaPerturbSeq_Re-stimulated.h5ad')
+    >>> adata.obs = adata.obs[['cluster_name']]
+    >>> del adata.obsp
+    >>> del adata.var['features']
+    >>> del adata.obsm['X_pca']
+    >>> del adata.uns
+    >>> del adata.raw
+    >>> del adata.varm
+    >>> adata.obs = adata.obs.reset_index()
+    >>> del adata.obs['index']
+    >>> sc.pp.subsample(adata, 0.03)
+    >>> adata.write('schmidt22_perturbseq.h5ad')
+    """
+    filepath, _ = urlretrieve(
+        "https://lamindb-test.s3.amazonaws.com/schmidt22_perturbseq.h5ad",
+        "schmidt22_perturbseq.h5ad",
+    )
+    return Path(filepath).rename(Path(basedir) / filepath)