seer-pas-sdk 0.3.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

seer_pas_sdk/objects/__init__.py

@@ -1,3 +1,4 @@
 from .platemap import PlateMap
 from .groupanalysis import GroupAnalysisPostData
 from .volcanoplot import *
+from .headers import *

seer_pas_sdk/objects/headers.py

@@ -0,0 +1,144 @@
+# headers.py
+# # This file contains entity headers for the Seer PAS SDK.
+
+
+PLATE_COLUMNS = [
+    "id",
+    "plate_name",
+    "plate_id",
+    "description",
+    "notes",
+    "created_by",
+    "created_timestamp",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "space",
+]
+
+PROJECT_COLUMNS = [
+    "id",
+    "project_name",
+    "description",
+    "notes",
+    "created_by",
+    "created_timestamp",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "plates",
+    "sampleTypes",
+    "space",
+]
+
+SAMPLE_COLUMNS = [
+    "id",
+    "plate_id",
+    "sample_name",
+    "sample_id",
+    "sample_type",
+    "species",
+    "description",
+    "notes",
+    "created_by",
+    "created_timestamp",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "sample_receipt_date",
+    "sample_collection_date",
+    "condition",
+    "plate_name",
+    "biological_replicate",
+    "technical_replicate",
+    "well_location",
+    "control",
+    "space",
+]
+
+ANALYSIS_COLUMNS = [
+    "id",
+    "analysis_name",
+    "description",
+    "notes",
+    "analysis_protocol_id",
+    "analyzed_by",
+    "start_time",
+    "end_time",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "status",
+    "result_folder",
+    "job_id",
+    "space",
+    "project_id",
+    "number_msdatafile",
+    "protein_group_count",
+    "single_protein_group_count",
+    "possible_protein_set_size",
+    "peptides_count",
+    "contains_control",
+    "job_log_stream_name",
+    "contains_sample",
+    "is_folder",
+    "folder_id",
+    "number_sample",
+    "total_file_size_mb",
+    "msdatafile_extensions",
+    "fasta",
+]
+
+ANALYSIS_PROTOCOL_COLUMNS = [
+    "id",
+    "analysis_protocol_name",
+    "analysis_type",
+    "version_number",
+    "description",
+    "notes",
+    "created_by",
+    "created_timestamp",
+    "parameter_file_path",
+    "species",
+    "alg_version",
+    "analysis_engine",
+    "offering_name",
+    "based_on",
+    "retired",
+    "use_normalization",
+    "pipeline_w_version",
+    "archived",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "go_version",
+    "space",
+    "fasta",
+]
+
+MSRUN_COLUMNS = [
+    "id",
+    "raw_file_path",
+    "sample_id",
+    "sample_id_tracking",
+    "well_location",
+    "nanoparticle",
+    "nanoparticle_id",
+    "control",
+    "control_id",
+    "instrument_name",
+    "date_sample_prep",
+    "sample_volume",
+    "peptide_concentration",
+    "peptide_mass_sample",
+    "dilution_factor",
+    "kit_id",
+    "created_by",
+    "created_timestamp",
+    "last_modified_by",
+    "last_modified_timestamp",
+    "injection_timestamp",
+    "ms_instrument_sn",
+    "recon_volume",
+    "gradient",
+    "assay_product",
+    "method_set_id",
+    "assay_method_id",
+    "sample_tube_id",
+    "space",
+]

seer_pas_sdk/objects/volcanoplot.py

@@ -147,14 +147,15 @@ class VolcanoPlotBuilder:
         Returns:
             dict: The row data
         """
-        self.protein_gene_map[data[self.feature_type_index]] = data["gene"]
+        if "gene" in data:
+            self.protein_gene_map[data[self.feature_type_index]] = data["gene"]
 
         row = dict(
             logFD=data["logFD"],
             negativeLog10P=data["negativeLog10P"],
             dataIndex=i,
             rowID=json.dumps(data),
-            gene=data["gene"],
+            gene=data.get("gene", ""),
             group=self.get_contrast_group_string(data),
             significant=self.get_significance_class(data),
             euclideanDistance=self.calculate_euclidean_distance(

{seer_pas_sdk-0.3.4.dist-info → seer_pas_sdk-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seer-pas-sdk
-Version: 0.3.4
+Version: 1.1.0
 Summary: SDK for Seer Proteograph Analysis Suite (PAS)
 Author-email: Ryan Sun <rsun@seer.bio>
 License: 
@@ -194,7 +194,6 @@ License-File: LICENSE.txt
 Requires-Dist: boto3>=1.26.152
 Requires-Dist: botocore>=1.29.152
 Requires-Dist: pandas>=2.0.1
-Requires-Dist: numpy<2.0.0,>=1.5.3
 Requires-Dist: PyJWT>=2.8.0
 Requires-Dist: python-dotenv>=1.0.0
 Requires-Dist: Requests>=2.31.0

seer_pas_sdk-1.1.0.dist-info/RECORD

@@ -0,0 +1,19 @@
+seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
+seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
+seer_pas_sdk/auth/auth.py,sha256=_SI5CdEkfqfr4o5BQ79BuPbxGeI9p7tqxJd7mUqSAkI,8854
+seer_pas_sdk/common/__init__.py,sha256=8r-xF0alzIdCRdtpQCWKs6pQFrOi9KYnO7EwP8Pm94A,23475
+seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
+seer_pas_sdk/common/groupanalysis.py,sha256=DxB-gbQfYzl7p9MTYWDIqghcH-IeakzdYdrRZrlIHek,1730
+seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
+seer_pas_sdk/core/sdk.py,sha256=OKN7z11hm0Uzx-1yO3YxiN4OCar_4tjDwpKQBjzXeD0,160092
+seer_pas_sdk/core/unsupported.py,sha256=7iAY2vrOq49YNXLzSMrEOK3f9wJhpTx8UyGBjMymLxI,68919
+seer_pas_sdk/objects/__init__.py,sha256=r-lY7axLTzToAI-Dme019YfcJLDe2ok1f_e6OQx3j64,130
+seer_pas_sdk/objects/groupanalysis.py,sha256=x3D_5NmYBoPDilNCQqUoCFARIfIeUq4FBY3_N6u8tfM,994
+seer_pas_sdk/objects/headers.py,sha256=RilNzB_Nhid3U8j93BxJYcRrgDmd_1bAuI0P465xd0g,2727
+seer_pas_sdk/objects/platemap.py,sha256=8IvJPAecs_e_FyqibzhCw-O4zjCFnf-zMUp_5krTEsg,5864
+seer_pas_sdk/objects/volcanoplot.py,sha256=lTrTOVg74nT3uo-P1edQJC1ZbdoiLMtQ3VJd9CnzmoM,9396
+seer_pas_sdk-1.1.0.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
+seer_pas_sdk-1.1.0.dist-info/METADATA,sha256=wcrzQ-A0gt3XJV3_km9Cuo02K2wOUBoCJb2NFrmHwSc,13413
+seer_pas_sdk-1.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+seer_pas_sdk-1.1.0.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
+seer_pas_sdk-1.1.0.dist-info/RECORD,,

seer_pas_sdk-0.3.4.dist-info/RECORD

@@ -1,18 +0,0 @@
-seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
-seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
-seer_pas_sdk/auth/auth.py,sha256=C9XQWg2dScHcvvypqnjmluRlH-GEuc4D9rYyG9_OnN0,2965
-seer_pas_sdk/common/__init__.py,sha256=jA5qm-t9x3qXMp5Q6v7vV2kZdLw32-lnbtf0fPY4lIw,22482
-seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
-seer_pas_sdk/common/groupanalysis.py,sha256=DxB-gbQfYzl7p9MTYWDIqghcH-IeakzdYdrRZrlIHek,1730
-seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
-seer_pas_sdk/core/sdk.py,sha256=NHhUCxuhea_KhCd3FLpojCwkOZDIZuvjU7K52h695KY,108508
-seer_pas_sdk/core/unsupported.py,sha256=XAPZ3tidqjnsgftf3NUdTGIzvnsjHy0e_eGRCAo6GPo,59890
-seer_pas_sdk/objects/__init__.py,sha256=HJLS6sOr7DfzdI14fv5dWcITEj5QQsKcdfED3YNvUrY,107
-seer_pas_sdk/objects/groupanalysis.py,sha256=x3D_5NmYBoPDilNCQqUoCFARIfIeUq4FBY3_N6u8tfM,994
-seer_pas_sdk/objects/platemap.py,sha256=8IvJPAecs_e_FyqibzhCw-O4zjCFnf-zMUp_5krTEsg,5864
-seer_pas_sdk/objects/volcanoplot.py,sha256=tKuCWDIdoO8FLJlhpXhuwHn0aMYnvudTugxAslDXyGs,9357
-seer_pas_sdk-0.3.4.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
-seer_pas_sdk-0.3.4.dist-info/METADATA,sha256=QuSAislG3NV9SE66n1xNF4Kf7Nk704jSEPCyefSoP_E,13448
-seer_pas_sdk-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-seer_pas_sdk-0.3.4.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
-seer_pas_sdk-0.3.4.dist-info/RECORD,,