mutts 1.0.4__tar.gz → 1.0.5__tar.gz

{mutts-1.0.4 → mutts-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mutts
-Version: 1.0.4
+Version: 1.0.5
 Summary: Metadata for User facility Template Transformations
 License: MIT
 Keywords: NMDC,US DOE user facilities,metadata translation
@@ -62,9 +62,10 @@ The documentation and setup instructions in this section are meant for any user
 
 This is required for running the examples in the [Usage](#usage) section below (after going through all the [Installation](#installation) steps).
 
-Create a `.env` file in your working directory:
+Create a `.env` file in your working directory with the following environment variables:
 ```bash
 echo "DATA_PORTAL_REFRESH_TOKEN=your_token_here" > .env
+echo "SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org" >> .env
 ```
 
 To get your access token:
@@ -187,7 +188,7 @@ The software consists of two main components:
 - The `sub_port_mapping` keyword specifies mappings between Submission Portal columns/slots (as dictated by the [NMDC submission schema](https://microbiomedata.github.io/submission-schema/)) and user facility template columns
 - Examples available in [input-files/](input-files/)
 
-1. **`mutts` CLI**
+2. **`mutts` CLI**
 - Command-line application that performs the metadata conversion
 - Consumes mapper files and submission data as inputs
 
@@ -215,9 +216,10 @@ This installs the `mutts` package in development mode and creates the `mutts` co
 cp .env.example .env  # if available, or create a new .env file
 ```
 
-Add your NMDC API token:
+Add your NMDC API token and submission portal base URL:
 ```
 DATA_PORTAL_REFRESH_TOKEN=your_token_here
+SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org
 ```
 
 Get your token from: https://data.microbiomedata.org/user

{mutts-1.0.4 → mutts-1.0.5}/README.md

@@ -38,9 +38,10 @@ The documentation and setup instructions in this section are meant for any user
 
 This is required for running the examples in the [Usage](#usage) section below (after going through all the [Installation](#installation) steps).
 
-Create a `.env` file in your working directory:
+Create a `.env` file in your working directory with the following environment variables:
 ```bash
 echo "DATA_PORTAL_REFRESH_TOKEN=your_token_here" > .env
+echo "SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org" >> .env
 ```
 
 To get your access token:
@@ -163,7 +164,7 @@ The software consists of two main components:
 - The `sub_port_mapping` keyword specifies mappings between Submission Portal columns/slots (as dictated by the [NMDC submission schema](https://microbiomedata.github.io/submission-schema/)) and user facility template columns
 - Examples available in [input-files/](input-files/)
 
-1. **`mutts` CLI**
+2. **`mutts` CLI**
 - Command-line application that performs the metadata conversion
 - Consumes mapper files and submission data as inputs
 
@@ -191,9 +192,10 @@ This installs the `mutts` package in development mode and creates the `mutts` co
 cp .env.example .env  # if available, or create a new .env file
 ```
 
-Add your NMDC API token:
+Add your NMDC API token and submission portal base URL:
 ```
 DATA_PORTAL_REFRESH_TOKEN=your_token_here
+SUBMISSION_PORTAL_BASE_URL=https://data.microbiomedata.org
 ```
 
 Get your token from: https://data.microbiomedata.org/user

{mutts-1.0.4 → mutts-1.0.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mutts"
-version = "1.0.4"  # dynamic versioning from git tags
+version = "1.0.5"  # dynamic versioning from git tags
 description = "Metadata for User facility Template Transformations"
 authors = [
     "Sujay Patil <spatil@lbl.gov>",

{mutts-1.0.4 → mutts-1.0.5}/src/mutts/cli.py

@@ -107,11 +107,13 @@ def cli(
         # Write the generated data to 'DATA SHEET'
         user_facility_spreadsheet.to_excel(writer, index=False, sheet_name='DATA SHEET')
 
-        # Check if mapper is one of the v15 JGI templates
+        # Check if mapper is one of the v15 or v16 JGI templates
         mapper_basename = os.path.basename(mapper)
         jgi_v15_mappers = ['jgi_mg_header_v15.json', 'jgi_mt_header_v15.json']
+        jgi_v16_mappers = ['jgi_mg_header_v16.json', 'jgi_mt_header_v16.json']
+        jgi_mappers = jgi_v15_mappers + jgi_v16_mappers
 
-        if mapper_basename in jgi_v15_mappers:
+        if mapper_basename in jgi_mappers:
             # Path to static JGI v15 Excel template
             static_excel_path = os.path.join(
                 os.path.dirname(__file__), 'static-excel-tabs', 'JGI.Metagenome.NA.v15.xlsx'

{mutts-1.0.4 → mutts-1.0.5}/src/mutts/retriever.py

@@ -189,7 +189,7 @@ class MetadataRetriever:
 
         # Address 'Was sample DNAse treated?' col
         # Change from 'yes/no' to 'Y/N'
-        if self.user_facility in ["jgi_mg", "jgi_mt"] and "dnase" in df.columns:
+        if self.user_facility in ["jgi_mg", "jgi_mt", "jgi_mg_lr"] and "dnase" in df.columns:
             df.loc[df["dnase"] == "yes", "dnase"] = "Y"
             df.loc[df["dnase"] == "no", "dnase"] = "N"